Starting phenix.real_space_refine
on Tue Nov 18 06:14:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5oyg_3861/11_2025/5oyg_3861.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5oyg_3861/11_2025/5oyg_3861.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5oyg_3861/11_2025/5oyg_3861.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5oyg_3861/11_2025/5oyg_3861.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5oyg_3861/11_2025/5oyg_3861.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5oyg_3861/11_2025/5oyg_3861.map"
  }
  resolution = 4.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    7566      2.51       5
     N    1906      2.21       5
     O    2052      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11596
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 709, 5798
          Classifications: {'peptide': 709}
          Link IDs: {'PTRANS': 31, 'TRANS': 677}
          Chain breaks: 4
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.01, per 1000 atoms: 0.43
  Number of scatterers: 11596
  At special positions: 0
  Unit cell: (85.995, 124.215, 121.485, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    2052      8.00
     N    1906      7.00
     C    7566      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 386 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 625 " - pdb=" SG  CYS A 630 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 386 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 625 " - pdb=" SG  CYS B 630 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 552.8 milliseconds
  

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2716

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      62.6% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
      removed outlier: 3.790A  pdb=" N   LEU A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 181
      removed outlier: 3.590A  pdb=" N   THR A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 205 through 211
    Processing helix  chain 'A' and resid 242 through 257
      removed outlier: 3.596A  pdb=" N   THR A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 275
      removed outlier: 3.704A  pdb=" N   GLY A 275 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 316 through 325
    Processing helix  chain 'A' and resid 325 through 359
      removed outlier: 3.643A  pdb=" N   GLY A 329 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ILE A 343 " --> pdb=" O   THR A 339 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
      removed outlier: 3.638A  pdb=" N   THR A 359 " --> pdb=" O   TYR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 363
      removed outlier: 3.767A  pdb=" N   ASN A 363 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 360 through 363'
    Processing helix  chain 'A' and resid 364 through 371
    Processing helix  chain 'A' and resid 395 through 405
    Processing helix  chain 'A' and resid 408 through 438
    Processing helix  chain 'A' and resid 452 through 466
      removed outlier: 3.833A  pdb=" N   ALA A 456 " --> pdb=" O   ASP A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 519
    Processing helix  chain 'A' and resid 523 through 527
      removed outlier: 4.420A  pdb=" N   SER A 526 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER A 527 " --> pdb=" O   MET A 524 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 523 through 527'
    Processing helix  chain 'A' and resid 536 through 569
      removed outlier: 3.538A  pdb=" N   ALA A 540 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   GLU A 555 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   VAL A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 569 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 601
      removed outlier: 3.816A  pdb=" N   LEU A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      Proline residue:  A 595  - end of helix
    Processing helix  chain 'A' and resid 630 through 656
      removed outlier: 3.952A  pdb=" N   LEU A 634 " --> pdb=" O   CYS A 630 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE A 640 " --> pdb=" O   ILE A 636 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 641 " --> pdb=" O   GLN A 637 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   GLN A 646 " --> pdb=" O   MET A 642 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   LEU A 647 " --> pdb=" O   LEU A 643 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   GLU A 654 " --> pdb=" O   ASN A 650 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ILE A 655 " --> pdb=" O   ASN A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 692
      removed outlier: 4.062A  pdb=" N   ASN A 692 " --> pdb=" O   GLU A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 715
      removed outlier: 4.249A  pdb=" N   GLU A 705 " --> pdb=" O   PRO A 701 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   MET A 706 " --> pdb=" O   GLU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 744
      removed outlier: 3.586A  pdb=" N   PHE A 726 " --> pdb=" O   LEU A 722 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ILE A 733 " --> pdb=" O   LEU A 729 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG A 736 " --> pdb=" O   ILE A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 781
      removed outlier: 4.009A  pdb=" N   ASN A 762 " --> pdb=" O   GLY A 758 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   VAL A 772 " --> pdb=" O   GLY A 768 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   ILE A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A 774 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 795
      removed outlier: 3.549A  pdb=" N   LEU A 789 " --> pdb=" O   PHE A 785 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR A 795 " --> pdb=" O   TYR A 791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 809
    Processing helix  chain 'A' and resid 854 through 886
      removed outlier: 4.038A  pdb=" N   TRP A 858 " --> pdb=" O   SER A 854 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASP A 883 " --> pdb=" O   SER A 879 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE A 886 " --> pdb=" O   VAL A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 909
      removed outlier: 3.510A  pdb=" N   SER A 894 " --> pdb=" O   PRO A 890 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 174
      removed outlier: 3.791A  pdb=" N   LEU B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 181
      removed outlier: 3.590A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 204
      No H-bonds generated for 'chain 'B' and resid 202 through 204'
    Processing helix  chain 'B' and resid 205 through 211
    Processing helix  chain 'B' and resid 242 through 257
      removed outlier: 3.597A  pdb=" N   THR B 257 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 275
      removed outlier: 3.703A  pdb=" N   GLY B 275 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 305
    Processing helix  chain 'B' and resid 316 through 325
    Processing helix  chain 'B' and resid 325 through 359
      removed outlier: 3.644A  pdb=" N   GLY B 329 " --> pdb=" O   GLY B 325 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ILE B 343 " --> pdb=" O   THR B 339 " (cutoff:3.500A)
      Proline residue:  B 344  - end of helix
      removed outlier: 3.638A  pdb=" N   THR B 359 " --> pdb=" O   TYR B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 363
      removed outlier: 3.766A  pdb=" N   ASN B 363 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 360 through 363'
    Processing helix  chain 'B' and resid 364 through 371
    Processing helix  chain 'B' and resid 395 through 405
    Processing helix  chain 'B' and resid 408 through 438
    Processing helix  chain 'B' and resid 452 through 466
      removed outlier: 3.833A  pdb=" N   ALA B 456 " --> pdb=" O   ASP B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 490 through 519
    Processing helix  chain 'B' and resid 523 through 527
      removed outlier: 4.421A  pdb=" N   SER B 526 " --> pdb=" O   ALA B 523 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER B 527 " --> pdb=" O   MET B 524 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 523 through 527'
    Processing helix  chain 'B' and resid 536 through 569
      removed outlier: 3.538A  pdb=" N   ALA B 540 " --> pdb=" O   VAL B 536 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   GLU B 555 " --> pdb=" O   ILE B 551 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   VAL B 556 " --> pdb=" O   LEU B 552 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL B 569 " --> pdb=" O   THR B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 601
      removed outlier: 3.815A  pdb=" N   LEU B 587 " --> pdb=" O   LYS B 583 " (cutoff:3.500A)
      Proline residue:  B 595  - end of helix
    Processing helix  chain 'B' and resid 630 through 656
      removed outlier: 3.951A  pdb=" N   LEU B 634 " --> pdb=" O   CYS B 630 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE B 640 " --> pdb=" O   ILE B 636 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 641 " --> pdb=" O   GLN B 637 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   GLN B 646 " --> pdb=" O   MET B 642 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   LEU B 647 " --> pdb=" O   LEU B 643 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLU B 654 " --> pdb=" O   ASN B 650 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ILE B 655 " --> pdb=" O   ASN B 651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 685 through 692
      removed outlier: 4.064A  pdb=" N   ASN B 692 " --> pdb=" O   GLU B 688 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 699 through 715
      removed outlier: 4.254A  pdb=" N   GLU B 705 " --> pdb=" O   PRO B 701 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   MET B 706 " --> pdb=" O   GLU B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 722 through 744
      removed outlier: 3.587A  pdb=" N   PHE B 726 " --> pdb=" O   LEU B 722 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ILE B 733 " --> pdb=" O   LEU B 729 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG B 736 " --> pdb=" O   ILE B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 781
      removed outlier: 4.008A  pdb=" N   ASN B 762 " --> pdb=" O   GLY B 758 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   VAL B 772 " --> pdb=" O   GLY B 768 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   ILE B 773 " --> pdb=" O   LYS B 769 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE B 774 " --> pdb=" O   LEU B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 795
      removed outlier: 3.549A  pdb=" N   LEU B 789 " --> pdb=" O   PHE B 785 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR B 795 " --> pdb=" O   TYR B 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 809
    Processing helix  chain 'B' and resid 854 through 886
      removed outlier: 4.036A  pdb=" N   TRP B 858 " --> pdb=" O   SER B 854 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP B 883 " --> pdb=" O   SER B 879 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE B 886 " --> pdb=" O   VAL B 882 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 909
      removed outlier: 3.510A  pdb=" N   SER B 894 " --> pdb=" O   PRO B 890 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189
      removed outlier: 4.024A  pdb=" N   SER A 196 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASP A 123 " --> pdb=" O   GLN A 199 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   PHE A 126 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218
    Processing sheet with id=AA3, first strand: chain 'A' and resid 615 through 616
      removed outlier: 3.658A  pdb=" N   PHE A 620 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 812 through 813
    Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 189
      removed outlier: 4.022A  pdb=" N   SER B 196 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASP B 123 " --> pdb=" O   GLN B 199 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   PHE B 126 " --> pdb=" O   SER B 278 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 217 through 218
    Processing sheet with id=AA7, first strand: chain 'B' and resid 615 through 616
      removed outlier: 3.659A  pdb=" N   PHE B 620 " --> pdb=" O   ILE B 616 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 812 through 813

    616 hydrogen bonds defined for protein.
