Starting phenix.real_space_refine
on Thu Jul 24 09:47:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sk0_10219/07_2025/6sk0_10219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sk0_10219/07_2025/6sk0_10219.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6sk0_10219/07_2025/6sk0_10219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sk0_10219/07_2025/6sk0_10219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sk0_10219/07_2025/6sk0_10219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sk0_10219/07_2025/6sk0_10219.cif"
  }
  resolution = 2.3
  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=   1.000
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      39      5.16       5
     C    3531      2.51       5
     N    1077      2.21       5
     O    1179      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5826
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1942
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 5, 'TRANS': 258}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 4.16, per 1000 atoms: 0.71
  Number of scatterers: 5826
  At special positions: 0
  Unit cell: (61.44, 57.344, 121.856, 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      39     16.00
     O    1179      8.00
     N    1077      7.00
     C    3531      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 801.1 milliseconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1410

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 3 sheets defined
      17.4% alpha, 39.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 567 through 571
    Processing helix  chain 'A' and resid 577 through 601
    Processing helix  chain 'A' and resid 607 through 619
      removed outlier: 3.845A  pdb=" N   GLN A 611 " --> pdb=" O   ASP A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 622
      No H-bonds generated for 'chain 'A' and resid 620 through 622'
    Processing helix  chain 'B' and resid 567 through 571
    Processing helix  chain 'B' and resid 577 through 601
    Processing helix  chain 'B' and resid 607 through 619
      removed outlier: 3.845A  pdb=" N   GLN B 611 " --> pdb=" O   ASP B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 622
      No H-bonds generated for 'chain 'B' and resid 620 through 622'
    Processing helix  chain 'C' and resid 567 through 571
    Processing helix  chain 'C' and resid 577 through 601
    Processing helix  chain 'C' and resid 607 through 619
      removed outlier: 3.846A  pdb=" N   GLN C 611 " --> pdb=" O   ASP C 607 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 620 through 622
      No H-bonds generated for 'chain 'C' and resid 620 through 622'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497
      removed outlier: 9.961A  pdb=" N   TRP B 551 " --> pdb=" O   ARG A 540 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   GLU A 542 " --> pdb=" O   TRP B 551 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   SER B 553 " --> pdb=" O   GLU A 542 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ALA A 544 " --> pdb=" O   SER B 553 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   ARG B 555 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LEU A 546 " --> pdb=" O   ARG B 555 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ILE B 552 " --> pdb=" O   PHE C 561 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   SER C 563 " --> pdb=" O   ILE B 552 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   ILE B 554 " --> pdb=" O   SER C 563 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ILE C 560 " --> pdb=" O   LEU C 627 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   HIS C 629 " --> pdb=" O   ILE C 560 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ILE C 562 " --> pdb=" O   HIS C 629 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLY A 635 " --> pdb=" O   LEU C 628 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   LEU B 642 " --> pdb=" O   GLY C 652 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   MET C 654 " --> pdb=" O   LEU B 642 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ILE B 644 " --> pdb=" O   MET C 654 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   PHE B 667 " --> pdb=" O   SER C 676 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   LEU C 678 " --> pdb=" O   PHE B 667 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL B 669 " --> pdb=" O   LEU C 678 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   GLN A 685 " --> pdb=" O   LEU C 677 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   SER C 679 " --> pdb=" O   GLN A 685 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU A 687 " --> pdb=" O   SER C 679 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   MET A 684 " --> pdb=" O   ASN B 694 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   GLN B 696 " --> pdb=" O   MET A 684 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A 686 " --> pdb=" O   GLN B 696 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   VAL B 693 " --> pdb=" O   SER C 703 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   SER C 705 " --> pdb=" O   VAL B 693 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ILE B 695 " --> pdb=" O   SER C 705 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ASP A 711 " --> pdb=" O   MET C 704 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   SER C 706 " --> pdb=" O   ASP A 711 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   GLN A 713 " --> pdb=" O   SER C 706 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   LEU A 752 " --> pdb=" O   LEU C 745 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 493 through 497
