Starting phenix.real_space_refine
on Sun Mar 10 23:01:58 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/03_2024/6sk0_10219.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/03_2024/6sk0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/03_2024/6sk0_10219.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/03_2024/6sk0_10219.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/03_2024/6sk0_10219.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/03_2024/6sk0_10219.pdb"
  }
  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
    Residue "A ARG  505": "NH1" <-> "NH2"
    Residue "A ASP  508": "OD1" <-> "OD2"
    Residue "A ARG  510": "NH1" <-> "NH2"
    Residue "A GLU  512": "OE1" <-> "OE2"
    Residue "A ARG  547": "NH1" <-> "NH2"
    Residue "A ASP  565": "OD1" <-> "OD2"
    Residue "A GLU  585": "OE1" <-> "OE2"
    Residue "A ASP  607": "OD1" <-> "OD2"
    Residue "A ASP  657": "OD1" <-> "OD2"
    Residue "A ASP  660": "OD1" <-> "OD2"
    Residue "B ARG  505": "NH1" <-> "NH2"
    Residue "B ASP  508": "OD1" <-> "OD2"
    Residue "B ARG  510": "NH1" <-> "NH2"
    Residue "B GLU  512": "OE1" <-> "OE2"
    Residue "B ARG  547": "NH1" <-> "NH2"
    Residue "B ASP  565": "OD1" <-> "OD2"
    Residue "B GLU  585": "OE1" <-> "OE2"
    Residue "B ASP  607": "OD1" <-> "OD2"
    Residue "B ASP  657": "OD1" <-> "OD2"
    Residue "B ASP  660": "OD1" <-> "OD2"
    Residue "C ARG  505": "NH1" <-> "NH2"
    Residue "C ASP  508": "OD1" <-> "OD2"
    Residue "C ARG  510": "NH1" <-> "NH2"
    Residue "C GLU  512": "OE1" <-> "OE2"
    Residue "C ARG  547": "NH1" <-> "NH2"
    Residue "C ASP  565": "OD1" <-> "OD2"
    Residue "C GLU  585": "OE1" <-> "OE2"
    Residue "C ASP  607": "OD1" <-> "OD2"
    Residue "C ASP  657": "OD1" <-> "OD2"
    Residue "C ASP  660": "OD1" <-> "OD2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 5826
  Number of models: 1
  Model: ""
    Number of chains: 3
    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}
    Chain: "B"
      Number of atoms: 1942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1942
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 5, 'TRANS': 258}
    Chain: "C"
      Number of atoms: 1942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1942
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 5, 'TRANS': 258}
  Time building chain proxies: 3.66, per 1000 atoms: 0.63
  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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.79
  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: 1.89

  Time building geometry restraints manager: 2.43 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:
       97.75 -   104.99: 69
      104.99 -   112.23: 3011
      112.23 -   119.47: 1902
      119.47 -   126.71: 2869
      126.71 -   133.95: 33
  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 2.440
  nonbonded pdb=" OH  TYR A 735 "
            pdb=" OE2 GLU A 744 "
     model   vdw
     2.203 2.440
  nonbonded pdb=" OH  TYR B 735 "
            pdb=" OE2 GLU B 744 "
     model   vdw
     2.203 2.440
  nonbonded pdb=" N   GLY A 673 "
            pdb=" O   GLN C 665 "
     model   vdw
     2.299 2.520
  nonbonded pdb=" O   GLN A 665 "
            pdb=" N   GLY B 673 "
     model   vdw
     2.311 2.520
  ... (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
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:             1.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          9.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.050
  Process input model:                     20.050
  Find NCS groups from input model:        0.340
  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:             0.010
  Load rotamer database and sin/cos tables:11.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.300
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.688 
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: 1.7443
  time to fit residues: 199.8545
Evaluate side-chains
  93 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.1281

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= 0.236
  Angle     :  0.595   5.201   7884  Z= 0.333
  Chirality :  0.047   0.151    912
  Planarity :  0.004   0.032   1056
  Dihedral  :  6.812  23.604    843
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 10.52 %
    Favored  : 88.83 %
  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 (0.26), residues: 786
  helix:  2.38 (0.45), residues: 114
  sheet:  0.22 (0.52), residues: 90
  loop : -1.89 (0.20), residues: 582

