Starting phenix.real_space_refine
on Tue Feb 11 13:55:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sk0_10219/02_2025/6sk0_10219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sk0_10219/02_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_10219/02_2025/6sk0_10219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sk0_10219/02_2025/6sk0_10219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sk0_10219/02_2025/6sk0_10219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sk0_10219/02_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.18, per 1000 atoms: 0.72
  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: 1.37
  Conformation dependent library (CDL) restraints added in 631.3 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: 0.90
  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: 2.03

  Time building geometry restraints manager: 1.61 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:             2.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.440
  Find NCS groups from input model:        0.110
  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:15.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.600
-------------------------------------------------------------------------------
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= 0.548
  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 

*********************** 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  : 0.739 
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: 1.8973
  time to fit residues: 217.2888
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  : 0.646 
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.8380

-------------------------------------------------------------------------------
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 = 0.108707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.096047 restraints weight = 4719.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 0.63
r_work: 0.3016 rms_B_bonded: 0.93 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 1.60 restraints_weight: 0.2500
r_work: 0.2640 rms_B_bonded: 4.38 restraints_weight: 0.1250
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5865  Z= 0.253
  Angle     :  0.617   4.741   7884  Z= 0.346
  Chirality :  0.048   0.150    912
  Planarity :  0.004   0.037   1056
  Dihedral  :  6.915  24.462    843
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.97 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.31 (0.26), residues: 786
  helix:  2.32 (0.46), residues: 114
  sheet:  0.20 (0.52), residues: 90
  loop : -1.88 (0.21), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 551 
 HIS   0.007   0.003   HIS B 514 
 PHE   0.006   0.002   PHE A 667 
 TYR   0.004   0.001   TYR A 521 
 ARG   0.004   0.001   ARG A 680 

*********************** 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  : 0.672 
Fit side-chains
   revert: symmetry clash
REVERT: A  654 MET cc_start: 0.9243 (mpt) cc_final: 0.8628 (mpt)
REVERT: B  684 MET cc_start: 0.9091 (ttm) cc_final: 0.8734 (ttm)
REVERT: B  737 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8430 (ttpp)
REVERT: C  713 GLN cc_start: 0.8967 (tt0) cc_final: 0.8744 (pm20)
REVERT: C  737 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8581 (ttpp)
  outliers start: 3
  outliers final: 1
  residues processed: 107
  average time/residue: 1.9363
  time to fit residues: 213.5681
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  : 0.781 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    0.2980
   chunk 35 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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 = 0.3275 r_free = 0.3275 target = 0.106824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.094321 restraints weight = 4735.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 0.62
r_work: 0.2992 rms_B_bonded: 0.91 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 1.57 restraints_weight: 0.2500
r_work: 0.2625 rms_B_bonded: 4.28 restraints_weight: 0.1250
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8955
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   5865  Z= 0.465
  Angle     :  0.740   6.136   7884  Z= 0.409
  Chirality :  0.052   0.153    912
  Planarity :  0.005   0.046   1056
  Dihedral  :  7.271  26.600    840
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.75 %
    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: -1.42 (0.26), residues: 786
  helix:  2.03 (0.46), residues: 114
  sheet: -0.20 (0.54), residues: 75
  loop : -1.81 (0.21), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 551 
 HIS   0.008   0.004   HIS B 514 
 PHE   0.009   0.003   PHE A 667 
 TYR   0.009   0.003   TYR B 735 
 ARG   0.006   0.001   ARG B 613 

