Starting phenix.real_space_refine
on Tue Mar  3 14:11:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sk0_10219/03_2026/6sk0_10219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sk0_10219/03_2026/6sk0_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_10219/03_2026/6sk0_10219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sk0_10219/03_2026/6sk0_10219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sk0_10219/03_2026/6sk0_10219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sk0_10219/03_2026/6sk0_10219.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    B, C
  Time building chain proxies: 1.27, per 1000 atoms: 0.22
  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: 0.53
  Conformation dependent library (CDL) restraints added in 364.0 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: 0.26
  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: 0.91

  Time building geometry restraints manager: 0.65 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             2.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.420
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:6.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.530
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (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
 ARG   0.003   0.000   ARG A 613 
 TYR   0.006   0.002   TYR B 521 
 PHE   0.005   0.002   PHE C 667 
 TRP   0.004   0.002   TRP A 551 
 HIS   0.007   0.003   HIS A 629 

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

*********************** 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  : 0.237 
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: 0.8354
  time to fit residues: 95.5545
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  : 0.228 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   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
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: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.108974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.096164 restraints weight = 4773.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 0.66
r_work: 0.3014 rms_B_bonded: 0.95 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 1.66 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:          0.1364

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   4.710   7884  Z= 0.340
  Chirality :  0.048   0.149    912
  Planarity :  0.004   0.036   1056
  Dihedral  :  6.858  24.402    843
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.32
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (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
 ARG   0.004   0.001   ARG A 680 
 TYR   0.004   0.001   TYR A 521 
 PHE   0.005   0.002   PHE A 667 
 TRP   0.004   0.001   TRP C 551 
 HIS   0.007   0.003   HIS B 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5865)
  covalent geometry    : angle       0.60740 ( 7884)
  hydrogen bonds       : bond        0.04450 (  294)
  hydrogen bonds       : angle       5.07887 (  810)

*********************** 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  : 0.268 
Fit side-chains
REVERT: A  654 MET cc_start: 0.9224 (mpt) cc_final: 0.8615 (mpt)
REVERT: B  684 MET cc_start: 0.9107 (ttm) cc_final: 0.8774 (ttm)
REVERT: B  737 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8485 (ttpp)
REVERT: C  713 GLN cc_start: 0.8958 (tt0) cc_final: 0.8726 (pm20)
REVERT: C  737 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8571 (ttpp)
  outliers start: 3
  outliers final: 1
  residues processed: 107
  average time/residue: 0.8569
  time to fit residues: 94.3981
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  : 0.214 
-------------------------------------------------------------------------------
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 17 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 68 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3299 r_free = 0.3299 target = 0.108453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.096025 restraints weight = 4679.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 0.61
r_work: 0.3020 rms_B_bonded: 0.90 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 1.57 restraints_weight: 0.2500
r_work: 0.2655 rms_B_bonded: 4.29 restraints_weight: 0.1250
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.1540

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= 0.246
  Angle     :  0.652   5.258   7884  Z= 0.361
  Chirality :  0.049   0.151    912
  Planarity :  0.004   0.041   1056
  Dihedral  :  6.970  25.123    840
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 14.08 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.26), residues: 786
  helix:  2.27 (0.46), residues: 114
  sheet: -0.41 (0.63), residues: 60
  loop : -1.84 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 680 
 TYR   0.007   0.002   TYR B 735 
 PHE   0.007   0.002   PHE A 667 
 TRP   0.004   0.001   TRP C 551 
 HIS   0.007   0.003   HIS B 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 5865)
  covalent geometry    : angle       0.65188 ( 7884)
  hydrogen bonds       : bond        0.04584 (  294)
  hydrogen bonds       : angle       4.99673 (  810)

*********************** 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
  108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  654 MET cc_start: 0.9230 (mpt) cc_final: 0.8732 (mpt)
REVERT: B  684 MET cc_start: 0.9089 (ttm) cc_final: 0.8748 (ttm)
REVERT: B  737 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8475 (ttpp)
REVERT: C  737 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8650 (ttpp)
  outliers start: 4
  outliers final: 0
  residues processed: 107
  average time/residue: 0.8669
  time to fit residues: 95.4043
Evaluate side-chains
  88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 694 ASN
A 696 GLN
A 750 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.106559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.094236 restraints weight = 4725.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 0.61
r_work: 0.2991 rms_B_bonded: 0.89 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 1.55 restraints_weight: 0.2500
r_work: 0.2623 rms_B_bonded: 4.26 restraints_weight: 0.1250
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8958
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050   5865  Z= 0.381
  Angle     :  0.777   7.404   7884  Z= 0.426
  Chirality :  0.052   0.150    912
  Planarity :  0.006   0.047   1056
  Dihedral  :  7.388  27.407    840
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.43 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.26), residues: 786
  helix:  1.86 (0.45), residues: 114
  sheet: -0.20 (0.45), residues: 105
  loop : -1.86 (0.21), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 680 
 TYR   0.011   0.003   TYR C 735 
 PHE   0.011   0.003   PHE A 667 
 TRP   0.008   0.002   TRP C 551 
 HIS   0.009   0.004   HIS B 629 

