Starting phenix.real_space_refine
on Tue Jul 29 20:47:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5oyg_3861/07_2025/5oyg_3861.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5oyg_3861/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5oyg_3861/07_2025/5oyg_3861.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5oyg_3861/07_2025/5oyg_3861.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5oyg_3861/07_2025/5oyg_3861.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5oyg_3861/07_2025/5oyg_3861.cif"
  }
  resolution = 4.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.35, per 1000 atoms: 0.98
  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: 2.62
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 1.35
  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: 3.17

  Time building geometry restraints manager: 3.08 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: 0.05
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:             1.210
  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:             0.000
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     31.600
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.380
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.021   0.003   TRP A 334 
 HIS   0.006   0.002   HIS A 402 
 PHE   0.026   0.003   PHE B 585 
 TYR   0.023   0.003   TYR B 761 
 ARG   0.007   0.001   ARG B 618 

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

*********************** 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  : 1.411 
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: 0.2977
  time to fit residues: 113.1711
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  : 1.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 71 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 109 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 127 optimal weight:    0.6980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 709 GLN
B 896 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.078517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.061088 restraints weight = 43484.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.062696 restraints weight = 25322.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.063661 restraints weight = 17644.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11898  Z= 0.152
  Angle     :  0.671  11.403  16110  Z= 0.343
  Chirality :  0.043   0.178   1774
  Planarity :  0.005   0.060   2020
  Dihedral  :  5.104  22.836   1562
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.93 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.22), residues: 1398
  helix:  0.56 (0.17), residues: 838
  sheet: -1.20 (0.91), residues: 28
  loop : -2.85 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 427 
 HIS   0.004   0.001   HIS B 402 
 PHE   0.043   0.001   PHE B 505 
 TYR   0.013   0.001   TYR A 331 
 ARG   0.006   0.001   ARG A 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04544 (  616)
  hydrogen bonds       : angle       4.75616 ( 1830)
  SS BOND              : bond        0.00597 (    8)
  SS BOND              : angle       1.27577 (   16)
  covalent geometry    : bond        0.00329 (11890)
  covalent geometry    : angle       0.66972 (16094)

*********************** 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
  213 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 211
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8478 (tmm) cc_final: 0.7374 (tmm)
REVERT: A  206 GLN cc_start: 0.9030 (tt0) cc_final: 0.8789 (tt0)
REVERT: A  252 GLU cc_start: 0.9157 (tp30) cc_final: 0.8761 (tp30)
REVERT: A  369 MET cc_start: 0.8569 (mtm) cc_final: 0.8263 (ttm)
REVERT: A  461 ARG cc_start: 0.7252 (ttm170) cc_final: 0.7008 (tmt170)
REVERT: A  702 GLU cc_start: 0.8712 (tp30) cc_final: 0.8340 (tp30)
REVERT: A  755 LYS cc_start: 0.9033 (ptmm) cc_final: 0.8770 (ptpt)
REVERT: A  840 ASP cc_start: 0.8619 (t0) cc_final: 0.8401 (t70)
REVERT: A  881 PHE cc_start: 0.8994 (t80) cc_final: 0.8499 (t80)
REVERT: B  117 MET cc_start: 0.8339 (tmm) cc_final: 0.7198 (tmm)
REVERT: B  206 GLN cc_start: 0.9101 (tt0) cc_final: 0.8850 (tt0)
REVERT: B  252 GLU cc_start: 0.9239 (tp30) cc_final: 0.8979 (tp30)
REVERT: B  300 LEU cc_start: 0.9691 (tt) cc_final: 0.9483 (tt)
REVERT: B  367 MET cc_start: 0.9014 (mtt) cc_final: 0.8800 (mtt)
REVERT: B  369 MET cc_start: 0.8743 (mtm) cc_final: 0.8342 (ttm)
REVERT: B  461 ARG cc_start: 0.7266 (ttm170) cc_final: 0.6979 (tmt170)
REVERT: B  702 GLU cc_start: 0.8718 (tp30) cc_final: 0.8329 (tp30)
REVERT: B  704 MET cc_start: 0.9055 (tpp) cc_final: 0.8813 (tpp)
REVERT: B  755 LYS cc_start: 0.9015 (ptmm) cc_final: 0.8682 (ptpp)
REVERT: B  794 MET cc_start: 0.7976 (mmp) cc_final: 0.7686 (mmp)
REVERT: B  840 ASP cc_start: 0.8585 (t0) cc_final: 0.8348 (t70)
REVERT: B  881 PHE cc_start: 0.9016 (t80) cc_final: 0.8553 (t80)
REVERT: B  904 MET cc_start: 0.9309 (tmm) cc_final: 0.9091 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 213
  average time/residue: 0.2346
  time to fit residues: 71.2842
Evaluate side-chains
  145 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 99 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 121 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0670
   chunk 47 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 136 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   overall best weight:    0.7120

