Starting phenix.real_space_refine
on Thu Jun 12 16:30:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d81_46624/06_2025/9d81_46624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d81_46624/06_2025/9d81_46624.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d81_46624/06_2025/9d81_46624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d81_46624/06_2025/9d81_46624.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d81_46624/06_2025/9d81_46624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d81_46624/06_2025/9d81_46624.cif"
  }
  resolution = 2.4
  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
-------------------------------------------------------------------------------
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=   0.015
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      93      5.16       5
     C    9156      2.51       5
     N    2487      2.21       5
     O    2739      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14475
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 625, 4825
          Classifications: {'peptide': 625}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 598}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 12.38, per 1000 atoms: 0.86
  Number of scatterers: 14475
  At special positions: 0
  Unit cell: (98.346, 94.802, 129.356, 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      93     16.00
     O    2739      8.00
     N    2487      7.00
     C    9156      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 596 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 520 " - pdb=" SG  CYS C 596 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 520 " - pdb=" SG  CYS B 596 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.96
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3342

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 27 sheets defined
      29.3% alpha, 30.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 462 through 469
    Processing helix  chain 'A' and resid 470 through 476
      removed outlier: 4.439A  pdb=" N   ALA A 473 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 491
    Processing helix  chain 'A' and resid 492 through 513
    Processing helix  chain 'A' and resid 524 through 529
    Processing helix  chain 'A' and resid 552 through 566
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 580 through 586
    Processing helix  chain 'A' and resid 604 through 609
    Processing helix  chain 'A' and resid 610 through 614
    Processing helix  chain 'A' and resid 615 through 633
    Processing helix  chain 'A' and resid 652 through 668
      removed outlier: 4.044A  pdb=" N   HIS A 656 " --> pdb=" O   PRO A 652 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR A 668 " --> pdb=" O   VAL A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 688
    Processing helix  chain 'A' and resid 695 through 712
    Processing helix  chain 'A' and resid 808 through 814
      removed outlier: 4.075A  pdb=" N   GLN A 812 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 885
    Processing helix  chain 'A' and resid 930 through 934
    Processing helix  chain 'A' and resid 938 through 943
    Processing helix  chain 'A' and resid 947 through 951
      removed outlier: 3.940A  pdb=" N   THR A 951 " --> pdb=" O   PHE A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 995
    Processing helix  chain 'A' and resid 1044 through 1048
      removed outlier: 4.136A  pdb=" N   GLY A1047 " --> pdb=" O   SER A1044 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 469
    Processing helix  chain 'B' and resid 470 through 476
      removed outlier: 4.440A  pdb=" N   ALA B 473 " --> pdb=" O   THR B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 491
    Processing helix  chain 'B' and resid 492 through 513
    Processing helix  chain 'B' and resid 524 through 529
    Processing helix  chain 'B' and resid 552 through 566
      Proline residue:  B 562  - end of helix
    Processing helix  chain 'B' and resid 580 through 586
    Processing helix  chain 'B' and resid 604 through 609
    Processing helix  chain 'B' and resid 610 through 614
    Processing helix  chain 'B' and resid 615 through 633
    Processing helix  chain 'B' and resid 652 through 668
      removed outlier: 4.044A  pdb=" N   HIS B 656 " --> pdb=" O   PRO B 652 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR B 668 " --> pdb=" O   VAL B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 688
    Processing helix  chain 'B' and resid 695 through 712
    Processing helix  chain 'B' and resid 808 through 814