    1830 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: 1.71

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3393
        1.33 -     1.46: 2108
        1.46 -     1.58: 6271
        1.58 -     1.70: 0
        1.70 -     1.82: 118
  Bond restraints: 11890
  Sorted by residual:
  bond pdb=" CA  ASP B 203 "
       pdb=" C   ASP B 203 "
    ideal  model  delta    sigma   weight residual
    1.521  1.548 -0.027 1.11e-02 8.12e+03 5.71e+00
  bond pdb=" C   MET A 176 "
       pdb=" N   PRO A 177 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.028 1.19e-02 7.06e+03 5.52e+00
  bond pdb=" CA  ILE B 657 "
       pdb=" C   ILE B 657 "
    ideal  model  delta    sigma   weight residual
    1.524  1.549 -0.024 1.05e-02 9.07e+03 5.42e+00
  bond pdb=" C   MET B 176 "
       pdb=" N   PRO B 177 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.028 1.19e-02 7.06e+03 5.42e+00
  bond pdb=" CA  ASP A 203 "
       pdb=" C   ASP A 203 "
    ideal  model  delta    sigma   weight residual
    1.521  1.547 -0.026 1.11e-02 8.12e+03 5.35e+00
  ... (remaining 11885 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 14295
        1.83 -     3.66: 1565
        3.66 -     5.49: 168
        5.49 -     7.32: 44
        7.32 -     9.15: 22
  Bond angle restraints: 16094
  Sorted by residual:
  angle pdb=" C   HIS B 453 "
        pdb=" N   PRO B 454 "
        pdb=" CA  PRO B 454 "
      ideal   model   delta    sigma   weight residual
     119.87  114.38    5.49 1.04e+00 9.25e-01 2.79e+01
  angle pdb=" C   HIS A 453 "
        pdb=" N   PRO A 454 "
        pdb=" CA  PRO A 454 "
      ideal   model   delta    sigma   weight residual
     119.87  114.45    5.42 1.04e+00 9.25e-01 2.71e+01
  angle pdb=" C   ILE B 657 "
        pdb=" N   PRO B 658 "
        pdb=" CA  PRO B 658 "
      ideal   model   delta    sigma   weight residual
     119.05  124.73   -5.68 1.11e+00 8.12e-01 2.62e+01
  angle pdb=" C   ILE A 657 "
        pdb=" N   PRO A 658 "
        pdb=" CA  PRO A 658 "
      ideal   model   delta    sigma   weight residual
     119.05  124.68   -5.63 1.11e+00 8.12e-01 2.57e+01
  angle pdb=" N   SER A 811 "
        pdb=" CA  SER A 811 "
        pdb=" C   SER A 811 "
      ideal   model   delta    sigma   weight residual
     110.91  116.32   -5.41 1.17e+00 7.31e-01 2.14e+01
  ... (remaining 16089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 6441
       16.26 -    32.52: 521
       32.52 -    48.79: 122
       48.79 -    65.05: 10
       65.05 -    81.31: 12
  Dihedral angle restraints: 7106
    sinusoidal: 2910
      harmonic: 4196
  Sorted by residual:
  dihedral pdb=" CB  CYS B 382 "
           pdb=" SG  CYS B 382 "
           pdb=" SG  CYS B 386 "
           pdb=" CB  CYS B 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.58  -68.42     1      1.00e+01 1.00e-02 6.07e+01
  dihedral pdb=" CB  CYS A 382 "
           pdb=" SG  CYS A 382 "
           pdb=" SG  CYS A 386 "
           pdb=" CB  CYS A 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.75  -68.25     1      1.00e+01 1.00e-02 6.04e+01
  dihedral pdb=" CB  CYS B 625 "
           pdb=" SG  CYS B 625 "
           pdb=" SG  CYS B 630 "
           pdb=" CB  CYS B 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.34  -66.34     1      1.00e+01 1.00e-02 5.75e+01
  ... (remaining 7103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 1249
       0.100 -    0.200: 442
       0.200 -    0.299: 59
       0.299 -    0.399: 17
       0.399 -    0.499: 7
  Chirality restraints: 1774
  Sorted by residual:
  chirality pdb=" CA  PHE A 505 "
            pdb=" N   PHE A 505 "
            pdb=" C   PHE A 505 "
            pdb=" CB  PHE A 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.22e+00
  chirality pdb=" CA  PHE B 505 "
            pdb=" N   PHE B 505 "
            pdb=" C   PHE B 505 "
            pdb=" CB  PHE B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.17e+00
  chirality pdb=" CA  THR A 594 "
            pdb=" N   THR A 594 "
            pdb=" C   THR A 594 "
            pdb=" CB  THR A 594 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.07    0.46 2.00e-01 2.50e+01 5.20e+00
  ... (remaining 1771 not shown)

  Planarity restraints: 2020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 406 "   -0.048 5.00e-02 4.00e+02   7.36e-02 8.68e+00
        pdb=" N   PRO A 407 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 407 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 407 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 406 "    0.048 5.00e-02 4.00e+02   7.36e-02 8.66e+00
        pdb=" N   PRO B 407 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 407 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 407 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 222 "   -0.043 5.00e-02 4.00e+02   6.53e-02 6.82e+00
        pdb=" N   PRO B 223 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 223 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 223 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2017 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2743
        2.81 -     3.33: 11084
        3.33 -     3.85: 18028
        3.85 -     4.38: 19669
        4.38 -     4.90: 33725
  Nonbonded interactions: 85249
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 791 "
            pdb=" O   HIS B 802 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OH  TYR A 791 "
            pdb=" O   HIS A 802 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" NH2 ARG A 515 "
            pdb=" O   MET A 622 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" NH2 ARG B 515 "
            pdb=" O   MET B 622 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" O   ALA A 600 "
            pdb=" OG1 THR A 782 "
     model   vdw
     2.336 3.040
  ... (remaining 85244 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.810
  Find NCS groups from input model:        0.090
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
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      :  0.007   0.037  11898  Z= 0.474
  Angle     :  1.269   9.151  16110  Z= 0.800
  Chirality :  0.103   0.499   1774
  Planarity :  0.007   0.074   2020
  Dihedral  : 12.530  81.310   4366
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  6.58 %
    Favored  : 91.44 %