Details of bonding type rmsd
  covalent geometry    : bond        0.00757 ( 5865)
  covalent geometry    : angle       0.77671 ( 7884)
  hydrogen bonds       : bond        0.05153 (  294)
  hydrogen bonds       : angle       5.17408 (  810)

*********************** 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
  106 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8823 (mtmm)
REVERT: A  654 MET cc_start: 0.9278 (mpt) cc_final: 0.8802 (mpt)
REVERT: B  684 MET cc_start: 0.9086 (ttm) cc_final: 0.8755 (ttm)
REVERT: B  737 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8537 (ttpp)
REVERT: C  737 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8658 (ttpp)
  outliers start: 6
  outliers final: 3
  residues processed: 103
  average time/residue: 0.8808
  time to fit residues: 93.3931
Evaluate side-chains
  100 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain C residue  573 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3322 r_free = 0.3322 target = 0.109965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.097430 restraints weight = 4794.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 0.63
r_work: 0.3044 rms_B_bonded: 0.93 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 1.61 restraints_weight: 0.2500
r_work: 0.2678 rms_B_bonded: 4.41 restraints_weight: 0.1250
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8911
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      :  0.004   0.028   5865  Z= 0.191
  Angle     :  0.612   6.409   7884  Z= 0.339
  Chirality :  0.048   0.146    912
  Planarity :  0.004   0.041   1056
  Dihedral  :  6.931  24.775    840
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 15.05 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.26), residues: 786
  helix:  2.18 (0.46), residues: 114
  sheet: -0.54 (0.64), residues: 60
  loop : -1.88 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 537 
 TYR   0.004   0.001   TYR B 521 
 PHE   0.008   0.002   PHE A 667 
 TRP   0.003   0.001   TRP C 551 
 HIS   0.005   0.003   HIS B 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5865)
  covalent geometry    : angle       0.61208 ( 7884)
  hydrogen bonds       : bond        0.04040 (  294)
  hydrogen bonds       : angle       4.86800 (  810)

*********************** 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
  104 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9110 (mtmm) cc_final: 0.8781 (mtmm)
REVERT: A  654 MET cc_start: 0.9161 (mpt) cc_final: 0.8478 (mpt)
REVERT: B  684 MET cc_start: 0.9032 (ttm) cc_final: 0.8686 (ttm)
REVERT: B  737 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8467 (ttpp)
REVERT: C  737 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8512 (ttpp)
  outliers start: 2
  outliers final: 0
  residues processed: 104
  average time/residue: 0.8335
  time to fit residues: 89.2729
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  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 42 optimal weight:    0.4980
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3324 r_free = 0.3324 target = 0.109992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.097417 restraints weight = 4757.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 0.63
r_work: 0.3046 rms_B_bonded: 0.93 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 1.60 restraints_weight: 0.2500
r_work: 0.2679 rms_B_bonded: 4.42 restraints_weight: 0.1250
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8909
moved from start:          0.1754

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= 0.200
  Angle     :  0.614   6.358   7884  Z= 0.340
  Chirality :  0.048   0.147    912
  Planarity :  0.004   0.041   1056
  Dihedral  :  6.879  24.743    840
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 14.24 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.26), residues: 786
  helix:  2.23 (0.47), residues: 114
  sheet: -0.53 (0.66), residues: 60
  loop : -1.88 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 680 
 TYR   0.005   0.001   TYR A 521 
 PHE   0.007   0.002   PHE A 667 
 TRP   0.004   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5865)
  covalent geometry    : angle       0.61435 ( 7884)
  hydrogen bonds       : bond        0.04020 (  294)
  hydrogen bonds       : angle       4.83137 (  810)