      removed outlier: 4.075A  pdb=" N   GLN B 812 " --> pdb=" O   PRO B 809 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 881 through 885
    Processing helix  chain 'B' and resid 930 through 934
    Processing helix  chain 'B' and resid 938 through 943
    Processing helix  chain 'B' and resid 947 through 951
      removed outlier: 3.940A  pdb=" N   THR B 951 " --> pdb=" O   PHE B 948 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 991 through 995
    Processing helix  chain 'B' and resid 1044 through 1048
      removed outlier: 4.136A  pdb=" N   GLY B1047 " --> pdb=" O   SER B1044 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 469
    Processing helix  chain 'C' and resid 470 through 476
      removed outlier: 4.439A  pdb=" N   ALA C 473 " --> pdb=" O   THR C 470 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 483 through 491
    Processing helix  chain 'C' and resid 492 through 513
    Processing helix  chain 'C' and resid 524 through 529
    Processing helix  chain 'C' and resid 552 through 566
      Proline residue:  C 562  - end of helix
    Processing helix  chain 'C' and resid 580 through 586
    Processing helix  chain 'C' and resid 604 through 609
    Processing helix  chain 'C' and resid 610 through 614
    Processing helix  chain 'C' and resid 615 through 633
    Processing helix  chain 'C' and resid 652 through 668
      removed outlier: 4.043A  pdb=" N   HIS C 656 " --> pdb=" O   PRO C 652 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR C 668 " --> pdb=" O   VAL C 664 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 683 through 688
    Processing helix  chain 'C' and resid 695 through 712
    Processing helix  chain 'C' and resid 808 through 814
      removed outlier: 4.075A  pdb=" N   GLN C 812 " --> pdb=" O   PRO C 809 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 881 through 885
    Processing helix  chain 'C' and resid 930 through 934
    Processing helix  chain 'C' and resid 938 through 943
    Processing helix  chain 'C' and resid 947 through 951
      removed outlier: 3.940A  pdb=" N   THR C 951 " --> pdb=" O   PHE C 948 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 991 through 995
    Processing helix  chain 'C' and resid 1044 through 1048
      removed outlier: 4.135A  pdb=" N   GLY C1047 " --> pdb=" O   SER C1044 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 568 through 573
      removed outlier: 8.251A  pdb=" N   PHE A 673 " --> pdb=" O   VAL A 637 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   VAL A 639 " --> pdb=" O   PHE A 673 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 537 through 538
    Processing sheet with id=3, first strand: chain 'A' and resid 726 through 728
    Processing sheet with id=4, first strand: chain 'A' and resid 726 through 728
      removed outlier: 5.384A  pdb=" N   VAL A 872 " --> pdb=" O   ASP A 790 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   ASP A 790 " --> pdb=" O   VAL A 872 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   SER A 874 " --> pdb=" O   LYS A 788 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A 782 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ALA A 783 " --> pdb=" O   ARG A 847 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   ARG A 847 " --> pdb=" O   ALA A 783 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE A 785 " --> pdb=" O   VAL A 845 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'A' and resid 737 through 741
    Processing sheet with id=6, first strand: chain 'A' and resid 898 through 906
      removed outlier: 6.568A  pdb=" N   TYR A 965 " --> pdb=" O   HIS A 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS A 987 " --> pdb=" O   TYR A 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU A 967 " --> pdb=" O   LEU A 985 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   LEU A 998 " --> pdb=" O   GLY A 982 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'A' and resid 898 through 906
      removed outlier: 6.568A  pdb=" N   TYR A 965 " --> pdb=" O   HIS A 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS A 987 " --> pdb=" O   TYR A 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU A 967 " --> pdb=" O   LEU A 985 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   LEU A 998 " --> pdb=" O   GLY A 982 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'A' and resid 920 through 921
    Processing sheet with id=9, first strand: chain 'A' and resid 1008 through 1011
      removed outlier: 6.801A  pdb=" N   ILE A1025 " --> pdb=" O   ILE A1010 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'B' and resid 568 through 573