  Cbeta Deviations :  0.74 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.35 (0.19), residues: 1398
  helix: -1.60 (0.15), residues: 790
  sheet: -1.66 (0.98), residues: 22
  loop : -3.11 (0.24), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 618 
 TYR   0.023   0.003   TYR B 761 
 PHE   0.026   0.003   PHE B 585 
 TRP   0.021   0.003   TRP A 334 
 HIS   0.006   0.002   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00734 (11890)
  covalent geometry    : angle       1.26853 (16094)
  SS BOND              : bond        0.00932 (    8)
  SS BOND              : angle       1.97410 (   16)
  hydrogen bonds       : bond        0.14090 (  616)
  hydrogen bonds       : angle       8.83446 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 268
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8397 (tmm) cc_final: 0.7400 (tmm)
REVERT: A  222 TYR cc_start: 0.9286 (p90) cc_final: 0.8994 (p90)
REVERT: A  342 LEU cc_start: 0.9863 (mt) cc_final: 0.9548 (tp)
REVERT: A  364 ILE cc_start: 0.9699 (mp) cc_final: 0.9355 (mm)
REVERT: A  391 MET cc_start: 0.9131 (tpt) cc_final: 0.8904 (tpp)
REVERT: A  424 MET cc_start: 0.9274 (mmt) cc_final: 0.8993 (mmt)
REVERT: A  429 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.9007 (mtm180)
REVERT: A  461 ARG cc_start: 0.7096 (ttm170) cc_final: 0.6807 (tmt170)
REVERT: A  551 ILE cc_start: 0.9748 (mt) cc_final: 0.9530 (mt)
REVERT: A  553 LEU cc_start: 0.9873 (tp) cc_final: 0.8714 (tp)
REVERT: A  557 TYR cc_start: 0.9245 (m-10) cc_final: 0.8433 (m-80)
REVERT: A  588 LYS cc_start: 0.9262 (ttmp) cc_final: 0.9052 (tttp)
REVERT: A  637 GLN cc_start: 0.9467 (tt0) cc_final: 0.9081 (tm-30)
REVERT: A  688 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8898 (mt-10)
REVERT: A  702 GLU cc_start: 0.8686 (tp30) cc_final: 0.7869 (tp30)
REVERT: A  734 GLU cc_start: 0.9315 (tp30) cc_final: 0.8854 (tp30)
REVERT: A  755 LYS cc_start: 0.9233 (ptmm) cc_final: 0.8699 (ptpt)
REVERT: A  904 MET cc_start: 0.9407 (tmt) cc_final: 0.9114 (tmm)
REVERT: B  117 MET cc_start: 0.8296 (tmm) cc_final: 0.7233 (tmm)
REVERT: B  182 TYR cc_start: 0.9253 (m-80) cc_final: 0.9042 (m-80)
REVERT: B  222 TYR cc_start: 0.9295 (p90) cc_final: 0.9006 (p90)
REVERT: B  342 LEU cc_start: 0.9855 (mt) cc_final: 0.9492 (tp)
REVERT: B  391 MET cc_start: 0.9168 (tpt) cc_final: 0.8947 (tpp)
REVERT: B  424 MET cc_start: 0.9281 (mmt) cc_final: 0.9018 (mmt)
REVERT: B  429 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.9027 (mtm180)
REVERT: B  461 ARG cc_start: 0.6959 (ttm170) cc_final: 0.6664 (tmt170)
REVERT: B  553 LEU cc_start: 0.9864 (tp) cc_final: 0.8702 (tp)
REVERT: B  557 TYR cc_start: 0.9178 (m-10) cc_final: 0.8347 (m-80)
REVERT: B  688 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8887 (mt-10)
REVERT: B  702 GLU cc_start: 0.8678 (tp30) cc_final: 0.7875 (tp30)
REVERT: B  734 GLU cc_start: 0.9310 (tp30) cc_final: 0.8863 (tp30)
REVERT: B  745 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8646 (mt-10)
REVERT: B  755 LYS cc_start: 0.9263 (ptmm) cc_final: 0.8740 (ptpt)
REVERT: B  904 MET cc_start: 0.9402 (tmt) cc_final: 0.9078 (tmm)
  outliers start: 25
  outliers final: 0
  residues processed: 285
  average time/residue: 0.1428
  time to fit residues: 54.2626
Evaluate side-chains
  175 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 173
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0030
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 646 GLN
A 896 GLN
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 646 GLN
B 896 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.080019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.062853 restraints weight = 43173.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.064449 restraints weight = 24880.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.065399 restraints weight = 17339.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.066017 restraints weight = 13837.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.066401 restraints weight = 11946.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11898  Z= 0.130
  Angle     :  0.662  11.415  16110  Z= 0.335
  Chirality :  0.042   0.178   1774
  Planarity :  0.005   0.059   2020
  Dihedral  :  5.097  22.220   1562
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.85 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.22), residues: 1398
  helix:  0.40 (0.17), residues: 838
  sheet: -1.14 (0.91), residues: 28
  loop : -2.90 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 213 
 TYR   0.012   0.001   TYR A 687 
 PHE   0.041   0.001   PHE B 505 
 TRP   0.028   0.002   TRP A 427 
 HIS   0.003   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (11890)
  covalent geometry    : angle       0.66102 (16094)
  SS BOND              : bond        0.00450 (    8)
  SS BOND              : angle       1.28227 (   16)
  hydrogen bonds       : bond        0.04491 (  616)
  hydrogen bonds       : angle       4.80472 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 220
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8378 (tmm) cc_final: 0.7334 (tmm)
REVERT: A  252 GLU cc_start: 0.9221 (tp30) cc_final: 0.8756 (tp30)
REVERT: A  300 LEU cc_start: 0.9697 (tt) cc_final: 0.9455 (tp)
REVERT: A  368 GLU cc_start: 0.8595 (mp0) cc_final: 0.8232 (mp0)
REVERT: A  369 MET cc_start: 0.8607 (mtm) cc_final: 0.8344 (ttm)
REVERT: A  416 MET cc_start: 0.9393 (mmp) cc_final: 0.9068 (mmm)
REVERT: A  461 ARG cc_start: 0.7248 (ttm170) cc_final: 0.7014 (tmt170)
REVERT: A  702 GLU cc_start: 0.8478 (tp30) cc_final: 0.7818 (tp30)
REVERT: A  755 LYS cc_start: 0.9019 (ptmm) cc_final: 0.8758 (ptpt)
REVERT: A  782 THR cc_start: 0.9513 (m) cc_final: 0.9302 (p)
REVERT: A  840 ASP cc_start: 0.8619 (t0) cc_final: 0.8350 (t70)
REVERT: A  881 PHE cc_start: 0.8978 (t80) cc_final: 0.8466 (t80)
REVERT: B  117 MET cc_start: 0.8346 (tmm) cc_final: 0.7214 (tmm)
REVERT: B  206 GLN cc_start: 0.9149 (tt0) cc_final: 0.8925 (tt0)
REVERT: B  252 GLU cc_start: 0.9310 (tp30) cc_final: 0.8990 (tp30)
REVERT: B  300 LEU cc_start: 0.9696 (tt) cc_final: 0.9459 (tt)
REVERT: B  367 MET cc_start: 0.9025 (mtt) cc_final: 0.8765 (mtt)
REVERT: B  368 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8645 (mm-30)
REVERT: B  369 MET cc_start: 0.8778 (mtm) cc_final: 0.8479 (ttm)