-------------------------------------------------------------------------------
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 709 GLN
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 731 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.079498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.062335 restraints weight = 44076.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.063965 restraints weight = 25257.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.064972 restraints weight = 17466.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11898  Z= 0.120
  Angle     :  0.625  10.020  16110  Z= 0.317
  Chirality :  0.042   0.179   1774
  Planarity :  0.004   0.057   2020
  Dihedral  :  4.728  21.205   1562
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.96 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.23), residues: 1398
  helix:  1.19 (0.17), residues: 842
  sheet: -1.88 (0.76), residues: 48
  loop : -2.71 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 427 
 HIS   0.002   0.000   HIS A 402 
 PHE   0.036   0.001   PHE A 505 
 TYR   0.014   0.001   TYR B 222 
 ARG   0.003   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  616)
  hydrogen bonds       : angle       4.29003 ( 1830)
  SS BOND              : bond        0.00541 (    8)
  SS BOND              : angle       1.08470 (   16)
  covalent geometry    : bond        0.00252 (11890)
  covalent geometry    : angle       0.62487 (16094)

*********************** 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
  194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8488 (tmm) cc_final: 0.7394 (tmm)
REVERT: A  252 GLU cc_start: 0.9139 (tp30) cc_final: 0.8741 (tp30)
REVERT: A  341 MET cc_start: 0.9226 (tpp) cc_final: 0.8867 (tpp)
REVERT: A  367 MET cc_start: 0.8876 (mtt) cc_final: 0.8618 (mtt)
REVERT: A  368 GLU cc_start: 0.8632 (mp0) cc_final: 0.8070 (mp0)
REVERT: A  369 MET cc_start: 0.8954 (mtt) cc_final: 0.8511 (ttm)
REVERT: A  461 ARG cc_start: 0.7212 (ttm170) cc_final: 0.6995 (tmt170)
REVERT: A  702 GLU cc_start: 0.8588 (tp30) cc_final: 0.7505 (tp30)
REVERT: A  734 GLU cc_start: 0.8881 (tp30) cc_final: 0.8547 (tp30)
REVERT: A  755 LYS cc_start: 0.9040 (ptmm) cc_final: 0.8730 (ptpt)
REVERT: A  840 ASP cc_start: 0.8554 (t0) cc_final: 0.8247 (t70)
REVERT: A  881 PHE cc_start: 0.8942 (t80) cc_final: 0.8461 (t80)
REVERT: B  117 MET cc_start: 0.8401 (tmm) cc_final: 0.7285 (tmm)
REVERT: B  199 GLN cc_start: 0.8330 (mp-120) cc_final: 0.7755 (mp10)
REVERT: B  252 GLU cc_start: 0.9297 (tp30) cc_final: 0.8975 (tp30)
REVERT: B  341 MET cc_start: 0.9386 (tpp) cc_final: 0.8902 (tpp)
REVERT: B  367 MET cc_start: 0.9118 (mtt) cc_final: 0.8904 (mtt)
REVERT: B  368 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8620 (mm-30)
REVERT: B  369 MET cc_start: 0.8981 (mtm) cc_final: 0.8455 (ttm)
REVERT: B  461 ARG cc_start: 0.7240 (ttm170) cc_final: 0.7020 (tmt170)
REVERT: B  694 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8665 (mm-30)
REVERT: B  702 GLU cc_start: 0.8568 (tp30) cc_final: 0.7518 (tp30)
REVERT: B  734 GLU cc_start: 0.8880 (tp30) cc_final: 0.8516 (tp30)
REVERT: B  794 MET cc_start: 0.8071 (mmp) cc_final: 0.7745 (mmp)
REVERT: B  840 ASP cc_start: 0.8503 (t0) cc_final: 0.8174 (t70)
REVERT: B  881 PHE cc_start: 0.8963 (t80) cc_final: 0.8492 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2325
  time to fit residues: 64.4370
Evaluate side-chains
  145 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 131 optimal weight:    8.9990
   chunk 124 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 127 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 29 optimal weight:   10.0000
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
** 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 = 0.3373 r_free = 0.3373 target = 0.079439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.062581 restraints weight = 43849.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.064190 restraints weight = 24954.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.065153 restraints weight = 17150.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3740