      removed outlier: 8.251A  pdb=" N   PHE B 673 " --> pdb=" O   VAL B 637 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   VAL B 639 " --> pdb=" O   PHE B 673 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'B' and resid 537 through 538
    Processing sheet with id=12, first strand: chain 'B' and resid 726 through 728
    Processing sheet with id=13, first strand: chain 'B' and resid 726 through 728
      removed outlier: 5.384A  pdb=" N   VAL B 872 " --> pdb=" O   ASP B 790 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   ASP B 790 " --> pdb=" O   VAL B 872 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER B 874 " --> pdb=" O   LYS B 788 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA B 782 " --> pdb=" O   ILE B 880 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ALA B 783 " --> pdb=" O   ARG B 847 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   ARG B 847 " --> pdb=" O   ALA B 783 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE B 785 " --> pdb=" O   VAL B 845 " (cutoff:3.500A)
    Processing sheet with id=14, first strand: chain 'B' and resid 737 through 741
    Processing sheet with id=15, first strand: chain 'B' and resid 898 through 906
      removed outlier: 6.569A  pdb=" N   TYR B 965 " --> pdb=" O   HIS B 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS B 987 " --> pdb=" O   TYR B 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU B 967 " --> pdb=" O   LEU B 985 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU B 998 " --> pdb=" O   GLY B 982 " (cutoff:3.500A)
    Processing sheet with id=16, first strand: chain 'B' and resid 898 through 906
      removed outlier: 6.569A  pdb=" N   TYR B 965 " --> pdb=" O   HIS B 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS B 987 " --> pdb=" O   TYR B 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU B 967 " --> pdb=" O   LEU B 985 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU B 998 " --> pdb=" O   GLY B 982 " (cutoff:3.500A)
    Processing sheet with id=17, first strand: chain 'B' and resid 920 through 921
    Processing sheet with id=18, first strand: chain 'B' and resid 1008 through 1011
      removed outlier: 6.800A  pdb=" N   ILE B1025 " --> pdb=" O   ILE B1010 " (cutoff:3.500A)
    Processing sheet with id=19, first strand: chain 'C' and resid 568 through 573
      removed outlier: 8.251A  pdb=" N   PHE C 673 " --> pdb=" O   VAL C 637 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   VAL C 639 " --> pdb=" O   PHE C 673 " (cutoff:3.500A)
    Processing sheet with id=20, first strand: chain 'C' and resid 537 through 538
    Processing sheet with id=21, first strand: chain 'C' and resid 726 through 728
    Processing sheet with id=22, first strand: chain 'C' and resid 726 through 728
      removed outlier: 5.384A  pdb=" N   VAL C 872 " --> pdb=" O   ASP C 790 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   ASP C 790 " --> pdb=" O   VAL C 872 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER C 874 " --> pdb=" O   LYS C 788 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA C 782 " --> pdb=" O   ILE C 880 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ALA C 783 " --> pdb=" O   ARG C 847 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   ARG C 847 " --> pdb=" O   ALA C 783 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE C 785 " --> pdb=" O   VAL C 845 " (cutoff:3.500A)
    Processing sheet with id=23, first strand: chain 'C' and resid 737 through 741
    Processing sheet with id=24, first strand: chain 'C' and resid 898 through 906
      removed outlier: 6.568A  pdb=" N   TYR C 965 " --> pdb=" O   HIS C 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS C 987 " --> pdb=" O   TYR C 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU C 967 " --> pdb=" O   LEU C 985 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU C 998 " --> pdb=" O   GLY C 982 " (cutoff:3.500A)
    Processing sheet with id=25, first strand: chain 'C' and resid 898 through 906
      removed outlier: 6.568A  pdb=" N   TYR C 965 " --> pdb=" O   HIS C 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS C 987 " --> pdb=" O   TYR C 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU C 967 " --> pdb=" O   LEU C 985 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU C 998 " --> pdb=" O   GLY C 982 " (cutoff:3.500A)
    Processing sheet with id=26, first strand: chain 'C' and resid 920 through 921
    Processing sheet with id=27, first strand: chain 'C' and resid 1008 through 1011
      removed outlier: 6.800A  pdb=" N   ILE C1025 " --> pdb=" O   ILE C1010 " (cutoff:3.500A)

    702 hydrogen bonds defined for protein.
