Starting phenix.real_space_refine
on Thu Dec  7 23:44:38 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/12_2023/6sk0_10219.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/12_2023/6sk0_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_10219/12_2023/6sk0_10219.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/12_2023/6sk0_10219.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/12_2023/6sk0_10219.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sk0_10219/12_2023/6sk0_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: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.80, per 1000 atoms: 0.65
  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: 2.15
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.81
  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: 1.96

  Time building geometry restraints manager: 2.34 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:             1.840
  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:          9.380
  Check model and map are aligned:         0.090
  Set scattering table:                    0.050
  Process input model:                     21.060
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.280
-------------------------------------------------------------------------------
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  : 0.649 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 111
  average time/residue: 1.7677
  time to fit residues: 202.4199
Evaluate side-chains
  75 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.644 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 0.8490
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 724 ASN
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1395

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= 0.239
  Angle     :  0.598   5.304   7884  Z= 0.334
  Chirality :  0.047   0.149    912
  Planarity :  0.004   0.033   1056
  Dihedral  :  6.768  23.592    840
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.33 %
    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:  2.37 (0.45), residues: 114
  sheet:  0.19 (0.52), residues: 90
  loop : -1.90 (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   0.003   0.001   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
  91 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 90
  average time/residue: 1.6413
  time to fit residues: 153.1087
Evaluate side-chains
  76 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.717 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 4
  residues processed: 0
  time to fit residues: 0.9551
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 694 ASN
C 696 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1535

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= 0.301
  Angle     :  0.634   5.431   7884  Z= 0.351
  Chirality :  0.048   0.150    912
  Planarity :  0.004   0.037   1056
  Dihedral  :  6.902  24.632    840
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.11 %
    Favored  : 86.25 %
  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:  2.41 (0.46), residues: 114
  sheet: -0.08 (0.51), residues: 90
  loop : -1.90 (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   0.006   0.002   PHE A 667 
   TYR   0.006   0.002   TYR A 521 
   ARG   0.004   0.001   ARG B 537 

*********************** 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
  90 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 89
  average time/residue: 1.7373
  time to fit residues: 160.0411
Evaluate side-chains
  81 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.750 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 2
  residues processed: 0
  time to fit residues: 1.0246
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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: 0.8121
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5865  Z= 0.349
  Angle     :  0.664   5.659   7884  Z= 0.368
  Chirality :  0.048   0.149    912
  Planarity :  0.004   0.037   1056
  Dihedral  :  7.043  25.603    840
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 12.78 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.26), residues: 786
  helix:  2.24 (0.45), residues: 114
  sheet:  0.03 (0.43), residues: 114
  loop : -1.90 (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   0.007   0.002   TYR A 521 
   ARG   0.004   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
  90 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 89
  average time/residue: 1.7568
  time to fit residues: 161.6552
Evaluate side-chains
  94 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.747 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 0.0616
  time to fit residues: 1.0841
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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: 0.8116
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   5865  Z= 0.326
  Angle     :  0.651   5.319   7884  Z= 0.361
  Chirality :  0.048   0.148    912
  Planarity :  0.004   0.038   1056
  Dihedral  :  7.020  25.363    840
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.43 %
    Favored  : 85.92 %
  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:  2.24 (0.45), residues: 114
  sheet: -0.03 (0.43), residues: 114
  loop : -1.91 (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
  89 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 89
  average time/residue: 1.7808
  time to fit residues: 163.8491
Evaluate side-chains
  83 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.708 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 0.9372
-------------------------------------------------------------------------------
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 18 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    0.4980
   chunk 72 optimal weight:    0.0870
   chunk 8 optimal weight:    3.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.5960