      removed outlier: 6.306A  pdb=" N   ILE A 552 " --> pdb=" O   PHE B 561 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   SER B 563 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   ILE A 554 " --> pdb=" O   SER B 563 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ILE B 560 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   HIS B 629 " --> pdb=" O   ILE B 560 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   ILE B 562 " --> pdb=" O   HIS B 629 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ARG A 643 " --> pdb=" O   MET C 636 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   SER C 638 " --> pdb=" O   ARG A 643 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   ALA A 645 " --> pdb=" O   SER C 638 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   LEU A 642 " --> pdb=" O   GLY B 652 " (cutoff:3.500A)
      removed outlier: 7.680A  pdb=" N   MET B 654 " --> pdb=" O   LEU A 642 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   ILE A 644 " --> pdb=" O   MET B 654 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   VAL B 651 " --> pdb=" O   ASP C 660 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   THR C 662 " --> pdb=" O   VAL B 651 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ILE B 653 " --> pdb=" O   THR C 662 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   THR A 668 " --> pdb=" O   ILE C 661 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   ALA C 663 " --> pdb=" O   THR A 668 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL A 670 " --> pdb=" O   ALA C 663 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   PHE A 667 " --> pdb=" O   SER B 676 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   LEU B 678 " --> pdb=" O   PHE A 667 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL A 669 " --> pdb=" O   LEU B 678 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   VAL A 693 " --> pdb=" O   SER B 703 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   SER B 705 " --> pdb=" O   VAL A 693 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ILE A 695 " --> pdb=" O   SER B 705 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   THR A 720 " --> pdb=" O   ILE C 712 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   SER C 714 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   SER A 722 " --> pdb=" O   SER C 714 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 493 through 497
      removed outlier: 9.976A  pdb=" N   TRP C 551 " --> pdb=" O   ARG B 540 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   GLU B 542 " --> pdb=" O   TRP C 551 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   SER C 553 " --> pdb=" O   GLU B 542 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ALA B 544 " --> pdb=" O   SER C 553 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   ARG C 555 " --> pdb=" O   ALA B 544 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU B 546 " --> pdb=" O   ARG C 555 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ILE A 560 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   HIS A 629 " --> pdb=" O   ILE A 560 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ILE A 562 " --> pdb=" O   HIS A 629 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   VAL A 651 " --> pdb=" O   ASP B 660 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   THR B 662 " --> pdb=" O   VAL A 651 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ILE A 653 " --> pdb=" O   THR B 662 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   MET B 684 " --> pdb=" O   ASN C 694 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   GLN C 696 " --> pdb=" O   MET B 684 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU B 686 " --> pdb=" O   GLN C 696 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   GLU A 726 " --> pdb=" O   VAL C 719 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   VAL C 721 " --> pdb=" O   GLU A 726 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ILE A 728 " --> pdb=" O   VAL C 721 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   ALA C 723 " --> pdb=" O   ILE A 728 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ALA A 730 " --> pdb=" O   ALA C 723 " (cutoff:3.500A)

    294 hydrogen bonds defined for protein.