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= 0.118
  Angle     :  0.608   9.489  16110  Z= 0.309
  Chirality :  0.042   0.204   1774
  Planarity :  0.004   0.051   2020
  Dihedral  :  4.557  20.315   1562
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.77 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.23), residues: 1398
  helix:  1.56 (0.18), residues: 836
  sheet: -1.55 (0.81), residues: 48
  loop : -2.59 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 427 
 HIS   0.002   0.000   HIS B 402 
 PHE   0.017   0.001   PHE B 505 
 TYR   0.014   0.001   TYR A 687 
 ARG   0.003   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03700 (  616)
  hydrogen bonds       : angle       4.08901 ( 1830)
  SS BOND              : bond        0.00396 (    8)
  SS BOND              : angle       1.52560 (   16)
  covalent geometry    : bond        0.00255 (11890)
  covalent geometry    : angle       0.60635 (16094)

*********************** 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
  187 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 2.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8459 (tmm) cc_final: 0.7419 (tmm)
REVERT: A  174 LEU cc_start: 0.9365 (mp) cc_final: 0.9132 (tt)
REVERT: A  252 GLU cc_start: 0.9222 (tp30) cc_final: 0.8806 (tp30)
REVERT: A  368 GLU cc_start: 0.8766 (mp0) cc_final: 0.8126 (mp0)
REVERT: A  416 MET cc_start: 0.9295 (mmp) cc_final: 0.9043 (mmm)
REVERT: A  461 ARG cc_start: 0.7456 (ttm170) cc_final: 0.7227 (tmt170)
REVERT: A  637 GLN cc_start: 0.9606 (tt0) cc_final: 0.9247 (tt0)
REVERT: A  702 GLU cc_start: 0.8610 (tp30) cc_final: 0.7450 (tp30)
REVERT: A  734 GLU cc_start: 0.8818 (tp30) cc_final: 0.8372 (tp30)
REVERT: A  755 LYS cc_start: 0.9159 (ptmm) cc_final: 0.8727 (ptpt)
REVERT: A  840 ASP cc_start: 0.8551 (t0) cc_final: 0.8235 (t70)
REVERT: A  881 PHE cc_start: 0.8911 (t80) cc_final: 0.8501 (t80)
REVERT: B  117 MET cc_start: 0.8459 (tmm) cc_final: 0.7378 (tmm)
REVERT: B  252 GLU cc_start: 0.9315 (tp30) cc_final: 0.9020 (tp30)
REVERT: B  367 MET cc_start: 0.9127 (mtt) cc_final: 0.8814 (mtt)
REVERT: B  368 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8628 (mm-30)
REVERT: B  702 GLU cc_start: 0.8582 (tp30) cc_final: 0.7746 (tp30)
REVERT: B  734 GLU cc_start: 0.8811 (tp30) cc_final: 0.8246 (tp30)
REVERT: B  794 MET cc_start: 0.8137 (mmp) cc_final: 0.7794 (mmp)
REVERT: B  840 ASP cc_start: 0.8479 (t0) cc_final: 0.8164 (t70)
REVERT: B  881 PHE cc_start: 0.8935 (t80) cc_final: 0.8527 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 187
  average time/residue: 0.3577
  time to fit residues: 95.5771
Evaluate side-chains
  151 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 2.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 137 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 74 optimal weight:    0.1980
   chunk 50 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 136 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 GLN ** 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 = 0.3383 r_free = 0.3383 target = 0.079554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.062738 restraints weight = 43735.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.064430 restraints weight = 23707.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.065477 restraints weight = 15899.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11898  Z= 0.111
  Angle     :  0.601   9.168  16110  Z= 0.300
  Chirality :  0.041   0.170   1774
  Planarity :  0.004   0.046   2020
  Dihedral  :  4.378  19.063   1562
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.69 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.24), residues: 1398
  helix:  1.78 (0.18), residues: 836
  sheet: -1.37 (0.83), residues: 48
  loop : -2.58 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 427 
 HIS   0.001   0.000   HIS A 426 
 PHE   0.021   0.001   PHE A 505 
 TYR   0.014   0.001   TYR B 222 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03464 (  616)
  hydrogen bonds       : angle       3.91713 ( 1830)
  SS BOND              : bond        0.00383 (    8)
  SS BOND              : angle       1.39126 (   16)
  covalent geometry    : bond        0.00235 (11890)
  covalent geometry    : angle       0.59968 (16094)