REVERT: B  391 MET cc_start: 0.8804 (tpt) cc_final: 0.8588 (tpp)
REVERT: B  461 ARG cc_start: 0.7259 (ttm170) cc_final: 0.6996 (tmt170)
REVERT: B  590 VAL cc_start: 0.9733 (t) cc_final: 0.9475 (p)
REVERT: B  702 GLU cc_start: 0.8688 (tp30) cc_final: 0.8011 (tp30)
REVERT: B  704 MET cc_start: 0.9032 (tpp) cc_final: 0.8777 (tpp)
REVERT: B  755 LYS cc_start: 0.9024 (ptmm) cc_final: 0.8740 (ptpt)
REVERT: B  782 THR cc_start: 0.9537 (m) cc_final: 0.9328 (p)
REVERT: B  794 MET cc_start: 0.8019 (mmp) cc_final: 0.7704 (mmp)
REVERT: B  840 ASP cc_start: 0.8506 (t0) cc_final: 0.8245 (t70)
REVERT: B  881 PHE cc_start: 0.9001 (t80) cc_final: 0.8518 (t80)
REVERT: B  904 MET cc_start: 0.9307 (tmm) cc_final: 0.9046 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1073
  time to fit residues: 34.3428
Evaluate side-chains
  152 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 126 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 128 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 75 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
A 206 GLN
B 183 HIS
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.074336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.057209 restraints weight = 45785.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.058685 restraints weight = 26080.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.059597 restraints weight = 17962.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.060196 restraints weight = 14289.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.060526 restraints weight = 12384.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  11898  Z= 0.286
  Angle     :  0.746  10.127  16110  Z= 0.394
  Chirality :  0.046   0.188   1774
  Planarity :  0.005   0.058   2020
  Dihedral  :  5.155  22.569   1562
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.72 %
    Favored  : 96.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.23), residues: 1398
  helix:  1.09 (0.17), residues: 844
  sheet: -2.04 (0.73), residues: 48
  loop : -2.86 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 837 
 TYR   0.016   0.002   TYR B 703 
 PHE   0.039   0.002   PHE A 505 
 TRP   0.021   0.002   TRP A 427 
 HIS   0.008   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00613 (11890)
  covalent geometry    : angle       0.74608 (16094)
  SS BOND              : bond        0.01477 (    8)
  SS BOND              : angle       0.82134 (   16)
  hydrogen bonds       : bond        0.05109 (  616)
  hydrogen bonds       : angle       4.81040 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8321 (tmm) cc_final: 0.7244 (tmm)
REVERT: A  252 GLU cc_start: 0.9253 (tp30) cc_final: 0.8953 (tp30)
REVERT: A  341 MET cc_start: 0.9385 (tpp) cc_final: 0.8910 (tpp)
REVERT: A  367 MET cc_start: 0.8945 (mtt) cc_final: 0.8699 (mtt)
REVERT: A  368 GLU cc_start: 0.8675 (mp0) cc_final: 0.8240 (mp0)
REVERT: A  378 MET cc_start: 0.8061 (mpp) cc_final: 0.7840 (mpp)
REVERT: A  461 ARG cc_start: 0.7285 (ttm170) cc_final: 0.6998 (tmt170)
REVERT: A  694 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8891 (mm-30)
REVERT: A  702 GLU cc_start: 0.8668 (tp30) cc_final: 0.8377 (tp30)
REVERT: A  734 GLU cc_start: 0.8891 (tp30) cc_final: 0.8191 (tp30)
REVERT: A  755 LYS cc_start: 0.9127 (ptmm) cc_final: 0.8714 (ptpp)
REVERT: A  840 ASP cc_start: 0.8824 (t0) cc_final: 0.8472 (t70)
REVERT: A  881 PHE cc_start: 0.8999 (t80) cc_final: 0.8511 (t80)
REVERT: B  117 MET cc_start: 0.8338 (tmm) cc_final: 0.7258 (tmm)
REVERT: B  252 GLU cc_start: 0.9322 (tp30) cc_final: 0.9119 (tp30)
REVERT: B  368 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8730 (mm-30)
REVERT: B  369 MET cc_start: 0.8806 (mtm) cc_final: 0.8531 (ttm)
REVERT: B  461 ARG cc_start: 0.7293 (ttm170) cc_final: 0.6978 (tmt170)
REVERT: B  694 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8800 (mm-30)
REVERT: B  704 MET cc_start: 0.9180 (tpp) cc_final: 0.8904 (tpp)
REVERT: B  734 GLU cc_start: 0.8827 (tp30) cc_final: 0.8115 (tp30)
REVERT: B  755 LYS cc_start: 0.9160 (ptmm) cc_final: 0.8604 (ptpp)
REVERT: B  794 MET cc_start: 0.8215 (mmp) cc_final: 0.7899 (mmp)
REVERT: B  840 ASP cc_start: 0.8786 (t0) cc_final: 0.8431 (t70)
REVERT: B  881 PHE cc_start: 0.9022 (t80) cc_final: 0.8572 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1128
  time to fit residues: 26.5289
Evaluate side-chains
  127 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 68 optimal weight:    0.1980
   chunk 136 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 122 optimal weight:    0.7980
   chunk 116 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 206 GLN
** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 709 GLN
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 GLN ** 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 = 0.3348 r_free = 0.3348 target = 0.077862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.060773 restraints weight = 45022.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.062416 restraints weight = 25017.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.063433 restraints weight = 16993.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.064046 restraints weight = 13298.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.064507 restraints weight = 11456.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11898  Z= 0.122
  Angle     :  0.626   9.750  16110  Z= 0.318
  Chirality :  0.042   0.211   1774
  Planarity :  0.004   0.053   2020
  Dihedral  :  4.722  21.182   1562
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.65 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.23), residues: 1398
  helix:  1.42 (0.18), residues: 840
  sheet: -2.04 (0.74), residues: 48
  loop : -2.68 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 213 
 TYR   0.018   0.001   TYR B 687 
 PHE   0.027   0.001   PHE A 171 
 TRP   0.017   0.001   TRP A 427 
 HIS   0.001   0.000   HIS B 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (11890)
  covalent geometry    : angle       0.62484 (16094)
  SS BOND              : bond        0.00447 (    8)
  SS BOND              : angle       1.19004 (   16)
  hydrogen bonds       : bond        0.03982 (  616)
  hydrogen bonds       : angle       4.18784 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8416 (tmm) cc_final: 0.7387 (tmm)