    810 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: 2.04

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2100
        1.34 -     1.45: 653
        1.45 -     1.57: 3043
        1.57 -     1.69: 0
        1.69 -     1.80: 69
  Bond restraints: 5865
  Sorted by residual:
  bond pdb=" CA  GLY B 746 "
       pdb=" C   GLY B 746 "
    ideal  model  delta    sigma   weight residual
    1.516  1.504  0.012 8.10e-03 1.52e+04 2.11e+00
  bond pdb=" CB  GLN A 696 "
       pdb=" CG  GLN A 696 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.09e+00
  bond pdb=" CA  GLU B 649 "
       pdb=" C   GLU B 649 "
    ideal  model  delta    sigma   weight residual
    1.527  1.513  0.014 9.80e-03 1.04e+04 2.05e+00
  bond pdb=" CB  GLN B 696 "
       pdb=" CG  GLN B 696 "
    ideal  model  delta    sigma   weight residual
    1.520  1.478  0.042 3.00e-02 1.11e+03 1.99e+00
  bond pdb=" CA  GLU A 649 "
       pdb=" C   GLU A 649 "
    ideal  model  delta    sigma   weight residual
    1.527  1.514  0.014 9.80e-03 1.04e+04 1.95e+00
  ... (remaining 5860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 7244
        1.28 -     2.55: 548
        2.55 -     3.83: 80
        3.83 -     5.11: 6
        5.11 -     6.39: 6
  Bond angle restraints: 7884
  Sorted by residual:
  angle pdb=" N   GLY C 523 "
        pdb=" CA  GLY C 523 "
        pdb=" C   GLY C 523 "
      ideal   model   delta    sigma   weight residual
     111.80  105.41    6.39 1.82e+00 3.02e-01 1.23e+01
  angle pdb=" N   GLY A 523 "
        pdb=" CA  GLY A 523 "
        pdb=" C   GLY A 523 "
      ideal   model   delta    sigma   weight residual
     111.80  105.42    6.38 1.82e+00 3.02e-01 1.23e+01
  angle pdb=" N   GLY B 523 "
        pdb=" CA  GLY B 523 "
        pdb=" C   GLY B 523 "
      ideal   model   delta    sigma   weight residual
     111.80  105.45    6.35 1.82e+00 3.02e-01 1.22e+01
  angle pdb=" C   LEU A 745 "
        pdb=" N   GLY A 746 "
        pdb=" CA  GLY A 746 "
      ideal   model   delta    sigma   weight residual
     122.33  120.46    1.87 7.30e-01 1.88e+00 6.57e+00
  angle pdb=" C   LEU B 745 "
        pdb=" N   GLY B 746 "
        pdb=" CA  GLY B 746 "
      ideal   model   delta    sigma   weight residual
     122.33  120.48    1.85 7.30e-01 1.88e+00 6.45e+00
  ... (remaining 7879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.76: 3247
       16.76 -    33.53: 272
       33.53 -    50.29: 81
       50.29 -    67.05: 18
       67.05 -    83.81: 18
  Dihedral angle restraints: 3636
    sinusoidal: 1431
      harmonic: 2205
  Sorted by residual:
  dihedral pdb=" CA  GLN B 696 "
           pdb=" C   GLN B 696 "
           pdb=" N   ALA B 697 "
           pdb=" CA  ALA B 697 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.68   25.32     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  GLN C 696 "
           pdb=" C   GLN C 696 "
           pdb=" N   ALA C 697 "
           pdb=" CA  ALA C 697 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.71   25.29     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  GLN A 696 "
           pdb=" C   GLN A 696 "
           pdb=" N   ALA A 697 "
           pdb=" CA  ALA A 697 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.72   25.28     0      5.00e+00 4.00e-02 2.56e+01
  ... (remaining 3633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 387
       0.026 -    0.051: 265
       0.051 -    0.077: 136
       0.077 -    0.103: 84
       0.103 -    0.129: 40
  Chirality restraints: 912
  Sorted by residual:
  chirality pdb=" CA  ILE B 496 "
            pdb=" N   ILE B 496 "
            pdb=" C   ILE B 496 "
            pdb=" CB  ILE B 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  ILE C 496 "
            pdb=" N   ILE C 496 "
            pdb=" C   ILE C 496 "
            pdb=" CB  ILE C 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  ILE A 496 "
            pdb=" N   ILE A 496 "
            pdb=" C   ILE A 496 "
            pdb=" CB  ILE A 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 909 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 665 "    0.015 2.00e-02 2.50e+03   2.93e-02 8.56e+00
        pdb=" C   GLN A 665 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   GLN A 665 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER A 666 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 665 "   -0.015 2.00e-02 2.50e+03   2.93e-02 8.56e+00
        pdb=" C   GLN B 665 "    0.051 2.00e-02 2.50e+03
        pdb=" O   GLN B 665 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER B 666 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C 665 "    0.015 2.00e-02 2.50e+03   2.91e-02 8.49e+00