*********************** 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  : 0.701 
Fit side-chains
REVERT: A  654 MET cc_start: 0.9276 (mpt) cc_final: 0.8803 (mpt)
REVERT: B  684 MET cc_start: 0.9116 (ttm) cc_final: 0.8792 (ttm)
REVERT: B  737 LYS cc_start: 0.9219 (ttmt) cc_final: 0.8490 (ttpp)
REVERT: C  737 LYS cc_start: 0.9224 (ttmt) cc_final: 0.8647 (ttpp)
  outliers start: 6
  outliers final: 1
  residues processed: 102
  average time/residue: 1.9222
  time to fit residues: 202.0700
Evaluate side-chains
  89 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3337 r_free = 0.3337 target = 0.110845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.098347 restraints weight = 4761.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 0.62
r_work: 0.3060 rms_B_bonded: 0.92 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 1.61 restraints_weight: 0.2500
r_work: 0.2692 rms_B_bonded: 4.42 restraints_weight: 0.1250
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5865  Z= 0.213
  Angle     :  0.581   4.559   7884  Z= 0.325
  Chirality :  0.047   0.149    912
  Planarity :  0.004   0.040   1056
  Dihedral  :  6.761  24.236    840
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 14.40 %
    Favored  : 84.95 %
  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:  2.36 (0.47), residues: 114
  sheet: -0.56 (0.64), residues: 60
  loop : -1.87 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 551 
 HIS   0.005   0.002   HIS A 514 
 PHE   0.008   0.002   PHE A 667 
 TYR   0.004   0.001   TYR B 521 
 ARG   0.003   0.000   ARG A 680 

*********************** 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
  108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8800 (mtmm)
REVERT: A  654 MET cc_start: 0.9144 (mpt) cc_final: 0.8466 (mpt)
REVERT: B  684 MET cc_start: 0.9006 (ttm) cc_final: 0.8661 (ttm)
REVERT: B  737 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8457 (ttpp)
REVERT: C  737 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8504 (ttpp)
  outliers start: 4
  outliers final: 1
  residues processed: 107
  average time/residue: 1.9008
  time to fit residues: 209.6472
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  : 0.654 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.107278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.094775 restraints weight = 4701.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 0.62
r_work: 0.3002 rms_B_bonded: 0.91 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 1.57 restraints_weight: 0.2500
r_work: 0.2633 rms_B_bonded: 4.30 restraints_weight: 0.1250
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8945
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   5865  Z= 0.452
  Angle     :  0.730   6.194   7884  Z= 0.402
  Chirality :  0.051   0.151    912
  Planarity :  0.005   0.045   1056
  Dihedral  :  7.251  26.781    840
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 14.08 %
    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:  2.00 (0.46), residues: 114
  sheet: -0.49 (0.53), residues: 75
  loop : -1.84 (0.21), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 551 
 HIS   0.009   0.004   HIS B 629 
 PHE   0.009   0.003   PHE A 667 
 TYR   0.009   0.003   TYR C 735 
 ARG   0.005   0.001   ARG B 613 

*********************** 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
  100 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8753 (mtmm)
REVERT: A  654 MET cc_start: 0.9275 (mpt) cc_final: 0.8786 (mpt)
REVERT: B  684 MET cc_start: 0.9078 (ttm) cc_final: 0.8759 (ttm)
REVERT: B  737 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8621 (ttpp)
REVERT: C  737 LYS cc_start: 0.9239 (ttmt) cc_final: 0.8664 (ttpp)
  outliers start: 3
  outliers final: 3
  residues processed: 99
  average time/residue: 1.9774
  time to fit residues: 201.6729
Evaluate side-chains
  99 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain B residue  605 GLN
Chi-restraints excluded: chain B residue  628 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3330 r_free = 0.3330 target = 0.110557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.098038 restraints weight = 4796.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 0.63
r_work: 0.3055 rms_B_bonded: 0.93 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 1.62 restraints_weight: 0.2500
r_work: 0.2688 rms_B_bonded: 4.43 restraints_weight: 0.1250
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8905
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5865  Z= 0.234
  Angle     :  0.600   5.594   7884  Z= 0.333
  Chirality :  0.048   0.147    912
  Planarity :  0.004   0.041   1056
  Dihedral  :  6.846  24.512    840
  Min Nonbonded Distance : 2.631

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: -1.49 (0.26), residues: 786
  helix:  2.26 (0.47), residues: 114
  sheet: -0.50 (0.65), residues: 60
  loop : -1.86 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 551 
 HIS   0.005   0.003   HIS A 514 
 PHE   0.007   0.002   PHE A 667 
 TYR   0.004   0.001   TYR B 521 
 ARG   0.004   0.000   ARG B 537 