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

*********************** 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
  105 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8166 (mtmt)
REVERT: A  654 MET cc_start: 0.8761 (mpt) cc_final: 0.8104 (mpt)
REVERT: B  516 LYS cc_start: 0.8669 (tttt) cc_final: 0.8320 (tttp)
REVERT: B  684 MET cc_start: 0.8195 (ttm) cc_final: 0.7636 (ttm)
REVERT: B  737 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7325 (ttpp)
REVERT: C  509 LYS cc_start: 0.8210 (tttt) cc_final: 0.7992 (ttmt)
REVERT: C  516 LYS cc_start: 0.8833 (tttt) cc_final: 0.8616 (ttpt)
REVERT: C  713 GLN cc_start: 0.7999 (tt0) cc_final: 0.7664 (pm20)
REVERT: C  737 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7369 (ttpp)
REVERT: C  750 GLN cc_start: 0.8081 (pt0) cc_final: 0.7851 (pp30)
  outliers start: 4
  outliers final: 3
  residues processed: 105
  average time/residue: 1.8044
  time to fit residues: 195.4142
Evaluate side-chains
  100 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain B residue  615 ASN
Chi-restraints excluded: chain C residue  536 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
C 694 ASN
C 696 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.1488

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= 0.228
  Angle     :  0.582   5.355   7884  Z= 0.325
  Chirality :  0.047   0.149    912
  Planarity :  0.004   0.035   1056
  Dihedral  :  6.669  23.502    840
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 11.33 %
    Favored  : 88.03 %
  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: -1.37 (0.26), residues: 786
  helix:  2.51 (0.46), residues: 114
  sheet: -0.18 (0.51), residues: 90
  loop : -1.91 (0.20), residues: 582

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   0.004   0.002   PHE A 667 
 TYR   0.004   0.001   TYR A 521 
 ARG   0.003   0.000   ARG C 643 

*********************** 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 fitting.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A  654 MET cc_start: 0.8766 (mpt) cc_final: 0.8031 (mpt)
REVERT: B  516 LYS cc_start: 0.8655 (tttt) cc_final: 0.8221 (tttp)
REVERT: B  684 MET cc_start: 0.8199 (ttm) cc_final: 0.7630 (ttm)
REVERT: B  737 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7332 (ttpp)
REVERT: C  516 LYS cc_start: 0.8834 (tttt) cc_final: 0.8622 (ttpt)
REVERT: C  713 GLN cc_start: 0.7990 (tt0) cc_final: 0.7664 (pm20)
REVERT: C  737 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7367 (ttpp)
  outliers start: 4
  outliers final: 2
  residues processed: 107
  average time/residue: 1.8717
  time to fit residues: 206.4941
Evaluate side-chains
  90 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain B residue  615 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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**
** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   5865  Z= 0.385
  Angle     :  0.687   6.040   7884  Z= 0.378
  Chirality :  0.049   0.151    912
  Planarity :  0.005   0.038   1056
  Dihedral  :  7.068  25.644    840
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 11.17 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.26), residues: 786
  helix:  2.24 (0.45), residues: 114
  sheet:  0.09 (0.44), residues: 114
  loop : -1.87 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 551 
 HIS   0.008   0.003   HIS B 514 
 PHE   0.009   0.002   PHE A 667 
 TYR   0.007   0.002   TYR A 521 
 ARG   0.005   0.001   ARG B 613 

*********************** 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
  105 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.642 
Fit side-chains
REVERT: B  516 LYS cc_start: 0.8650 (tttt) cc_final: 0.8311 (tttt)
REVERT: B  684 MET cc_start: 0.8253 (ttm) cc_final: 0.7698 (ttm)
REVERT: B  737 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7366 (ttpp)
REVERT: C  737 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7451 (ttpp)
REVERT: C  750 GLN cc_start: 0.8198 (pt0) cc_final: 0.7987 (pt0)
  outliers start: 6
  outliers final: 4
  residues processed: 104
  average time/residue: 1.8695
  time to fit residues: 200.3614
Evaluate side-chains
  102 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain C residue  536 SER
Chi-restraints excluded: chain C residue  547 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    1.3388