        pdb=" C   GLN C 665 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLN C 665 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER C 666 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 516
        2.74 -     3.28: 5764
        3.28 -     3.82: 11472
        3.82 -     4.36: 14173
        4.36 -     4.90: 22912
  Nonbonded interactions: 54837
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 735 "
            pdb=" OE2 GLU C 744 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OH  TYR A 735 "
            pdb=" OE2 GLU A 744 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OH  TYR B 735 "
            pdb=" OE2 GLU B 744 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" N   GLY A 673 "
            pdb=" O   GLN C 665 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" O   GLN A 665 "
            pdb=" N   GLY B 673 "
     model   vdw
     2.311 3.120
  ... (remaining 54832 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.870
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.120
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:17.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
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      :  0.008   0.049   5865  Z= 0.401
  Angle     :  0.738   6.386   7884  Z= 0.431
  Chirality :  0.049   0.129    912
  Planarity :  0.004   0.032   1056
  Dihedral  : 15.851  83.813   2226
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  6.31 %
    Favored  : 92.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.30 (0.25), residues: 786
  helix:  1.47 (0.44), residues: 114
  sheet:  0.81 (0.46), residues: 105
  loop : -1.85 (0.20), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP A 551 
 HIS   0.007   0.003   HIS A 629 
 PHE   0.005   0.002   PHE C 667 
 TYR   0.006   0.002   TYR B 521 
 ARG   0.003   0.000   ARG A 613 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13147 (  294)
  hydrogen bonds       : angle       6.27502 (  810)
  covalent geometry    : bond        0.00801 ( 5865)
  covalent geometry    : angle       0.73780 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8238 (mtmm)
REVERT: A  654 MET cc_start: 0.8853 (mpt) cc_final: 0.8135 (mpt)
REVERT: A  737 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8232 (ttpp)
REVERT: B  516 LYS cc_start: 0.8835 (tttt) cc_final: 0.8485 (tttt)
REVERT: B  537 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7556 (mpt-90)
REVERT: B  566 MET cc_start: 0.8185 (tpp) cc_final: 0.7931 (tpp)
REVERT: B  573 LYS cc_start: 0.8892 (mmtp) cc_final: 0.8564 (mmtp)
REVERT: B  684 MET cc_start: 0.8374 (ttm) cc_final: 0.7769 (ttm)
REVERT: B  737 LYS cc_start: 0.8522 (ttmt) cc_final: 0.7427 (ttpp)
REVERT: C  509 LYS cc_start: 0.8236 (tttt) cc_final: 0.8028 (ttmt)
REVERT: C  737 LYS cc_start: 0.8509 (ttmt) cc_final: 0.7508 (ttpp)
  outliers start: 6
  outliers final: 3
  residues processed: 111
  average time/residue: 1.8374
  time to fit residues: 210.3577
Evaluate side-chains
  93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain B residue  722 SER
Chi-restraints excluded: chain C residue  722 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 502 ASN
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS
A 583 GLN
A 725 GLN
B 502 ASN
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 583 GLN
C 502 ASN
** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 531 HIS
C 583 GLN
C 750 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.108983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.096192 restraints weight = 4754.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 0.66
r_work: 0.3015 rms_B_bonded: 0.95 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 1.65 restraints_weight: 0.2500
r_work: 0.2638 rms_B_bonded: 4.48 restraints_weight: 0.1250
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8925
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5865  Z= 0.187
  Angle     :  0.607   4.709   7884  Z= 0.340
  Chirality :  0.048   0.149    912
  Planarity :  0.004   0.036   1056
  Dihedral  :  6.857  24.402    843
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 12.30 %
    Favored  : 87.22 %
  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: -1.32 (0.26), residues: 786
  helix:  2.33 (0.46), residues: 114
  sheet:  0.17 (0.52), residues: 90
  loop : -1.88 (0.21), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 551 
 HIS   0.007   0.003   HIS B 514 
 PHE   0.005   0.002   PHE A 667 