*********************** 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
  102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8713 (mtmm)
REVERT: A  654 MET cc_start: 0.9186 (mpt) cc_final: 0.8695 (mpt)
REVERT: B  684 MET cc_start: 0.9036 (ttm) cc_final: 0.8698 (ttm)
REVERT: B  737 LYS cc_start: 0.9182 (ttmt) cc_final: 0.8461 (ttpp)
REVERT: C  737 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8522 (ttpp)
  outliers start: 4
  outliers final: 2
  residues processed: 101
  average time/residue: 0.8262
  time to fit residues: 86.0864
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  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 41 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 3 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3338 r_free = 0.3338 target = 0.111187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.098633 restraints weight = 4812.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 0.63
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: 0.2697 rms_B_bonded: 4.46 restraints_weight: 0.1250
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.1831

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= 0.173
  Angle     :  0.587   4.715   7884  Z= 0.326
  Chirality :  0.047   0.145    912
  Planarity :  0.004   0.039   1056
  Dihedral  :  6.745  24.112    840
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 14.40 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.26), residues: 786
  helix:  2.30 (0.47), residues: 114
  sheet: -0.53 (0.67), residues: 60
  loop : -1.90 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 497 
 TYR   0.010   0.001   TYR A 735 
 PHE   0.006   0.002   PHE A 667 
 TRP   0.003   0.001   TRP C 551 
 HIS   0.005   0.003   HIS B 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5865)
  covalent geometry    : angle       0.58692 ( 7884)
  hydrogen bonds       : bond        0.03771 (  294)
  hydrogen bonds       : angle       4.75568 (  810)

*********************** 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
  105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9049 (mtmm) cc_final: 0.8677 (mtmm)
REVERT: A  654 MET cc_start: 0.9171 (mpt) cc_final: 0.8650 (mpt)
REVERT: B  684 MET cc_start: 0.9034 (ttm) cc_final: 0.8704 (ttm)
REVERT: B  737 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8440 (ttpp)
REVERT: C  737 LYS cc_start: 0.9165 (ttmt) cc_final: 0.8536 (ttpp)
  outliers start: 6
  outliers final: 3
  residues processed: 103
  average time/residue: 0.8330
  time to fit residues: 88.4519
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  : 0.191 
-------------------------------------------------------------------------------
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 41 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 3 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0020
   chunk 64 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3352 r_free = 0.3352 target = 0.112021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.099436 restraints weight = 4785.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 0.64
r_work: 0.3079 rms_B_bonded: 0.94 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 1.64 restraints_weight: 0.2500
r_work: 0.2715 rms_B_bonded: 4.50 restraints_weight: 0.1250
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8880
moved from start:          0.1940

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= 0.151
  Angle     :  0.571   4.594   7884  Z= 0.318
  Chirality :  0.047   0.142    912
  Planarity :  0.004   0.039   1056
  Dihedral  :  6.611  23.178    840
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 15.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.26), residues: 786
  helix:  2.40 (0.47), residues: 114
  sheet: -0.52 (0.68), residues: 60
  loop : -1.91 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 497 
 TYR   0.004   0.001   TYR A 521 
 PHE   0.006   0.001   PHE A 667 
 TRP   0.002   0.001   TRP C 551 
 HIS   0.005   0.003   HIS A 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5865)
  covalent geometry    : angle       0.57136 ( 7884)
  hydrogen bonds       : bond        0.03557 (  294)
  hydrogen bonds       : angle       4.67571 (  810)

*********************** 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
  107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9058 (mtmm) cc_final: 0.8690 (mtmm)
REVERT: A  654 MET cc_start: 0.9162 (mpt) cc_final: 0.8648 (mpt)
REVERT: B  684 MET cc_start: 0.9015 (ttm) cc_final: 0.8683 (ttm)
REVERT: B  737 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8427 (ttpp)
REVERT: C  713 GLN cc_start: 0.8906 (tt0) cc_final: 0.8690 (pm20)
REVERT: C  737 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8528 (ttpp)
REVERT: C  739 SER cc_start: 0.8902 (p) cc_final: 0.8558 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 105
  average time/residue: 0.8242
  time to fit residues: 89.2631
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  : 0.226 
-------------------------------------------------------------------------------
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 23 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 70 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 72 optimal weight:    0.1980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3333 r_free = 0.3333 target = 0.110681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.098178 restraints weight = 4801.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 0.62
r_work: 0.3059 rms_B_bonded: 0.92 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 1.60 restraints_weight: 0.2500
r_work: 0.2693 rms_B_bonded: 4.40 restraints_weight: 0.1250
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8903
moved from start:          0.1852