-------------------------------------------------------------------------------
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**
C 750 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   5865  Z= 0.320
  Angle     :  0.646   6.060   7884  Z= 0.357
  Chirality :  0.048   0.147    912
  Planarity :  0.004   0.036   1056
  Dihedral  :  6.993  25.361    840
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.65 %
    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: -1.32 (0.26), residues: 786
  helix:  2.23 (0.45), residues: 114
  sheet: -0.03 (0.44), residues: 114
  loop : -1.89 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 551 
 HIS   0.007   0.003   HIS B 514 
 PHE   0.007   0.002   PHE A 667 
 TYR   0.006   0.002   TYR A 521 
 ARG   0.004   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
  104 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.700 
Fit side-chains
REVERT: B  516 LYS cc_start: 0.8646 (tttt) cc_final: 0.8213 (tttp)
REVERT: B  684 MET cc_start: 0.8213 (ttm) cc_final: 0.7679 (ttm)
REVERT: B  737 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7340 (ttpp)
REVERT: C  737 LYS cc_start: 0.8397 (ttmt) cc_final: 0.7535 (ttpp)
REVERT: C  750 GLN cc_start: 0.8103 (pt0) cc_final: 0.7852 (pt0)
  outliers start: 5
  outliers final: 3
  residues processed: 103
  average time/residue: 1.8496
  time to fit residues: 196.3663
Evaluate side-chains
  100 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain C residue  536 SER
Chi-restraints excluded: chain C residue  547 ARG
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 18 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   5865  Z= 0.262
  Angle     :  0.607   5.341   7884  Z= 0.336
  Chirality :  0.047   0.147    912
  Planarity :  0.004   0.036   1056
  Dihedral  :  6.836  24.419    840
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.65 %
    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: -1.33 (0.26), residues: 786
  helix:  2.36 (0.46), residues: 114
  sheet: -0.11 (0.44), residues: 114
  loop : -1.92 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.006   0.002   PHE A 667 
 TYR   0.005   0.001   TYR A 521 
 ARG   0.003   0.000   ARG A 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 fitting.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8031 (mtmm)
REVERT: B  516 LYS cc_start: 0.8647 (tttt) cc_final: 0.8217 (tttp)
REVERT: B  684 MET cc_start: 0.8181 (ttm) cc_final: 0.7657 (ttm)
REVERT: B  737 LYS cc_start: 0.8412 (ttmt) cc_final: 0.7363 (ttpp)
REVERT: C  713 GLN cc_start: 0.7992 (tt0) cc_final: 0.7605 (pm20)
REVERT: C  737 LYS cc_start: 0.8377 (ttmt) cc_final: 0.7525 (ttpp)
  outliers start: 5
  outliers final: 3
  residues processed: 104
  average time/residue: 1.8443
  time to fit residues: 197.8443
Evaluate side-chains
  100 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain C residue  536 SER
Chi-restraints excluded: chain C residue  547 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1717

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= 0.228
  Angle     :  0.587   5.059   7884  Z= 0.325
  Chirality :  0.046   0.146    912
  Planarity :  0.003   0.035   1056
  Dihedral  :  6.700  24.060    840
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.65 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.26), residues: 786
  helix:  2.47 (0.46), residues: 114
  sheet: -0.20 (0.44), residues: 114
  loop : -1.95 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.006   0.002   PHE A 667 
 TYR   0.004   0.001   TYR A 521 
 ARG   0.004   0.000   ARG A 537 

*********************** 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
  106 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8021 (mtmm)
REVERT: B  516 LYS cc_start: 0.8650 (tttt) cc_final: 0.8220 (tttp)
REVERT: B  684 MET cc_start: 0.8181 (ttm) cc_final: 0.7659 (ttm)
REVERT: B  737 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7366 (ttpp)
REVERT: C  713 GLN cc_start: 0.7996 (tt0) cc_final: 0.7629 (pm20)
REVERT: C  737 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7316 (ttpp)
  outliers start: 7
  outliers final: 3
  residues processed: 103
  average time/residue: 1.8373
  time to fit residues: 195.0911
Evaluate side-chains
  101 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain C residue  536 SER
Chi-restraints excluded: chain C residue  547 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   5865  Z= 0.318
  Angle     :  0.646   5.499   7884  Z= 0.356
  Chirality :  0.048   0.149    912
  Planarity :  0.004   0.038   1056
  Dihedral  :  6.920  25.227    840
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.14 %
    Favored  : 87.06 %
  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: -1.34 (0.26), residues: 786
  helix:  2.33 (0.46), residues: 114
  sheet: -0.11 (0.44), residues: 114
  loop : -1.92 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.008   0.002   PHE A 667 
 TYR   0.006   0.002   TYR A 521 
 ARG   0.004   0.001   ARG B 613 