 TYR   0.004   0.001   TYR A 521 
 ARG   0.004   0.001   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04449 (  294)
  hydrogen bonds       : angle       5.07882 (  810)
  covalent geometry    : bond        0.00359 ( 5865)
  covalent geometry    : angle       0.60742 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
REVERT: A  654 MET cc_start: 0.9225 (mpt) cc_final: 0.8616 (mpt)
REVERT: B  684 MET cc_start: 0.9107 (ttm) cc_final: 0.8774 (ttm)
REVERT: B  737 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8483 (ttpp)
REVERT: C  713 GLN cc_start: 0.8953 (tt0) cc_final: 0.8726 (pm20)
REVERT: C  737 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8569 (ttpp)
  outliers start: 3
  outliers final: 1
  residues processed: 107
  average time/residue: 1.8751
  time to fit residues: 206.7644
Evaluate side-chains
  94 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  615 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 ASN
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 571 GLN
** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.107154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.094687 restraints weight = 4727.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 0.62
r_work: 0.2997 rms_B_bonded: 0.90 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 1.57 restraints_weight: 0.2500
r_work: 0.2630 rms_B_bonded: 4.29 restraints_weight: 0.1250
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5865  Z= 0.324
  Angle     :  0.718   5.993   7884  Z= 0.397
  Chirality :  0.051   0.152    912
  Planarity :  0.005   0.044   1056
  Dihedral  :  7.210  26.407    840
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.59 %
    Favored  : 85.44 %
  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: -1.43 (0.26), residues: 786
  helix:  2.09 (0.46), residues: 114
  sheet: -0.26 (0.54), residues: 75
  loop : -1.83 (0.21), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 551 
 HIS   0.008   0.003   HIS B 514 
 PHE   0.008   0.003   PHE A 667 
 TYR   0.009   0.003   TYR B 735 
 ARG   0.005   0.001   ARG B 613 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04999 (  294)
  hydrogen bonds       : angle       5.13918 (  810)
  covalent geometry    : bond        0.00639 ( 5865)
  covalent geometry    : angle       0.71804 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A  654 MET cc_start: 0.9267 (mpt) cc_final: 0.8802 (mpt)
REVERT: B  684 MET cc_start: 0.9120 (ttm) cc_final: 0.8803 (ttm)
REVERT: B  737 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8492 (ttpp)
REVERT: C  737 LYS cc_start: 0.9224 (ttmt) cc_final: 0.8660 (ttpp)
  outliers start: 6
  outliers final: 1
  residues processed: 102
  average time/residue: 1.7757
  time to fit residues: 187.0173
Evaluate side-chains
  100 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  495 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 571 GLN
** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.109400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.096869 restraints weight = 4759.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 0.62
r_work: 0.3035 rms_B_bonded: 0.92 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 1.60 restraints_weight: 0.2500
r_work: 0.2667 rms_B_bonded: 4.39 restraints_weight: 0.1250
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8920
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5865  Z= 0.211
  Angle     :  0.617   4.794   7884  Z= 0.345
  Chirality :  0.048   0.148    912
  Planarity :  0.004   0.040   1056
  Dihedral  :  6.940  24.979    840
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 14.24 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.26), residues: 786
  helix:  2.21 (0.46), residues: 114
  sheet: -0.50 (0.64), residues: 60
  loop : -1.86 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.008   0.002   PHE A 667 
 TYR   0.005   0.002   TYR B 735 
 ARG   0.004   0.001   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  294)
  hydrogen bonds       : angle       4.93265 (  810)
  covalent geometry    : bond        0.00408 ( 5865)
  covalent geometry    : angle       0.61740 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  654 MET cc_start: 0.9184 (mpt) cc_final: 0.8710 (mpt)
REVERT: B  684 MET cc_start: 0.9051 (ttm) cc_final: 0.8715 (ttm)
REVERT: B  737 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8479 (ttpp)
REVERT: C  737 LYS cc_start: 0.9190 (ttmt) cc_final: 0.8657 (ttpp)
  outliers start: 2
  outliers final: 1
  residues processed: 107
  average time/residue: 2.0364
  time to fit residues: 224.7410