REVERT: A  176 MET cc_start: 0.9107 (tpp) cc_final: 0.8899 (tpp)
REVERT: A  252 GLU cc_start: 0.9224 (tp30) cc_final: 0.8863 (tp30)
REVERT: A  341 MET cc_start: 0.9406 (tpp) cc_final: 0.8918 (tpp)
REVERT: A  351 ILE cc_start: 0.9656 (OUTLIER) cc_final: 0.9454 (mp)
REVERT: A  368 GLU cc_start: 0.8759 (mp0) cc_final: 0.8154 (mp0)
REVERT: A  369 MET cc_start: 0.8799 (mmm) cc_final: 0.8413 (mpp)
REVERT: A  378 MET cc_start: 0.7973 (mpp) cc_final: 0.7677 (mpp)
REVERT: A  461 ARG cc_start: 0.7353 (ttm170) cc_final: 0.7118 (tmt170)
REVERT: A  702 GLU cc_start: 0.8485 (tp30) cc_final: 0.7659 (tp30)
REVERT: A  734 GLU cc_start: 0.8843 (tp30) cc_final: 0.8117 (tp30)
REVERT: A  738 ASP cc_start: 0.8096 (m-30) cc_final: 0.6841 (m-30)
REVERT: A  755 LYS cc_start: 0.9182 (ptmm) cc_final: 0.8798 (ptpt)
REVERT: A  840 ASP cc_start: 0.8470 (t0) cc_final: 0.8095 (t70)
REVERT: A  881 PHE cc_start: 0.8886 (t80) cc_final: 0.8466 (t80)
REVERT: B  117 MET cc_start: 0.8435 (tmm) cc_final: 0.7392 (tmm)
REVERT: B  176 MET cc_start: 0.9071 (tpp) cc_final: 0.8795 (tpp)
REVERT: B  252 GLU cc_start: 0.9290 (tp30) cc_final: 0.9001 (tp30)
REVERT: B  341 MET cc_start: 0.9348 (tpp) cc_final: 0.8941 (tpp)
REVERT: B  367 MET cc_start: 0.9163 (mtm) cc_final: 0.8734 (mtt)
REVERT: B  368 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8619 (mm-30)
REVERT: B  461 ARG cc_start: 0.7239 (ttm170) cc_final: 0.6999 (tmt170)
REVERT: B  702 GLU cc_start: 0.8176 (tp30) cc_final: 0.7205 (tp30)
REVERT: B  734 GLU cc_start: 0.8771 (tp30) cc_final: 0.8140 (tp30)
REVERT: B  755 LYS cc_start: 0.9131 (ptmm) cc_final: 0.8740 (ptpt)
REVERT: B  763 ILE cc_start: 0.9652 (mm) cc_final: 0.9374 (mp)
REVERT: B  794 MET cc_start: 0.8181 (mmp) cc_final: 0.7783 (mmp)
REVERT: B  840 ASP cc_start: 0.8515 (t0) cc_final: 0.8140 (t70)
REVERT: B  881 PHE cc_start: 0.8898 (t80) cc_final: 0.8505 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1091
  time to fit residues: 28.8110
Evaluate side-chains
  146 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 88 optimal weight:    0.0030
   chunk 81 optimal weight:    0.1980
   chunk 37 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   chunk 115 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 80 optimal weight:    0.2980
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
A 206 GLN
A 215 GLN
** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 731 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.078700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.061542 restraints weight = 44246.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.063220 restraints weight = 24827.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.064275 restraints weight = 16824.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.064878 restraints weight = 13205.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.065312 restraints weight = 11405.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11898  Z= 0.110
  Angle     :  0.600   9.108  16110  Z= 0.302
  Chirality :  0.042   0.171   1774
  Planarity :  0.004   0.047   2020
  Dihedral  :  4.427  19.316   1562
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.61 %
    Favored  : 97.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.24), residues: 1398
  helix:  1.68 (0.18), residues: 836
  sheet: -1.73 (0.78), residues: 48
  loop : -2.64 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 128 
 TYR   0.015   0.001   TYR A 687 
 PHE   0.021   0.001   PHE A 505 
 TRP   0.013   0.001   TRP A 427 
 HIS   0.002   0.000   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (11890)
  covalent geometry    : angle       0.59785 (16094)
  SS BOND              : bond        0.00605 (    8)
  SS BOND              : angle       1.70748 (   16)
  hydrogen bonds       : bond        0.03619 (  616)
  hydrogen bonds       : angle       3.93947 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8433 (tmm) cc_final: 0.7397 (tmm)
REVERT: A  252 GLU cc_start: 0.9157 (tp30) cc_final: 0.8798 (tp30)
REVERT: A  341 MET cc_start: 0.9361 (tpp) cc_final: 0.8888 (tpp)
REVERT: A  369 MET cc_start: 0.8773 (mmm) cc_final: 0.8431 (mpp)
REVERT: A  378 MET cc_start: 0.8038 (mpp) cc_final: 0.7747 (mpp)
REVERT: A  461 ARG cc_start: 0.7454 (ttm170) cc_final: 0.7228 (tmt170)
REVERT: A  690 ASP cc_start: 0.8672 (m-30) cc_final: 0.8471 (m-30)
REVERT: A  702 GLU cc_start: 0.8390 (tp30) cc_final: 0.7529 (tp30)
REVERT: A  734 GLU cc_start: 0.8762 (tp30) cc_final: 0.8295 (tp30)
REVERT: A  755 LYS cc_start: 0.9115 (ptmm) cc_final: 0.8590 (ptpp)
REVERT: A  840 ASP cc_start: 0.8546 (t0) cc_final: 0.8158 (t70)
REVERT: A  881 PHE cc_start: 0.8848 (t80) cc_final: 0.8485 (t80)
REVERT: B  117 MET cc_start: 0.8436 (tmm) cc_final: 0.7397 (tmm)
REVERT: B  252 GLU cc_start: 0.9296 (tp30) cc_final: 0.9000 (tp30)
REVERT: B  341 MET cc_start: 0.9347 (tpp) cc_final: 0.8940 (tpp)
REVERT: B  367 MET cc_start: 0.9158 (mtm) cc_final: 0.8718 (mtt)
REVERT: B  368 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8588 (mm-30)
REVERT: B  461 ARG cc_start: 0.7336 (ttm170) cc_final: 0.7136 (tmt170)
REVERT: B  557 TYR cc_start: 0.8757 (m-10) cc_final: 0.8286 (m-80)
REVERT: B  702 GLU cc_start: 0.7935 (tp30) cc_final: 0.7187 (tp30)
REVERT: B  734 GLU cc_start: 0.8719 (tp30) cc_final: 0.7995 (tp30)
REVERT: B  738 ASP cc_start: 0.8083 (m-30) cc_final: 0.6277 (m-30)
REVERT: B  755 LYS cc_start: 0.9101 (ptmm) cc_final: 0.8621 (ptpp)
REVERT: B  763 ILE cc_start: 0.9484 (mm) cc_final: 0.9261 (mp)
REVERT: B  794 MET cc_start: 0.8122 (mmp) cc_final: 0.7792 (mmp)
REVERT: B  840 ASP cc_start: 0.8509 (t0) cc_final: 0.8173 (t70)
REVERT: B  881 PHE cc_start: 0.8870 (t80) cc_final: 0.8532 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1084
  time to fit residues: 30.0095
Evaluate side-chains
  148 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 138 optimal weight:    0.6980
   chunk 111 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 206 GLN
** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** 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 = 0.3355 r_free = 0.3355 target = 0.078113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.061256 restraints weight = 44513.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.062825 restraints weight = 25028.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.063867 restraints weight = 17197.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.064501 restraints weight = 13416.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.064959 restraints weight = 11542.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11898  Z= 0.115
  Angle     :  0.602   8.818  16110  Z= 0.302
  Chirality :  0.041   0.167   1774
  Planarity :  0.004   0.043   2020
  Dihedral  :  4.316  19.439   1562
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.24), residues: 1398
  helix:  1.85 (0.18), residues: 840
  sheet: -1.69 (0.79), residues: 48
  loop : -2.65 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 125 
 TYR   0.018   0.001   TYR A 687 
 PHE   0.026   0.001   PHE B 505 
 TRP   0.011   0.001   TRP A 427 
 HIS   0.002   0.000   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (11890)
  covalent geometry    : angle       0.60090 (16094)
  SS BOND              : bond        0.00347 (    8)
  SS BOND              : angle       1.31766 (   16)
  hydrogen bonds       : bond        0.03582 (  616)
  hydrogen bonds       : angle       3.88292 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.9182 (tp30) cc_final: 0.8818 (tp30)
REVERT: A  341 MET cc_start: 0.9343 (tpp) cc_final: 0.8932 (tpp)
REVERT: A  367 MET cc_start: 0.9080 (mmt) cc_final: 0.8576 (mpp)
REVERT: A  369 MET cc_start: 0.8717 (mmm) cc_final: 0.8448 (mpp)
REVERT: A  378 MET cc_start: 0.8137 (mpp) cc_final: 0.7843 (mpp)
REVERT: A  416 MET cc_start: 0.9302 (mmp) cc_final: 0.9068 (tpp)
REVERT: A  702 GLU cc_start: 0.8448 (tp30) cc_final: 0.7633 (tp30)
REVERT: A  734 GLU cc_start: 0.8716 (tp30) cc_final: 0.8236 (tp30)
REVERT: A  755 LYS cc_start: 0.9135 (ptmm) cc_final: 0.8645 (ptpp)
REVERT: A  840 ASP cc_start: 0.8450 (t0) cc_final: 0.8044 (t70)
REVERT: A  881 PHE cc_start: 0.8847 (t80) cc_final: 0.8440 (t80)
REVERT: B  117 MET cc_start: 0.8437 (tmm) cc_final: 0.7416 (tmm)
REVERT: B  252 GLU cc_start: 0.9259 (tp30) cc_final: 0.9001 (tp30)
REVERT: B  341 MET cc_start: 0.9339 (tpp) cc_final: 0.8999 (tpp)
REVERT: B  367 MET cc_start: 0.9162 (mtm) cc_final: 0.8738 (mtt)
REVERT: B  369 MET cc_start: 0.8861 (mtp) cc_final: 0.8351 (ttm)
REVERT: B  461 ARG cc_start: 0.7387 (ttm170) cc_final: 0.7170 (tmt170)
REVERT: B  557 TYR cc_start: 0.8725 (m-10) cc_final: 0.8167 (m-80)
REVERT: B  702 GLU cc_start: 0.8040 (tp30) cc_final: 0.7326 (tp30)
REVERT: B  734 GLU cc_start: 0.8694 (tp30) cc_final: 0.8073 (tp30)
REVERT: B  755 LYS cc_start: 0.9039 (ptmm) cc_final: 0.8529 (ptpp)
REVERT: B  763 ILE cc_start: 0.9518 (mm) cc_final: 0.9294 (mp)
REVERT: B  794 MET cc_start: 0.8100 (mmp) cc_final: 0.7773 (mmp)
REVERT: B  840 ASP cc_start: 0.8499 (t0) cc_final: 0.8081 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1057
  time to fit residues: 29.1479
Evaluate side-chains
  143 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 108 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.077847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.060923 restraints weight = 44229.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.062477 restraints weight = 25792.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.063426 restraints weight = 17887.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.064062 restraints weight = 14231.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.064425 restraints weight = 12307.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11898  Z= 0.126
  Angle     :  0.627   9.703  16110  Z= 0.314
  Chirality :  0.043   0.208   1774
  Planarity :  0.004   0.040   2020
  Dihedral  :  4.313  17.761   1562
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.24), residues: 1398
  helix:  1.98 (0.18), residues: 840
  sheet: -1.56 (0.80), residues: 48
  loop : -2.61 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 128 
 TYR   0.019   0.001   TYR A 687 
 PHE   0.013   0.001   PHE A 589 
 TRP   0.012   0.001   TRP A 760 
 HIS   0.002   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (11890)
  covalent geometry    : angle       0.62644 (16094)
  SS BOND              : bond        0.00334 (    8)
  SS BOND              : angle       1.30943 (   16)
  hydrogen bonds       : bond        0.03648 (  616)
  hydrogen bonds       : angle       3.93134 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8453 (tmm) cc_final: 0.7883 (tmm)
REVERT: A  252 GLU cc_start: 0.9204 (tp30) cc_final: 0.8952 (tp30)
REVERT: A  341 MET cc_start: 0.9347 (tpp) cc_final: 0.8887 (tpp)
REVERT: A  367 MET cc_start: 0.9071 (mmt) cc_final: 0.8420 (mpp)
REVERT: A  368 GLU cc_start: 0.8798 (mp0) cc_final: 0.8281 (mp0)
REVERT: A  369 MET cc_start: 0.8706 (mmm) cc_final: 0.8425 (mpp)
REVERT: A  378 MET cc_start: 0.8179 (mpp) cc_final: 0.7848 (mpp)
REVERT: A  416 MET cc_start: 0.9326 (mmp) cc_final: 0.9020 (tpp)
REVERT: A  637 GLN cc_start: 0.9640 (tt0) cc_final: 0.9337 (tt0)
REVERT: A  702 GLU cc_start: 0.8400 (tp30) cc_final: 0.7552 (tp30)
REVERT: A  734 GLU cc_start: 0.8720 (tp30) cc_final: 0.8272 (tp30)
REVERT: A  755 LYS cc_start: 0.9032 (ptmm) cc_final: 0.8681 (ptpp)
REVERT: A  840 ASP cc_start: 0.8456 (t0) cc_final: 0.8057 (t70)
REVERT: A  878 MET cc_start: 0.8892 (mmm) cc_final: 0.8675 (mmm)
REVERT: A  881 PHE cc_start: 0.8830 (t80) cc_final: 0.8432 (t80)
REVERT: B  252 GLU cc_start: 0.9271 (tp30) cc_final: 0.9001 (tp30)
REVERT: B  341 MET cc_start: 0.9335 (tpp) cc_final: 0.9030 (tpp)
REVERT: B  367 MET cc_start: 0.9153 (mtm) cc_final: 0.8742 (mtt)
REVERT: B  368 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8772 (mm-30)
REVERT: B  461 ARG cc_start: 0.7389 (ttm170) cc_final: 0.7171 (tmt170)
REVERT: B  702 GLU cc_start: 0.8028 (tp30) cc_final: 0.7334 (tp30)
REVERT: B  734 GLU cc_start: 0.8730 (tp30) cc_final: 0.8115 (tp30)
REVERT: B  755 LYS cc_start: 0.9036 (ptmm) cc_final: 0.8604 (ptpp)
REVERT: B  763 ILE cc_start: 0.9547 (mm) cc_final: 0.9315 (mp)
REVERT: B  794 MET cc_start: 0.8140 (mmp) cc_final: 0.7812 (mmp)
REVERT: B  840 ASP cc_start: 0.8415 (t0) cc_final: 0.8014 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1112
  time to fit residues: 29.0384
Evaluate side-chains
  142 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 56 optimal weight:    0.6980