*********************** 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 fitting.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8240 (mttp)
REVERT: B  516 LYS cc_start: 0.8679 (tttt) cc_final: 0.8250 (tttp)
REVERT: B  684 MET cc_start: 0.8178 (ttm) cc_final: 0.7655 (ttm)
REVERT: B  737 LYS cc_start: 0.8438 (ttmt) cc_final: 0.7365 (ttpp)
REVERT: C  737 LYS cc_start: 0.8358 (ttmt) cc_final: 0.7480 (ttpp)
  outliers start: 5
  outliers final: 4
  residues processed: 102
  average time/residue: 1.8733
  time to fit residues: 196.9743
Evaluate side-chains
  101 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain C residue  536 SER
Chi-restraints excluded: chain C residue  547 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 694 ASN
B 696 GLN
** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5865  Z= 0.346
  Angle     :  0.667   5.894   7884  Z= 0.367
  Chirality :  0.048   0.148    912
  Planarity :  0.004   0.038   1056
  Dihedral  :  7.002  25.428    840
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.30 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.26), residues: 786
  helix:  2.25 (0.45), residues: 114
  sheet: -0.04 (0.44), residues: 114
  loop : -1.89 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP C 551 
 HIS   0.007   0.003   HIS B 514 
 PHE   0.008   0.002   PHE A 667 
 TYR   0.006   0.002   TYR A 521 
 ARG   0.004   0.001   ARG B 613 

*********************** 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
  103 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8257 (mttp)
REVERT: B  516 LYS cc_start: 0.8680 (tttt) cc_final: 0.8250 (tttp)
REVERT: B  684 MET cc_start: 0.8177 (ttm) cc_final: 0.7656 (ttm)
REVERT: B  737 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7351 (ttpp)
REVERT: C  737 LYS cc_start: 0.8363 (ttmt) cc_final: 0.7310 (ttpp)
  outliers start: 5
  outliers final: 4
  residues processed: 102
  average time/residue: 1.8437
  time to fit residues: 193.8830
Evaluate side-chains
  101 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain C residue  536 SER
Chi-restraints excluded: chain C residue  547 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.2984

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   5865  Z= 0.313
  Angle     :  0.647   5.422   7884  Z= 0.356
  Chirality :  0.048   0.148    912
  Planarity :  0.004   0.037   1056
  Dihedral  :  6.973  24.945    840
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.46 %
    Favored  : 86.57 %
  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: -1.33 (0.26), residues: 786
  helix:  2.30 (0.46), residues: 114
  sheet: -0.10 (0.44), residues: 114
  loop : -1.90 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 551 
 HIS   0.007   0.003   HIS B 514 
 PHE   0.007   0.002   PHE A 667 
 TYR   0.006   0.002   TYR A 521 
 ARG   0.004   0.001   ARG B 613 

********************** 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
  104 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.752 
Fit side-chains
REVERT: A  596 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8241 (mttp)
REVERT: B  516 LYS cc_start: 0.8676 (tttt) cc_final: 0.8251 (tttp)
REVERT: B  684 MET cc_start: 0.8168 (ttm) cc_final: 0.7652 (ttm)
REVERT: B  737 LYS cc_start: 0.8438 (ttmt) cc_final: 0.7357 (ttpp)
REVERT: C  737 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7313 (ttpp)
  outliers start: 6
  outliers final: 4
  residues processed: 102
  average time/residue: 1.9577
  time to fit residues: 205.9624
Evaluate side-chains
  101 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 ASN
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain C residue  536 SER
Chi-restraints excluded: chain C residue  547 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3338 r_free = 0.3338 target = 0.110823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.098176 restraints weight = 4663.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 0.62
r_work: 0.3060 rms_B_bonded: 0.91 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 1.60 restraints_weight: 0.2500
r_work: 0.2690 rms_B_bonded: 4.38 restraints_weight: 0.1250
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5865  Z= 0.248
  Angle     :  0.608   5.421   7884  Z= 0.336
  Chirality :  0.047   0.145    912
  Planarity :  0.004   0.036   1056
  Dihedral  :  6.787  23.411    840
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.62 %
    Favored  : 86.73 %
  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: -1.33 (0.26), residues: 786
  helix:  2.43 (0.46), residues: 114
  sheet: -0.17 (0.44), residues: 114
  loop : -1.92 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 551 
 HIS   0.006   0.003   HIS B 514 
 PHE   0.006   0.002   PHE A 667 
 TYR   0.004   0.001   TYR A 521 
 ARG   0.005   0.000   ARG A 537 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3407.53 seconds
wall clock time: 60 minutes 52.06 seconds (3652.06 seconds total)