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= 0.204
  Angle     :  0.615   4.777   7884  Z= 0.341
  Chirality :  0.048   0.145    912
  Planarity :  0.004   0.044   1056
  Dihedral  :  6.791  24.223    840
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 15.70 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.26), residues: 786
  helix:  2.32 (0.47), residues: 114
  sheet: -0.54 (0.67), residues: 60
  loop : -1.89 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 497 
 TYR   0.006   0.002   TYR C 521 
 PHE   0.006   0.002   PHE A 667 
 TRP   0.004   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 5865)
  covalent geometry    : angle       0.61496 ( 7884)
  hydrogen bonds       : bond        0.03951 (  294)
  hydrogen bonds       : angle       4.75911 (  810)

*********************** 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
  104 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8684 (mtmm)
REVERT: A  654 MET cc_start: 0.9192 (mpt) cc_final: 0.8687 (mpt)
REVERT: B  684 MET cc_start: 0.9008 (ttm) cc_final: 0.8673 (ttm)
REVERT: B  737 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8462 (ttpp)
REVERT: C  737 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8470 (ttpp)
REVERT: C  739 SER cc_start: 0.8887 (p) cc_final: 0.8636 (p)
  outliers start: 5
  outliers final: 3
  residues processed: 102
  average time/residue: 0.8582
  time to fit residues: 90.1779
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  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  495 VAL
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 2 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3345 r_free = 0.3345 target = 0.111414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.098919 restraints weight = 4807.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 0.62
r_work: 0.3071 rms_B_bonded: 0.92 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 1.61 restraints_weight: 0.2500
r_work: 0.2706 rms_B_bonded: 4.44 restraints_weight: 0.1250
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8893
moved from start:          0.1904

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= 0.181
  Angle     :  0.601   4.703   7884  Z= 0.333
  Chirality :  0.048   0.144    912
  Planarity :  0.004   0.046   1056
  Dihedral  :  6.725  23.841    840
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.26), residues: 786
  helix:  2.35 (0.47), residues: 114
  sheet: -0.55 (0.67), residues: 60
  loop : -1.90 (0.20), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 497 
 TYR   0.006   0.001   TYR B 735 
 PHE   0.006   0.002   PHE A 667 
 TRP   0.003   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5865)
  covalent geometry    : angle       0.60070 ( 7884)
  hydrogen bonds       : bond        0.03773 (  294)
  hydrogen bonds       : angle       4.71780 (  810)

********************** 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  : 0.203 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.9075 (mtmm) cc_final: 0.8689 (mtmm)
REVERT: A  654 MET cc_start: 0.9171 (mpt) cc_final: 0.8638 (mpt)
REVERT: B  684 MET cc_start: 0.8992 (ttm) cc_final: 0.8663 (ttm)
REVERT: B  737 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8454 (ttpp)
REVERT: C  737 LYS cc_start: 0.9168 (ttmt) cc_final: 0.8449 (ttpp)
REVERT: C  739 SER cc_start: 0.8861 (p) cc_final: 0.8594 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 101
  average time/residue: 0.8532
  time to fit residues: 88.7135
Evaluate side-chains
  100 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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 74 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 750 GLN
** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 709 ASN ** 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 = 0.3282 r_free = 0.3282 target = 0.107283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.094734 restraints weight = 4770.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 0.62
r_work: 0.3003 rms_B_bonded: 0.91 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 1.58 restraints_weight: 0.2500
r_work: 0.2634 rms_B_bonded: 4.31 restraints_weight: 0.1250
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050   5865  Z= 0.407
  Angle     :  0.791   6.434   7884  Z= 0.434
  Chirality :  0.054   0.151    912
  Planarity :  0.006   0.051   1056
  Dihedral  :  7.367  27.033    840
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 15.86 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.26), residues: 786
  helix:  1.85 (0.46), residues: 114
  sheet: -0.43 (0.55), residues: 75
  loop : -1.82 (0.21), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 497 
 TYR   0.016   0.004   TYR A 735 
 PHE   0.009   0.003   PHE B 667 
 TRP   0.010   0.003   TRP C 551 
 HIS   0.011   0.004   HIS B 629 

Details of bonding type rmsd
  covalent geometry    : bond        0.00818 ( 5865)
  covalent geometry    : angle       0.79100 ( 7884)
  hydrogen bonds       : bond        0.05084 (  294)
  hydrogen bonds       : angle       5.09342 (  810)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2671.59 seconds
wall clock time: 46 minutes 8.82 seconds (2768.82 seconds total)