   chunk 116 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 30 optimal weight:    0.8980
   chunk 115 optimal weight:    2.9990
   chunk 118 optimal weight:    9.9990
   chunk 130 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.076917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.059975 restraints weight = 45117.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.061482 restraints weight = 26059.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.062284 restraints weight = 18220.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.062952 restraints weight = 14948.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.063373 restraints weight = 12953.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.4588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11898  Z= 0.149
  Angle     :  0.635   9.379  16110  Z= 0.322
  Chirality :  0.043   0.191   1774
  Planarity :  0.004   0.042   2020
  Dihedral  :  4.422  19.475   1562
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.24), residues: 1398
  helix:  2.04 (0.18), residues: 840
  sheet: -1.62 (0.78), residues: 48
  loop : -2.58 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 455 
 TYR   0.016   0.001   TYR B 687 
 PHE   0.016   0.001   PHE A 712 
 TRP   0.010   0.001   TRP A 427 
 HIS   0.003   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (11890)
  covalent geometry    : angle       0.63400 (16094)
  SS BOND              : bond        0.00338 (    8)
  SS BOND              : angle       1.19774 (   16)
  hydrogen bonds       : bond        0.03737 (  616)
  hydrogen bonds       : angle       3.99448 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.9209 (tp30) cc_final: 0.8967 (tp30)
REVERT: A  341 MET cc_start: 0.9338 (tpp) cc_final: 0.8928 (tpp)
REVERT: A  367 MET cc_start: 0.9114 (mmt) cc_final: 0.8790 (mpp)
REVERT: A  368 GLU cc_start: 0.8771 (mp0) cc_final: 0.8324 (mp0)
REVERT: A  369 MET cc_start: 0.8724 (mmm) cc_final: 0.8445 (mpp)
REVERT: A  378 MET cc_start: 0.8199 (mpp) cc_final: 0.7842 (mpp)
REVERT: A  416 MET cc_start: 0.9370 (mmp) cc_final: 0.9053 (tpp)
REVERT: A  702 GLU cc_start: 0.8439 (tp30) cc_final: 0.7729 (tp30)
REVERT: A  734 GLU cc_start: 0.8705 (tp30) cc_final: 0.8091 (tp30)
REVERT: A  755 LYS cc_start: 0.9180 (ptmm) cc_final: 0.8812 (ptpp)
REVERT: A  840 ASP cc_start: 0.8486 (t0) cc_final: 0.8100 (t70)
REVERT: A  878 MET cc_start: 0.8885 (mmm) cc_final: 0.8660 (mmm)
REVERT: A  881 PHE cc_start: 0.8857 (t80) cc_final: 0.8464 (t80)
REVERT: B  252 GLU cc_start: 0.9269 (tp30) cc_final: 0.9013 (tp30)
REVERT: B  341 MET cc_start: 0.9338 (tpp) cc_final: 0.9023 (tpp)
REVERT: B  367 MET cc_start: 0.9147 (mtm) cc_final: 0.8736 (mtt)
REVERT: B  368 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8779 (mm-30)
REVERT: B  461 ARG cc_start: 0.7398 (ttm170) cc_final: 0.7163 (tmt170)
REVERT: B  702 GLU cc_start: 0.8037 (tp30) cc_final: 0.7597 (tp30)
REVERT: B  734 GLU cc_start: 0.8732 (tp30) cc_final: 0.7966 (tp30)
REVERT: B  738 ASP cc_start: 0.8155 (m-30) cc_final: 0.5931 (m-30)
REVERT: B  755 LYS cc_start: 0.9183 (ptmm) cc_final: 0.8791 (ptpp)
REVERT: B  763 ILE cc_start: 0.9556 (mm) cc_final: 0.9330 (mp)
REVERT: B  794 MET cc_start: 0.8177 (mmp) cc_final: 0.7851 (mmp)
REVERT: B  840 ASP cc_start: 0.8457 (t0) cc_final: 0.8067 (t70)
REVERT: B  880 ASP cc_start: 0.8208 (t0) cc_final: 0.7979 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1126
  time to fit residues: 27.7283
Evaluate side-chains
  134 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 101 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 139 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 108 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.075650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.058795 restraints weight = 44786.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.060219 restraints weight = 26166.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.061133 restraints weight = 18356.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.061744 restraints weight = 14801.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.062095 restraints weight = 12849.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.4655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11898  Z= 0.186
  Angle     :  0.669   9.345  16110  Z= 0.343
  Chirality :  0.044   0.181   1774
  Planarity :  0.004   0.041   2020
  Dihedral  :  4.616  22.944   1562
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.24), residues: 1398
  helix:  1.97 (0.18), residues: 846
  sheet: -1.66 (0.77), residues: 48
  loop : -2.56 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 686 
 TYR   0.015   0.002   TYR A 687 
 PHE   0.018   0.002   PHE B 505 
 TRP   0.010   0.001   TRP A 760 
 HIS   0.004   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (11890)
  covalent geometry    : angle       0.66723 (16094)
  SS BOND              : bond        0.00294 (    8)
  SS BOND              : angle       1.71450 (   16)
  hydrogen bonds       : bond        0.04026 (  616)
  hydrogen bonds       : angle       4.14178 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.9263 (tp30) cc_final: 0.9049 (tp30)
REVERT: A  341 MET cc_start: 0.9351 (tpp) cc_final: 0.8924 (tpp)
REVERT: A  367 MET cc_start: 0.9076 (mmt) cc_final: 0.8819 (mpp)
REVERT: A  368 GLU cc_start: 0.8739 (mp0) cc_final: 0.8310 (mp0)
REVERT: A  369 MET cc_start: 0.8531 (mmm) cc_final: 0.8218 (mpp)
REVERT: A  378 MET cc_start: 0.8090 (mpp) cc_final: 0.7745 (mpp)
REVERT: A  702 GLU cc_start: 0.8467 (tp30) cc_final: 0.8129 (tp30)
REVERT: A  734 GLU cc_start: 0.8746 (tp30) cc_final: 0.7902 (tp30)
REVERT: A  738 ASP cc_start: 0.8284 (m-30) cc_final: 0.6044 (m-30)
REVERT: A  755 LYS cc_start: 0.9196 (ptmm) cc_final: 0.8714 (ptpt)
REVERT: A  779 ILE cc_start: 0.9759 (tt) cc_final: 0.9527 (tt)
REVERT: A  840 ASP cc_start: 0.8594 (t0) cc_final: 0.8140 (t70)
REVERT: A  878 MET cc_start: 0.8856 (mmm) cc_final: 0.8649 (mmm)
REVERT: A  881 PHE cc_start: 0.8863 (t80) cc_final: 0.8455 (t80)
REVERT: B  252 GLU cc_start: 0.9300 (tp30) cc_final: 0.9064 (tp30)
REVERT: B  341 MET cc_start: 0.9336 (tpp) cc_final: 0.8926 (tpp)
REVERT: B  367 MET cc_start: 0.9101 (mtm) cc_final: 0.8701 (mtt)
REVERT: B  461 ARG cc_start: 0.7415 (ttm170) cc_final: 0.7206 (tmt170)