*********************** 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
  178 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 176
  time to evaluate  : 1.349 
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: 0.8471 (tmm) cc_final: 0.7436 (tmm)
REVERT: A  252 GLU cc_start: 0.9191 (tp30) cc_final: 0.8752 (tp30)
REVERT: A  341 MET cc_start: 0.9295 (tpp) cc_final: 0.8964 (tpp)
REVERT: A  378 MET cc_start: 0.7804 (mpp) cc_final: 0.7407 (mpp)
REVERT: A  416 MET cc_start: 0.9277 (mmp) cc_final: 0.9074 (mmm)
REVERT: A  557 TYR cc_start: 0.8838 (m-10) cc_final: 0.8368 (m-80)
REVERT: A  637 GLN cc_start: 0.9613 (tt0) cc_final: 0.9183 (tt0)
REVERT: A  641 ILE cc_start: 0.8659 (mt) cc_final: 0.8423 (mt)
REVERT: A  702 GLU cc_start: 0.8568 (tp30) cc_final: 0.7606 (tp30)
REVERT: A  704 MET cc_start: 0.9252 (tpp) cc_final: 0.8855 (tpp)
REVERT: A  734 GLU cc_start: 0.8814 (tp30) cc_final: 0.8384 (tp30)
REVERT: A  755 LYS cc_start: 0.9112 (ptmm) cc_final: 0.8731 (ptpt)
REVERT: A  840 ASP cc_start: 0.8532 (t0) cc_final: 0.8222 (t70)
REVERT: B  252 GLU cc_start: 0.9281 (tp30) cc_final: 0.8970 (tp30)
REVERT: B  341 MET cc_start: 0.9291 (tpp) cc_final: 0.8910 (tpp)
REVERT: B  367 MET cc_start: 0.9106 (mtt) cc_final: 0.8780 (mtt)
REVERT: B  368 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8758 (mm-30)
REVERT: B  557 TYR cc_start: 0.8711 (m-10) cc_final: 0.8155 (m-80)
REVERT: B  702 GLU cc_start: 0.8536 (tp30) cc_final: 0.7590 (tp30)
REVERT: B  734 GLU cc_start: 0.8799 (tp30) cc_final: 0.8364 (tp30)
REVERT: B  794 MET cc_start: 0.8218 (mmp) cc_final: 0.7882 (mmp)
REVERT: B  840 ASP cc_start: 0.8633 (t0) cc_final: 0.8275 (t70)
REVERT: B  881 PHE cc_start: 0.8914 (t80) cc_final: 0.8486 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 178
  average time/residue: 0.3185
  time to fit residues: 85.2334
Evaluate side-chains
  147 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 127 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 109 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 137 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 133 optimal weight:    6.9990
   chunk 105 optimal weight:    3.9990
   chunk 116 optimal weight:    5.9990
   overall best weight:    1.4382

-------------------------------------------------------------------------------
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**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 229 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 = 0.3350 r_free = 0.3350 target = 0.078059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.061409 restraints weight = 44658.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.062990 restraints weight = 25410.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.063954 restraints weight = 17443.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.4228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11898  Z= 0.140
  Angle     :  0.622   9.318  16110  Z= 0.313
  Chirality :  0.042   0.167   1774
  Planarity :  0.004   0.043   2020
  Dihedral  :  4.413  18.775   1562
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.24), residues: 1398
  helix:  1.95 (0.18), residues: 842
  sheet: -1.47 (0.83), residues: 48
  loop : -2.62 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 427 
 HIS   0.003   0.001   HIS B 402 
 PHE   0.026   0.001   PHE A 505 
 TYR   0.013   0.001   TYR B 222 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  616)
  hydrogen bonds       : angle       3.98138 ( 1830)
  SS BOND              : bond        0.00387 (    8)
  SS BOND              : angle       1.22972 (   16)
  covalent geometry    : bond        0.00310 (11890)
  covalent geometry    : angle       0.62073 (16094)