*********************** 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
  105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9094 (mtmm) cc_final: 0.8799 (mtmm)
REVERT: A  654 MET cc_start: 0.9151 (mpt) cc_final: 0.8651 (mpt)
REVERT: B  684 MET cc_start: 0.9051 (ttm) cc_final: 0.8714 (ttm)
REVERT: B  737 LYS cc_start: 0.9184 (ttmt) cc_final: 0.8456 (ttpp)
REVERT: C  737 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8550 (ttpp)
  outliers start: 4
  outliers final: 3
  residues processed: 104
  average time/residue: 1.9287
  time to fit residues: 206.8174
Evaluate side-chains
  101 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain B residue  605 GLN
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:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 750 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 = 0.3295 r_free = 0.3295 target = 0.108173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.095709 restraints weight = 4745.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 0.62
r_work: 0.3016 rms_B_bonded: 0.91 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 1.58 restraints_weight: 0.2500
r_work: 0.2648 rms_B_bonded: 4.33 restraints_weight: 0.1250
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8936
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   5865  Z= 0.392
  Angle     :  0.694   6.018   7884  Z= 0.383
  Chirality :  0.050   0.149    912
  Planarity :  0.005   0.044   1056
  Dihedral  :  7.165  26.182    840
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 14.24 %
    Favored  : 84.95 %
  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:  2.06 (0.46), residues: 114
  sheet: -0.44 (0.64), residues: 60
  loop : -1.83 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 551 
 HIS   0.007   0.003   HIS B 629 
 PHE   0.009   0.002   PHE A 667 
 TYR   0.010   0.003   TYR A 735 
 ARG   0.008   0.001   ARG B 497 

*********************** 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
  103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8804 (mtmm)
REVERT: A  654 MET cc_start: 0.9255 (mpt) cc_final: 0.8758 (mpt)
REVERT: B  684 MET cc_start: 0.9036 (ttm) cc_final: 0.8721 (ttm)
REVERT: B  737 LYS cc_start: 0.9219 (ttmt) cc_final: 0.8627 (ttpp)
REVERT: C  737 LYS cc_start: 0.9227 (ttmt) cc_final: 0.8543 (ttpp)
  outliers start: 5
  outliers final: 3
  residues processed: 102
  average time/residue: 1.9312
  time to fit residues: 202.9455
Evaluate side-chains
  101 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain B residue  605 GLN
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:    0.0870
   chunk 52 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 750 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 = 0.3346 r_free = 0.3346 target = 0.111652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.099214 restraints weight = 4708.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 0.62
r_work: 0.3076 rms_B_bonded: 0.92 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 1.60 restraints_weight: 0.2500
r_work: 0.2709 rms_B_bonded: 4.44 restraints_weight: 0.1250
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5865  Z= 0.201
  Angle     :  0.579   4.666   7884  Z= 0.322
  Chirality :  0.047   0.145    912
  Planarity :  0.004   0.040   1056
  Dihedral  :  6.741  24.071    840
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 15.05 %
    Favored  : 84.30 %
  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: -1.48 (0.26), residues: 786
  helix:  2.32 (0.47), residues: 114
  sheet: -0.50 (0.66), residues: 60
  loop : -1.87 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 551 
 HIS   0.005   0.003   HIS A 531 
 PHE   0.007   0.001   PHE A 667 
 TYR   0.004   0.001   TYR B 521 
 ARG   0.009   0.001   ARG B 497 