Evaluate side-chains
  99 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0770
   chunk 21 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.1542

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 694 ASN
A 696 GLN
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.109170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.096799 restraints weight = 4688.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 0.61
r_work: 0.3035 rms_B_bonded: 0.91 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 1.57 restraints_weight: 0.2500
r_work: 0.2669 rms_B_bonded: 4.32 restraints_weight: 0.1250
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8919
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5865  Z= 0.229
  Angle     :  0.637   4.930   7884  Z= 0.353
  Chirality :  0.048   0.149    912
  Planarity :  0.004   0.041   1056
  Dihedral  :  6.962  25.105    840
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 14.40 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.51 (0.26), residues: 786
  helix:  2.22 (0.47), residues: 114
  sheet: -0.52 (0.64), residues: 60
  loop : -1.87 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.008   0.002   PHE A 667 
 TYR   0.006   0.002   TYR A 521 
 ARG   0.004   0.001   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  294)
  hydrogen bonds       : angle       4.91158 (  810)
  covalent geometry    : bond        0.00447 ( 5865)
  covalent geometry    : angle       0.63710 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  654 MET cc_start: 0.9210 (mpt) cc_final: 0.8718 (mpt)
REVERT: B  684 MET cc_start: 0.9045 (ttm) cc_final: 0.8705 (ttm)
REVERT: B  737 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8472 (ttpp)
REVERT: C  737 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8664 (ttpp)
  outliers start: 2
  outliers final: 0
  residues processed: 102
  average time/residue: 2.3690
  time to fit residues: 249.0067
Evaluate side-chains
  97 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 69 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 HIS ** 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 = 0.3328 r_free = 0.3328 target = 0.110376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.097884 restraints weight = 4805.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 0.63
r_work: 0.3051 rms_B_bonded: 0.94 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 1.61 restraints_weight: 0.2500
r_work: 0.2685 rms_B_bonded: 4.44 restraints_weight: 0.1250
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8907
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5865  Z= 0.190
  Angle     :  0.601   5.272   7884  Z= 0.334
  Chirality :  0.048   0.148    912
  Planarity :  0.004   0.040   1056
  Dihedral  :  6.822  24.315    840
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 14.56 %
    Favored  : 84.79 %
  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: -1.52 (0.26), residues: 786
  helix:  2.29 (0.47), residues: 114
  sheet: -0.55 (0.65), residues: 60
  loop : -1.88 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.006   0.002   PHE A 667 
 TYR   0.007   0.001   TYR A 735 
 ARG   0.003   0.001   ARG B 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03945 (  294)
  hydrogen bonds       : angle       4.83126 (  810)
  covalent geometry    : bond        0.00368 ( 5865)
  covalent geometry    : angle       0.60117 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8753 (mtmm)
REVERT: A  654 MET cc_start: 0.9184 (mpt) cc_final: 0.8669 (mpt)
REVERT: B  684 MET cc_start: 0.9070 (ttm) cc_final: 0.8758 (ttm)
REVERT: B  737 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8447 (ttpp)
REVERT: C  737 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8545 (ttpp)
  outliers start: 4
  outliers final: 2
  residues processed: 107
  average time/residue: 1.8455
  time to fit residues: 203.7054
Evaluate side-chains
  101 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  615 ASN
Chi-restraints excluded: chain C residue  563 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:    0.1980
   chunk 6 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 HIS ** 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 = 0.3332 r_free = 0.3332 target = 0.110633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.098026 restraints weight = 4806.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 0.64
r_work: 0.3056 rms_B_bonded: 0.94 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 1.64 restraints_weight: 0.2500
r_work: 0.2688 rms_B_bonded: 4.50 restraints_weight: 0.1250