*********************** 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
  162 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 2.367 
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: 0.8479 (tmm) cc_final: 0.7804 (tmm)
REVERT: A  252 GLU cc_start: 0.9232 (tp30) cc_final: 0.8896 (tp30)
REVERT: A  341 MET cc_start: 0.9346 (tpp) cc_final: 0.8951 (tpp)
REVERT: A  367 MET cc_start: 0.9153 (mmt) cc_final: 0.8572 (mpp)
REVERT: A  378 MET cc_start: 0.7393 (mpp) cc_final: 0.6574 (mpp)
REVERT: A  416 MET cc_start: 0.9315 (mmp) cc_final: 0.9094 (mmm)
REVERT: A  557 TYR cc_start: 0.8641 (m-10) cc_final: 0.8077 (m-80)
REVERT: A  637 GLN cc_start: 0.9614 (tt0) cc_final: 0.9332 (tt0)
REVERT: A  702 GLU cc_start: 0.8616 (tp30) cc_final: 0.7910 (tp30)
REVERT: A  704 MET cc_start: 0.9305 (tpp) cc_final: 0.8988 (tpp)
REVERT: A  734 GLU cc_start: 0.8761 (tp30) cc_final: 0.8221 (tp30)
REVERT: A  755 LYS cc_start: 0.9031 (ptmm) cc_final: 0.8806 (ptpp)
REVERT: A  840 ASP cc_start: 0.8507 (t0) cc_final: 0.8204 (t70)
REVERT: B  117 MET cc_start: 0.8419 (tmm) cc_final: 0.7795 (tmm)
REVERT: B  252 GLU cc_start: 0.9274 (tp30) cc_final: 0.9013 (tp30)
REVERT: B  367 MET cc_start: 0.9105 (mtt) cc_final: 0.8793 (mtt)
REVERT: B  368 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8767 (mm-30)
REVERT: B  369 MET cc_start: 0.8878 (mtp) cc_final: 0.8353 (ttm)
REVERT: B  702 GLU cc_start: 0.8589 (tp30) cc_final: 0.8047 (tp30)
REVERT: B  734 GLU cc_start: 0.8744 (tp30) cc_final: 0.8196 (tp30)
REVERT: B  794 MET cc_start: 0.8304 (mmp) cc_final: 0.7939 (mmp)
REVERT: B  840 ASP cc_start: 0.8475 (t0) cc_final: 0.8125 (t70)
REVERT: B  881 PHE cc_start: 0.8924 (t80) cc_final: 0.8478 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.3022
  time to fit residues: 75.2264
Evaluate side-chains
  130 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 3.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 131 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 138 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 132 optimal weight:    2.9990
   chunk 119 optimal weight:    7.9990
   chunk 135 optimal weight:    0.9980
   chunk 60 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 206 GLN
** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 896 GLN
B 206 GLN
** B 229 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 = 0.3313 r_free = 0.3313 target = 0.076409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.059444 restraints weight = 45664.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.060945 restraints weight = 26220.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.061910 restraints weight = 18201.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.4294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11898  Z= 0.185
  Angle     :  0.671  10.005  16110  Z= 0.342
  Chirality :  0.044   0.202   1774
  Planarity :  0.004   0.041   2020
  Dihedral  :  4.575  19.233   1562
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.24), residues: 1398
  helix:  2.00 (0.18), residues: 840
  sheet: -1.21 (0.81), residues: 48
  loop : -2.64 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 427 
 HIS   0.004   0.001   HIS B 402 
 PHE   0.019   0.001   PHE A 712 
 TYR   0.015   0.002   TYR B 687 
 ARG   0.003   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04001 (  616)
  hydrogen bonds       : angle       4.14292 ( 1830)
  SS BOND              : bond        0.00380 (    8)
  SS BOND              : angle       1.16058 (   16)
  covalent geometry    : bond        0.00409 (11890)
  covalent geometry    : angle       0.67005 (16094)

*********************** 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
  157 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8479 (tmm) cc_final: 0.7470 (tmm)
REVERT: A  125 ARG cc_start: 0.8572 (tpp80) cc_final: 0.8321 (tpp80)
REVERT: A  252 GLU cc_start: 0.9302 (tp30) cc_final: 0.8992 (tp30)
REVERT: A  341 MET cc_start: 0.9412 (tpp) cc_final: 0.8966 (tpp)
REVERT: A  367 MET cc_start: 0.9062 (mmt) cc_final: 0.8835 (mpp)
REVERT: A  368 GLU cc_start: 0.8776 (mp0) cc_final: 0.8261 (mp0)
REVERT: A  378 MET cc_start: 0.7564 (mpp) cc_final: 0.6943 (mpp)
REVERT: A  557 TYR cc_start: 0.8879 (m-10) cc_final: 0.8221 (m-80)
REVERT: A  637 GLN cc_start: 0.9647 (tt0) cc_final: 0.9365 (tt0)
REVERT: A  702 GLU cc_start: 0.8661 (tp30) cc_final: 0.8091 (tp30)
REVERT: A  734 GLU cc_start: 0.8802 (tp30) cc_final: 0.8269 (tp30)
REVERT: A  755 LYS cc_start: 0.9094 (ptmm) cc_final: 0.8776 (ptpt)
REVERT: A  786 ILE cc_start: 0.9837 (mm) cc_final: 0.9636 (mt)
REVERT: A  840 ASP cc_start: 0.8672 (t0) cc_final: 0.8296 (t70)
REVERT: B  125 ARG cc_start: 0.8615 (tpp80) cc_final: 0.8363 (tpp80)
REVERT: B  252 GLU cc_start: 0.9340 (tp30) cc_final: 0.9090 (tp30)
REVERT: B  367 MET cc_start: 0.9107 (mtt) cc_final: 0.8801 (mtt)
REVERT: B  368 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8762 (mm-30)
REVERT: B  369 MET cc_start: 0.8934 (mtp) cc_final: 0.8412 (ttm)
REVERT: B  424 MET cc_start: 0.8682 (mmm) cc_final: 0.8420 (mmm)
REVERT: B  702 GLU cc_start: 0.8584 (tp30) cc_final: 0.8024 (tp30)
REVERT: B  734 GLU cc_start: 0.8778 (tp30) cc_final: 0.8245 (tp30)
REVERT: B  786 ILE cc_start: 0.9844 (mm) cc_final: 0.9635 (mt)
REVERT: B  794 MET cc_start: 0.8343 (mmp) cc_final: 0.7957 (mmp)
REVERT: B  840 ASP cc_start: 0.8665 (t0) cc_final: 0.8247 (t70)
REVERT: B  881 PHE cc_start: 0.8900 (t80) cc_final: 0.8491 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2156
  time to fit residues: 50.8698
Evaluate side-chains
  123 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   chunk 117 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   chunk 135 optimal weight:    3.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 229 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 = 0.3319 r_free = 0.3319 target = 0.076795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.059891 restraints weight = 44845.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.061423 restraints weight = 25814.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.062390 restraints weight = 17893.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.4425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11898  Z= 0.155
  Angle     :  0.654   8.880  16110  Z= 0.331
  Chirality :  0.043   0.188   1774
  Planarity :  0.004   0.047   2020
  Dihedral  :  4.585  19.595   1562
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.24), residues: 1398
  helix:  2.05 (0.18), residues: 838
  sheet: -1.18 (0.81), residues: 48
  loop : -2.58 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 402 
 PHE   0.021   0.001   PHE A 712 
 TYR   0.020   0.001   TYR A 687 
 ARG   0.003   0.000   ARG B 837 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03839 (  616)
  hydrogen bonds       : angle       4.08017 ( 1830)
  SS BOND              : bond        0.00287 (    8)
  SS BOND              : angle       2.06282 (   16)
  covalent geometry    : bond        0.00347 (11890)
  covalent geometry    : angle       0.65081 (16094)