*********************** 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
  103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9046 (mtmm) cc_final: 0.8727 (mtmm)
REVERT: A  654 MET cc_start: 0.9141 (mpt) cc_final: 0.8643 (mpt)
REVERT: B  684 MET cc_start: 0.9030 (ttm) cc_final: 0.8693 (ttm)
REVERT: B  737 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8465 (ttpp)
REVERT: C  737 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8541 (ttpp)
  outliers start: 4
  outliers final: 2
  residues processed: 102
  average time/residue: 1.9123
  time to fit residues: 201.1751
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  : 0.700 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 8 optimal weight:    0.2980
   chunk 46 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3348 r_free = 0.3348 target = 0.111671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.099241 restraints weight = 4722.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 0.62
r_work: 0.3076 rms_B_bonded: 0.92 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 1.61 restraints_weight: 0.2500
r_work: 0.2712 rms_B_bonded: 4.43 restraints_weight: 0.1250
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8887
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5865  Z= 0.213
  Angle     :  0.582   4.613   7884  Z= 0.324
  Chirality :  0.047   0.144    912
  Planarity :  0.004   0.040   1056
  Dihedral  :  6.669  23.678    840
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  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: -1.49 (0.26), residues: 786
  helix:  2.38 (0.47), residues: 114
  sheet: -0.49 (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   0.002   PHE A 667 
 TYR   0.005   0.001   TYR A 735 
 ARG   0.010   0.001   ARG B 497 

*********************** 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
  108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9041 (mtmm) cc_final: 0.8640 (mtmm)
REVERT: A  654 MET cc_start: 0.9154 (mpt) cc_final: 0.8648 (mpt)
REVERT: B  684 MET cc_start: 0.9008 (ttm) cc_final: 0.8709 (ttm)
REVERT: B  737 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8454 (ttpp)
REVERT: C  713 GLN cc_start: 0.8891 (tt0) cc_final: 0.8684 (pm20)
REVERT: C  737 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8545 (ttpp)
REVERT: C  739 SER cc_start: 0.8908 (p) cc_final: 0.8579 (p)
  outliers start: 5
  outliers final: 2
  residues processed: 107
  average time/residue: 1.8424
  time to fit residues: 203.4484
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  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  605 GLN
Chi-restraints excluded: chain C residue  563 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3304 r_free = 0.3304 target = 0.108698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.096091 restraints weight = 4758.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 0.63
r_work: 0.3024 rms_B_bonded: 0.92 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 1.60 restraints_weight: 0.2500
r_work: 0.2654 rms_B_bonded: 4.38 restraints_weight: 0.1250
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   5865  Z= 0.396
  Angle     :  0.695   5.765   7884  Z= 0.384
  Chirality :  0.050   0.147    912
  Planarity :  0.005   0.049   1056
  Dihedral  :  7.111  25.684    840
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 15.70 %
    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: -1.48 (0.26), residues: 786
  helix:  2.14 (0.47), residues: 114
  sheet: -0.48 (0.65), residues: 60
  loop : -1.82 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 551 
 HIS   0.008   0.004   HIS B 629 
 PHE   0.010   0.003   PHE A 667 
 TYR   0.012   0.003   TYR A 735 
 ARG   0.010   0.001   ARG B 497 

********************** 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
  102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8658 (mtmm)
REVERT: A  654 MET cc_start: 0.9259 (mpt) cc_final: 0.8760 (mpt)
REVERT: B  684 MET cc_start: 0.9042 (ttm) cc_final: 0.8734 (ttm)
REVERT: B  737 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8507 (ttpp)
REVERT: C  737 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8537 (ttpp)
  outliers start: 3
  outliers final: 2
  residues processed: 102
  average time/residue: 1.9690
  time to fit residues: 206.8525
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 63 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0570
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.112011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.099498 restraints weight = 4791.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 0.63
r_work: 0.3080 rms_B_bonded: 0.93 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 1.62 restraints_weight: 0.2500
r_work: 0.2716 rms_B_bonded: 4.47 restraints_weight: 0.1250
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8883
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5865  Z= 0.201
  Angle     :  0.581   4.689   7884  Z= 0.323
  Chirality :  0.047   0.143    912
  Planarity :  0.004   0.048   1056
  Dihedral  :  6.724  23.742    840
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 15.70 %
    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: -1.48 (0.26), residues: 786
  helix:  2.35 (0.47), residues: 114
  sheet: -0.50 (0.67), residues: 60
  loop : -1.87 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.007   0.001   PHE A 667 
 TYR   0.004   0.001   TYR B 735 
 ARG   0.010   0.001   ARG B 497 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5551.16 seconds
wall clock time: 98 minutes 39.09 seconds (5919.09 seconds total)