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5865  Z= 0.191
  Angle     :  0.567   4.704   7884  Z= 0.316
  Chirality :  0.046   0.148    912
  Planarity :  0.003   0.035   1056
  Dihedral  :  6.631  23.482    840
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.59 %
    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 (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: -1.35 (0.26), residues: 786
  helix:  2.52 (0.46), residues: 114
  sheet: -0.19 (0.43), residues: 114
  loop : -1.96 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.002   0.001   TRP C 551 
   HIS   0.005   0.003   HIS A 514 
   PHE   0.005   0.001   PHE A 667 
   TYR   0.004   0.001   TYR B 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
  84 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.754 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 83
  average time/residue: 1.6857
  time to fit residues: 144.9345
Evaluate side-chains
  79 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.621 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 0.8181
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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: 0.8118
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5865  Z= 0.362
  Angle     :  0.668   5.775   7884  Z= 0.370
  Chirality :  0.049   0.150    912
  Planarity :  0.004   0.039   1056
  Dihedral  :  7.015  25.659    840
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.94 %
    Favored  : 86.25 %
  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:  2.28 (0.46), residues: 114
  sheet: -0.04 (0.43), residues: 114
  loop : -1.91 (0.21), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.002   TRP C 551 
   HIS   0.007   0.003   HIS C 629 
   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 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
  82 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.755 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 81
  average time/residue: 1.6948
  time to fit residues: 142.2076
Evaluate side-chains
  83 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.704 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 4
  residues processed: 0
  time to fit residues: 0.9298
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5865  Z= 0.281
  Angle     :  0.618   5.282   7884  Z= 0.344
  Chirality :  0.047   0.148    912
  Planarity :  0.004   0.036   1056
  Dihedral  :  6.878  24.733    840
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.11 %
    Favored  : 86.08 %
  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:  2.33 (0.46), residues: 114
  sheet: -0.13 (0.43), residues: 114
  loop : -1.93 (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   0.004   0.001   ARG A 537 

*********************** 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
  86 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.783 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 85
  average time/residue: 1.7290
  time to fit residues: 152.1886
Evaluate side-chains
  85 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.683 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 4
  residues processed: 0
  time to fit residues: 0.8798
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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: 0.8136
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   5865  Z= 0.500
  Angle     :  0.760   6.658   7884  Z= 0.418
  Chirality :  0.052   0.175    912
  Planarity :  0.006   0.043   1056
  Dihedral  :  7.333  27.194    840
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.94 %
    Favored  : 86.41 %
  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: -1.39 (0.26), residues: 786
  helix:  1.91 (0.45), residues: 114
  sheet: -0.02 (0.42), residues: 117
  loop : -1.90 (0.21), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.003   TRP C 551 
   HIS   0.009   0.004   HIS C 629 
   PHE   0.010   0.003   PHE A 667 
   TYR   0.009   0.003   TYR A 521 
   ARG   0.007   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
  86 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.680 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 86
  average time/residue: 1.7710
  time to fit residues: 157.4884
Evaluate side-chains
  86 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.752 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 4
  residues processed: 0
  time to fit residues: 0.9840
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 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: 0.8094
moved from start:          0.1766

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= 0.229
  Angle     :  0.601   4.961   7884  Z= 0.333
  Chirality :  0.047   0.146    912
  Planarity :  0.004   0.034   1056
  Dihedral  :  6.842  24.024    840
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.43 %
    Favored  : 85.92 %
  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: -0.06 (0.43), residues: 114
  loop : -1.93 (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 A 531 
   PHE   0.005   0.002   PHE A 667 
   TYR   0.005   0.001   TYR B 521 
   ARG   0.004   0.000   ARG B 537 

********************** 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
  84 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.667 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 84
  average time/residue: 1.6592
  time to fit residues: 144.2794
Evaluate side-chains
  82 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.713 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 0.9415
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3295 r_free = 0.3295 target = 0.108071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.095568 restraints weight = 4692.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 0.62
r_work: 0.3016 rms_B_bonded: 0.90 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 1.56 restraints_weight: 0.2500
r_work: 0.2650 rms_B_bonded: 4.28 restraints_weight: 0.1250
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
moved from start:          0.1698

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= 0.406
  Angle     :  0.709   6.116   7884  Z= 0.389
  Chirality :  0.050   0.148    912
  Planarity :  0.005   0.041   1056
  Dihedral  :  7.182  25.708    840
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.75 %
    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 (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:  2.16 (0.46), residues: 114
  sheet: -0.06 (0.42), residues: 117
  loop : -1.90 (0.21), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.002   TRP C 551 
   HIS   0.008   0.004   HIS C 629 
   PHE   0.009   0.003   PHE A 667 
   TYR   0.008   0.002   TYR A 521 
   ARG   0.005   0.001   ARG B 613 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3021.67 seconds
wall clock time: 54 minutes 1.82 seconds (3241.82 seconds total)