*********************** 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
  157 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.266 
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: 0.8508 (tmm) cc_final: 0.8300 (tmm)
REVERT: A  125 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8279 (tpp80)
REVERT: A  252 GLU cc_start: 0.9275 (tp30) cc_final: 0.8995 (tp30)
REVERT: A  341 MET cc_start: 0.9380 (tpp) cc_final: 0.8956 (tpp)
REVERT: A  367 MET cc_start: 0.9071 (mmt) cc_final: 0.8848 (mpp)
REVERT: A  368 GLU cc_start: 0.8778 (mp0) cc_final: 0.8152 (mp0)
REVERT: A  378 MET cc_start: 0.7510 (mpp) cc_final: 0.7131 (mpp)
REVERT: A  406 ASN cc_start: 0.9192 (t0) cc_final: 0.8968 (t0)
REVERT: A  637 GLN cc_start: 0.9627 (tt0) cc_final: 0.9358 (tt0)
REVERT: A  702 GLU cc_start: 0.8537 (tp30) cc_final: 0.7986 (tp30)
REVERT: A  734 GLU cc_start: 0.8744 (tp30) cc_final: 0.8053 (tp30)
REVERT: A  738 ASP cc_start: 0.8265 (m-30) cc_final: 0.6782 (m-30)
REVERT: A  755 LYS cc_start: 0.9141 (ptmm) cc_final: 0.8735 (ptpp)
REVERT: A  840 ASP cc_start: 0.8576 (t0) cc_final: 0.8170 (t70)
REVERT: B  125 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8311 (tpp80)
REVERT: B  252 GLU cc_start: 0.9308 (tp30) cc_final: 0.9065 (tp30)
REVERT: B  367 MET cc_start: 0.9109 (mtt) cc_final: 0.8850 (mtt)
REVERT: B  368 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8802 (mm-30)
REVERT: B  554 ASP cc_start: 0.9233 (t0) cc_final: 0.8951 (t0)
REVERT: B  702 GLU cc_start: 0.8508 (tp30) cc_final: 0.7939 (tp30)
REVERT: B  734 GLU cc_start: 0.8709 (tp30) cc_final: 0.8021 (tp30)
REVERT: B  738 ASP cc_start: 0.8280 (m-30) cc_final: 0.6764 (m-30)
REVERT: B  794 MET cc_start: 0.8394 (mmp) cc_final: 0.8004 (mmp)
REVERT: B  840 ASP cc_start: 0.8524 (t0) cc_final: 0.8088 (t70)
REVERT: B  881 PHE cc_start: 0.8881 (t80) cc_final: 0.8489 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2060
  time to fit residues: 48.4655
Evaluate side-chains
  119 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 92 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9990
   chunk 119 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 125 optimal weight:    3.9990
   chunk 132 optimal weight:    0.8980
   chunk 70 optimal weight:    9.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 229 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 = 0.075718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.058751 restraints weight = 45764.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.060231 restraints weight = 26249.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.061195 restraints weight = 18249.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11898  Z= 0.196
  Angle     :  0.686  11.958  16110  Z= 0.350
  Chirality :  0.044   0.178   1774
  Planarity :  0.004   0.046   2020
  Dihedral  :  4.686  19.811   1562
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.23), residues: 1398
  helix:  2.00 (0.18), residues: 836
  sheet: -1.05 (0.83), residues: 48
  loop : -2.63 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 334 
 HIS   0.005   0.001   HIS B 402 
 PHE   0.019   0.002   PHE A 505 
 TYR   0.017   0.002   TYR A 687 
 ARG   0.003   0.000   ARG A 837 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  616)
  hydrogen bonds       : angle       4.15823 ( 1830)
  SS BOND              : bond        0.00396 (    8)
  SS BOND              : angle       1.91726 (   16)
  covalent geometry    : bond        0.00433 (11890)
  covalent geometry    : angle       0.68407 (16094)