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5865  Z= 0.182
  Angle     :  0.594   5.677   7884  Z= 0.330
  Chirality :  0.048   0.147    912
  Planarity :  0.004   0.039   1056
  Dihedral  :  6.762  24.005    840
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.72 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.26), residues: 786
  helix:  2.31 (0.47), residues: 114
  sheet: -0.54 (0.66), residues: 60
  loop : -1.89 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.007   0.002   PHE A 667 
 TYR   0.005   0.001   TYR C 521 
 ARG   0.008   0.001   ARG B 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03846 (  294)
  hydrogen bonds       : angle       4.78038 (  810)
  covalent geometry    : bond        0.00353 ( 5865)
  covalent geometry    : angle       0.59444 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8714 (mtmm)
REVERT: A  654 MET cc_start: 0.9177 (mpt) cc_final: 0.8639 (mpt)
REVERT: B  684 MET cc_start: 0.9045 (ttm) cc_final: 0.8725 (ttm)
REVERT: B  737 LYS cc_start: 0.9188 (ttmt) cc_final: 0.8448 (ttpp)
REVERT: C  737 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8506 (ttpp)
  outliers start: 7
  outliers final: 3
  residues processed: 106
  average time/residue: 1.7900
  time to fit residues: 195.7328
Evaluate side-chains
  103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  605 GLN
Chi-restraints excluded: chain B residue  615 ASN
Chi-restraints excluded: chain C residue  563 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0070
   chunk 4 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.4006

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 HIS ** 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 = 0.3308 r_free = 0.3308 target = 0.108948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.096584 restraints weight = 4693.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 0.61
r_work: 0.3032 rms_B_bonded: 0.90 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 1.57 restraints_weight: 0.2500
r_work: 0.2664 rms_B_bonded: 4.33 restraints_weight: 0.1250
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8924
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5865  Z= 0.259
  Angle     :  0.661   5.468   7884  Z= 0.365
  Chirality :  0.049   0.148    912
  Planarity :  0.004   0.042   1056
  Dihedral  :  7.037  25.222    840
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 15.21 %
    Favored  : 83.98 %
  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: -1.51 (0.26), residues: 786
  helix:  2.18 (0.47), residues: 114
  sheet: -0.52 (0.65), residues: 60
  loop : -1.86 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 551 
 HIS   0.007   0.003   HIS C 629 
 PHE   0.008   0.002   PHE A 667 
 TYR   0.007   0.002   TYR A 521 
 ARG   0.010   0.001   ARG B 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04371 (  294)
  hydrogen bonds       : angle       4.90464 (  810)
  covalent geometry    : bond        0.00510 ( 5865)
  covalent geometry    : angle       0.66074 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8768 (mtmm)
REVERT: A  654 MET cc_start: 0.9239 (mpt) cc_final: 0.8737 (mpt)
REVERT: B  684 MET cc_start: 0.9029 (ttm) cc_final: 0.8678 (ttm)
REVERT: B  737 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8483 (ttpp)
REVERT: C  737 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8541 (ttpp)
  outliers start: 5
  outliers final: 2
  residues processed: 103
  average time/residue: 1.8738
  time to fit residues: 198.8344
Evaluate side-chains
  99 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  605 GLN
Chi-restraints excluded: chain C residue  563 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    0.3980
   chunk 50 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 HIS ** 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 = 0.3345 r_free = 0.3345 target = 0.111537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.099109 restraints weight = 4740.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 0.62
r_work: 0.3072 rms_B_bonded: 0.93 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 1.61 restraints_weight: 0.2500
r_work: 0.2708 rms_B_bonded: 4.45 restraints_weight: 0.1250
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5865  Z= 0.164
  Angle     :  0.584   4.687   7884  Z= 0.325
  Chirality :  0.047   0.144    912
  Planarity :  0.004   0.039   1056
  Dihedral  :  6.731  23.747    840
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 15.37 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.26), residues: 786