REVERT: B  702 GLU cc_start: 0.8079 (tp30) cc_final: 0.7585 (tp30)
REVERT: B  734 GLU cc_start: 0.8812 (tp30) cc_final: 0.7985 (tp30)
REVERT: B  738 ASP cc_start: 0.8193 (m-30) cc_final: 0.6153 (m-30)
REVERT: B  755 LYS cc_start: 0.9239 (ptmm) cc_final: 0.8686 (ptpt)
REVERT: B  763 ILE cc_start: 0.9590 (mm) cc_final: 0.9371 (mp)
REVERT: B  794 MET cc_start: 0.8154 (mmp) cc_final: 0.7849 (mmp)
REVERT: B  840 ASP cc_start: 0.8592 (t0) cc_final: 0.8150 (t70)
REVERT: B  880 ASP cc_start: 0.8183 (t0) cc_final: 0.7961 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1072
  time to fit residues: 25.1254
Evaluate side-chains
  124 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 119 optimal weight:    0.0980
   chunk 118 optimal weight:    1.9990
   chunk 135 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 133 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0010
   chunk 77 optimal weight:    6.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
B 215 GLN
** B 709 GLN ** 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 = 0.3342 r_free = 0.3342 target = 0.077940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.061042 restraints weight = 44202.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.062588 restraints weight = 25632.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.063558 restraints weight = 17827.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.064185 restraints weight = 14253.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.064633 restraints weight = 12362.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.4830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  11898  Z= 0.114
  Angle     :  0.636   9.060  16110  Z= 0.317
  Chirality :  0.042   0.175   1774
  Planarity :  0.004   0.044   2020
  Dihedral  :  4.441  20.905   1562
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.32 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.24), residues: 1398
  helix:  2.04 (0.18), residues: 838
  sheet: -1.75 (0.77), residues: 48
  loop : -2.54 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 128 
 TYR   0.020   0.001   TYR B 687 
 PHE   0.019   0.001   PHE B 505 
 TRP   0.014   0.001   TRP A 427 
 HIS   0.002   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (11890)
  covalent geometry    : angle       0.63354 (16094)
  SS BOND              : bond        0.00502 (    8)
  SS BOND              : angle       1.93682 (   16)
  hydrogen bonds       : bond        0.03540 (  616)
  hydrogen bonds       : angle       3.92032 ( 1830)

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.9212 (tp30) cc_final: 0.8990 (tp30)
REVERT: A  341 MET cc_start: 0.9337 (tpp) cc_final: 0.8877 (tpp)
REVERT: A  367 MET cc_start: 0.9089 (mmt) cc_final: 0.8759 (mpp)
REVERT: A  368 GLU cc_start: 0.8708 (mp0) cc_final: 0.8191 (mp0)
REVERT: A  369 MET cc_start: 0.8530 (mmm) cc_final: 0.8228 (mpp)
REVERT: A  416 MET cc_start: 0.9334 (mmp) cc_final: 0.9027 (tpp)
REVERT: A  702 GLU cc_start: 0.8177 (tp30) cc_final: 0.7132 (tp30)
REVERT: A  705 GLU cc_start: 0.8017 (mp0) cc_final: 0.7789 (pm20)
REVERT: A  734 GLU cc_start: 0.8665 (tp30) cc_final: 0.8135 (tp30)
REVERT: A  738 ASP cc_start: 0.8174 (m-30) cc_final: 0.6923 (m-30)
REVERT: A  755 LYS cc_start: 0.9115 (ptmm) cc_final: 0.8757 (ptpt)
REVERT: A  840 ASP cc_start: 0.8472 (t0) cc_final: 0.8083 (t70)
REVERT: A  878 MET cc_start: 0.8844 (mmm) cc_final: 0.8604 (mmm)
REVERT: A  880 ASP cc_start: 0.8121 (t0) cc_final: 0.7907 (t0)
REVERT: A  881 PHE cc_start: 0.8860 (t80) cc_final: 0.8440 (t80)
REVERT: B  252 GLU cc_start: 0.9291 (tp30) cc_final: 0.9041 (tp30)
REVERT: B  341 MET cc_start: 0.9358 (tpp) cc_final: 0.8916 (tpp)
REVERT: B  367 MET cc_start: 0.9089 (mtm) cc_final: 0.8693 (mtt)
REVERT: B  368 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8749 (mm-30)
REVERT: B  369 MET cc_start: 0.8833 (mtp) cc_final: 0.8479 (mtm)
REVERT: B  406 ASN cc_start: 0.9290 (t0) cc_final: 0.9066 (t0)
REVERT: B  416 MET cc_start: 0.9293 (mmp) cc_final: 0.8992 (tpp)
REVERT: B  461 ARG cc_start: 0.7386 (ttm170) cc_final: 0.7146 (tmt170)
REVERT: B  499 PHE cc_start: 0.8906 (t80) cc_final: 0.8686 (t80)
REVERT: B  702 GLU cc_start: 0.7874 (tp30) cc_final: 0.7253 (tp30)
REVERT: B  734 GLU cc_start: 0.8670 (tp30) cc_final: 0.7949 (tp30)
REVERT: B  738 ASP cc_start: 0.8034 (m-30) cc_final: 0.6160 (m-30)
REVERT: B  755 LYS cc_start: 0.9079 (ptmm) cc_final: 0.8715 (ptpp)
REVERT: B  763 ILE cc_start: 0.9477 (mm) cc_final: 0.9213 (mp)
REVERT: B  794 MET cc_start: 0.8210 (mmp) cc_final: 0.7918 (mmp)
REVERT: B  840 ASP cc_start: 0.8444 (t0) cc_final: 0.8044 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1011
  time to fit residues: 27.2386
Evaluate side-chains
  140 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 131 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.074676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.058017 restraints weight = 45504.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.059434 restraints weight = 26463.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.060371 restraints weight = 18565.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.060919 restraints weight = 14837.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.061302 restraints weight = 13016.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  11898  Z= 0.233
  Angle     :  0.723  14.591  16110  Z= 0.372
  Chirality :  0.045   0.173   1774
  Planarity :  0.005   0.044   2020
  Dihedral  :  4.663  21.169   1562
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.23), residues: 1398
  helix:  1.87 (0.17), residues: 846
  sheet: -1.88 (0.73), residues: 48
  loop : -2.71 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 128 
 TYR   0.027   0.002   TYR B 761 
 PHE   0.024   0.002   PHE A 499 
 TRP   0.017   0.002   TRP B 760 
 HIS   0.006   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (11890)
  covalent geometry    : angle       0.72124 (16094)
  SS BOND              : bond        0.00368 (    8)
  SS BOND              : angle       1.91238 (   16)
  hydrogen bonds       : bond        0.04233 (  616)
  hydrogen bonds       : angle       4.27092 ( 1830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1750.32 seconds
wall clock time: 31 minutes 6.48 seconds (1866.48 seconds total)