*********************** 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
  149 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8485 (tmm) cc_final: 0.8233 (tmm)
REVERT: A  125 ARG cc_start: 0.8511 (tpp80) cc_final: 0.8271 (tpp80)
REVERT: A  252 GLU cc_start: 0.9297 (tp30) cc_final: 0.9024 (tp30)
REVERT: A  341 MET cc_start: 0.9375 (tpp) cc_final: 0.8949 (tpp)
REVERT: A  367 MET cc_start: 0.9111 (mmt) cc_final: 0.8876 (mpp)
REVERT: A  368 GLU cc_start: 0.8809 (mp0) cc_final: 0.8178 (mp0)
REVERT: A  378 MET cc_start: 0.7223 (mpp) cc_final: 0.6933 (mpp)
REVERT: A  416 MET cc_start: 0.9350 (mmp) cc_final: 0.9128 (mmm)
REVERT: A  424 MET cc_start: 0.8675 (mmm) cc_final: 0.8368 (mmm)
REVERT: A  622 MET cc_start: 0.8005 (pmm) cc_final: 0.7764 (pmm)
REVERT: A  637 GLN cc_start: 0.9635 (tt0) cc_final: 0.9362 (tt0)
REVERT: A  702 GLU cc_start: 0.8633 (tp30) cc_final: 0.8227 (tp30)
REVERT: A  734 GLU cc_start: 0.8863 (tp30) cc_final: 0.7924 (tp30)
REVERT: A  738 ASP cc_start: 0.8322 (m-30) cc_final: 0.5869 (m-30)
REVERT: A  755 LYS cc_start: 0.9148 (ptmm) cc_final: 0.8794 (ptpt)
REVERT: A  840 ASP cc_start: 0.8654 (t0) cc_final: 0.8210 (t70)
REVERT: B  125 ARG cc_start: 0.8557 (tpp80) cc_final: 0.8322 (tpp80)
REVERT: B  252 GLU cc_start: 0.9296 (tp30) cc_final: 0.9064 (tp30)
REVERT: B  367 MET cc_start: 0.9096 (mtt) cc_final: 0.8854 (mtt)
REVERT: B  368 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8802 (mm-30)
REVERT: B  369 MET cc_start: 0.8892 (mtp) cc_final: 0.8621 (mtm)
REVERT: B  702 GLU cc_start: 0.8563 (tp30) cc_final: 0.8205 (tp30)
REVERT: B  734 GLU cc_start: 0.8875 (tp30) cc_final: 0.8074 (tp30)
REVERT: B  786 ILE cc_start: 0.9751 (mt) cc_final: 0.9309 (tt)
REVERT: B  794 MET cc_start: 0.8307 (mmp) cc_final: 0.7917 (mmp)
REVERT: B  840 ASP cc_start: 0.8664 (t0) cc_final: 0.8178 (t70)
REVERT: B  881 PHE cc_start: 0.8914 (t80) cc_final: 0.8500 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2295
  time to fit residues: 52.3949
Evaluate side-chains
  115 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 103 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 229 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 = 0.3342 r_free = 0.3342 target = 0.077861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.061059 restraints weight = 44703.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.062577 restraints weight = 25645.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.063561 restraints weight = 17749.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.4678

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= 0.118
  Angle     :  0.647   8.715  16110  Z= 0.319
  Chirality :  0.042   0.170   1774
  Planarity :  0.004   0.040   2020
  Dihedral  :  4.504  18.685   1562
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.24), residues: 1398
  helix:  2.01 (0.18), residues: 848
  sheet: -1.24 (0.82), residues: 48
  loop : -2.58 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 427 
 HIS   0.002   0.000   HIS B 426 
 PHE   0.020   0.001   PHE A 505 
 TYR   0.018   0.001   TYR A 687 
 ARG   0.006   0.000   ARG A 765 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03547 (  616)
  hydrogen bonds       : angle       3.92001 ( 1830)
  SS BOND              : bond        0.00413 (    8)
  SS BOND              : angle       1.81834 (   16)
  covalent geometry    : bond        0.00262 (11890)
  covalent geometry    : angle       0.64488 (16094)