  helix:  2.34 (0.47), residues: 114
  sheet: -0.50 (0.67), residues: 60
  loop : -1.88 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.008   0.001   PHE A 667 
 TYR   0.004   0.001   TYR A 521 
 ARG   0.009   0.001   ARG B 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  294)
  hydrogen bonds       : angle       4.75735 (  810)
  covalent geometry    : bond        0.00319 ( 5865)
  covalent geometry    : angle       0.58398 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9039 (mtmm) cc_final: 0.8723 (mtmm)
REVERT: A  654 MET cc_start: 0.9173 (mpt) cc_final: 0.8651 (mpt)
REVERT: B  684 MET cc_start: 0.9008 (ttm) cc_final: 0.8679 (ttm)
REVERT: B  737 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8453 (ttpp)
REVERT: C  737 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8514 (ttpp)
  outliers start: 5
  outliers final: 1
  residues processed: 104
  average time/residue: 1.7655
  time to fit residues: 189.5417
Evaluate side-chains
  97 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  563 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 76 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 HIS ** 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 = 0.3317 r_free = 0.3317 target = 0.109511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.096911 restraints weight = 4773.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 0.63
r_work: 0.3039 rms_B_bonded: 0.93 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 1.61 restraints_weight: 0.2500
r_work: 0.2670 rms_B_bonded: 4.41 restraints_weight: 0.1250
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5865  Z= 0.246
  Angle     :  0.655   5.850   7884  Z= 0.362
  Chirality :  0.049   0.148    912
  Planarity :  0.004   0.049   1056
  Dihedral  :  6.981  24.962    840
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 16.02 %
    Favored  : 83.50 %
  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: -1.49 (0.26), residues: 786
  helix:  2.22 (0.47), residues: 114
  sheet: -0.47 (0.66), residues: 60
  loop : -1.86 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 551 
 HIS   0.007   0.003   HIS B 514 
 PHE   0.009   0.002   PHE A 667 
 TYR   0.009   0.002   TYR C 521 
 ARG   0.010   0.001   ARG B 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  294)
  hydrogen bonds       : angle       4.88570 (  810)
  covalent geometry    : bond        0.00485 ( 5865)
  covalent geometry    : angle       0.65465 ( 7884)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 1.204 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9050 (mtmm) cc_final: 0.8720 (mtmm)
REVERT: A  654 MET cc_start: 0.9241 (mpt) cc_final: 0.8716 (mpt)
REVERT: B  684 MET cc_start: 0.9040 (ttm) cc_final: 0.8700 (ttm)
REVERT: B  737 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8475 (ttpp)
REVERT: C  737 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8522 (ttpp)
  outliers start: 3
  outliers final: 1
  residues processed: 100
  average time/residue: 2.5474
  time to fit residues: 263.2888
Evaluate side-chains
  98 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  563 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 HIS ** 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 = 0.3340 r_free = 0.3340 target = 0.111100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.098466 restraints weight = 4809.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 0.64
r_work: 0.3062 rms_B_bonded: 0.94 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 1.63 restraints_weight: 0.2500
r_work: 0.2695 rms_B_bonded: 4.48 restraints_weight: 0.1250
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5865  Z= 0.183
  Angle     :  0.602   4.803   7884  Z= 0.335
  Chirality :  0.048   0.146    912
  Planarity :  0.004   0.046   1056
  Dihedral  :  6.809  24.245    840
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 16.34 %
    Favored  : 83.17 %
  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: -1.49 (0.26), residues: 786
  helix:  2.31 (0.47), residues: 114
  sheet: -0.49 (0.67), residues: 60
  loop : -1.87 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.008   0.002   PHE A 667 
 TYR   0.005   0.001   TYR C 521 
 ARG   0.010   0.001   ARG B 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03837 (  294)
  hydrogen bonds       : angle       4.76756 (  810)
  covalent geometry    : bond        0.00357 ( 5865)
  covalent geometry    : angle       0.60249 ( 7884)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6226.58 seconds
wall clock time: 109 minutes 8.90 seconds (6548.90 seconds total)