********************** 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
  169 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 ARG cc_start: 0.8435 (tpp80) cc_final: 0.8184 (tpp80)
REVERT: A  252 GLU cc_start: 0.9267 (tp30) cc_final: 0.9004 (tp30)
REVERT: A  341 MET cc_start: 0.9374 (tpp) cc_final: 0.8959 (tpp)
REVERT: A  368 GLU cc_start: 0.8681 (mp0) cc_final: 0.8156 (mp0)
REVERT: A  378 MET cc_start: 0.7056 (mpp) cc_final: 0.6811 (mpp)
REVERT: A  416 MET cc_start: 0.9311 (mmp) cc_final: 0.9081 (mmm)
REVERT: A  424 MET cc_start: 0.8515 (mmm) cc_final: 0.8222 (mmm)
REVERT: A  637 GLN cc_start: 0.9628 (tt0) cc_final: 0.9346 (tt0)
REVERT: A  702 GLU cc_start: 0.8411 (tp30) cc_final: 0.7901 (tp30)
REVERT: A  734 GLU cc_start: 0.8688 (tp30) cc_final: 0.8035 (tp30)
REVERT: A  738 ASP cc_start: 0.8224 (m-30) cc_final: 0.6699 (m-30)
REVERT: A  755 LYS cc_start: 0.9154 (ptmm) cc_final: 0.8727 (ptpt)
REVERT: A  840 ASP cc_start: 0.8502 (t0) cc_final: 0.8119 (t70)
REVERT: B  125 ARG cc_start: 0.8451 (tpp80) cc_final: 0.8196 (tpp80)
REVERT: B  252 GLU cc_start: 0.9210 (tp30) cc_final: 0.8968 (tp30)
REVERT: B  367 MET cc_start: 0.9094 (mtt) cc_final: 0.8847 (mtt)
REVERT: B  368 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8793 (mm-30)
REVERT: B  369 MET cc_start: 0.8881 (mtp) cc_final: 0.8514 (mtm)
REVERT: B  499 PHE cc_start: 0.8960 (t80) cc_final: 0.8758 (t80)
REVERT: B  554 ASP cc_start: 0.9193 (t0) cc_final: 0.8990 (t0)
REVERT: B  702 GLU cc_start: 0.8391 (tp30) cc_final: 0.7897 (tp30)
REVERT: B  734 GLU cc_start: 0.8727 (tp30) cc_final: 0.8007 (tp30)
REVERT: B  738 ASP cc_start: 0.8181 (m-30) cc_final: 0.6622 (m-30)
REVERT: B  775 ASN cc_start: 0.9265 (m-40) cc_final: 0.8850 (m-40)
REVERT: B  794 MET cc_start: 0.8375 (mmp) cc_final: 0.7968 (mmp)
REVERT: B  840 ASP cc_start: 0.8495 (t0) cc_final: 0.8088 (t70)
REVERT: B  881 PHE cc_start: 0.8865 (t80) cc_final: 0.8463 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2129
  time to fit residues: 55.1926
Evaluate side-chains
  130 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 110 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 111 optimal weight:    0.7980
   chunk 94 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 229 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 = 0.3303 r_free = 0.3303 target = 0.075963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.059453 restraints weight = 45298.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.060861 restraints weight = 25619.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.061767 restraints weight = 17868.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.4731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11898  Z= 0.182
  Angle     :  0.680  11.244  16110  Z= 0.345
  Chirality :  0.044   0.168   1774
  Planarity :  0.004   0.044   2020
  Dihedral  :  4.568  18.505   1562
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.23), residues: 1398
  helix:  1.96 (0.18), residues: 844
  sheet: -1.34 (0.79), residues: 48
  loop : -2.61 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 760 
 HIS   0.004   0.001   HIS B 402 
 PHE   0.020   0.002   PHE A 505 
 TYR   0.016   0.001   TYR A 687 
 ARG   0.004   0.000   ARG B 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  616)
  hydrogen bonds       : angle       4.08830 ( 1830)
  SS BOND              : bond        0.00389 (    8)
  SS BOND              : angle       1.80748 (   16)
  covalent geometry    : bond        0.00405 (11890)
  covalent geometry    : angle       0.67822 (16094)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3761.72 seconds
wall clock time: 69 minutes 31.84 seconds (4171.84 seconds total)