    1764 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: 5.73

  Time building geometry restraints manager: 4.38 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 2379
        1.30 -     1.43: 4212
        1.43 -     1.55: 8112
        1.55 -     1.68: 0
        1.68 -     1.80: 156
  Bond restraints: 14859
  Sorted by residual:
  bond pdb=" CA  TYR A 835 "
       pdb=" C   TYR A 835 "
    ideal  model  delta    sigma   weight residual
    1.525  1.446  0.079 1.27e-02 6.20e+03 3.85e+01
  bond pdb=" CA  TYR B 835 "
       pdb=" C   TYR B 835 "
    ideal  model  delta    sigma   weight residual
    1.525  1.447  0.079 1.27e-02 6.20e+03 3.83e+01
  bond pdb=" CA  TYR C 835 "
       pdb=" C   TYR C 835 "
    ideal  model  delta    sigma   weight residual
    1.525  1.447  0.078 1.27e-02 6.20e+03 3.82e+01
  bond pdb=" CA  GLY C 837 "
       pdb=" C   GLY C 837 "
    ideal  model  delta    sigma   weight residual
    1.516  1.469  0.046 8.10e-03 1.52e+04 3.28e+01
  bond pdb=" CA  GLY B 837 "
       pdb=" C   GLY B 837 "
    ideal  model  delta    sigma   weight residual
    1.516  1.469  0.046 8.10e-03 1.52e+04 3.27e+01
  ... (remaining 14854 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 19933
        3.09 -     6.18: 215
        6.18 -     9.27: 30
        9.27 -    12.37: 18
       12.37 -    15.46: 6
  Bond angle restraints: 20202
  Sorted by residual:
  angle pdb=" N   PRO C 839 "
        pdb=" CA  PRO C 839 "
        pdb=" CB  PRO C 839 "
      ideal   model   delta    sigma   weight residual
     103.31   96.72    6.59 8.90e-01 1.26e+00 5.48e+01
  angle pdb=" N   PRO A 839 "
        pdb=" CA  PRO A 839 "
        pdb=" CB  PRO A 839 "
      ideal   model   delta    sigma   weight residual
     103.31   96.73    6.58 8.90e-01 1.26e+00 5.46e+01
  angle pdb=" N   PRO B 839 "
        pdb=" CA  PRO B 839 "
        pdb=" CB  PRO B 839 "
      ideal   model   delta    sigma   weight residual
     103.31   96.74    6.57 8.90e-01 1.26e+00 5.45e+01
  angle pdb=" C   LEU C 522 "
        pdb=" N   GLY C 523 "
        pdb=" CA  GLY C 523 "
      ideal   model   delta    sigma   weight residual
     121.70  134.29  -12.59 1.80e+00 3.09e-01 4.90e+01
  angle pdb=" C   LEU B 522 "
        pdb=" N   GLY B 523 "
        pdb=" CA  GLY B 523 "
      ideal   model   delta    sigma   weight residual
     121.70  134.29  -12.59 1.80e+00 3.09e-01 4.89e+01
  ... (remaining 20197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 7537
       16.71 -    33.42: 797
       33.42 -    50.13: 204
       50.13 -    66.84: 36
       66.84 -    83.55: 9
  Dihedral angle restraints: 8583
    sinusoidal: 3261
      harmonic: 5322
  Sorted by residual:
  dihedral pdb=" CA  GLN B1020 "
           pdb=" C   GLN B1020 "
           pdb=" N   PRO B1021 "
           pdb=" CA  PRO B1021 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  129.08   50.92     0      5.00e+00 4.00e-02 1.04e+02
  dihedral pdb=" CA  GLN C1020 "
           pdb=" C   GLN C1020 "
           pdb=" N   PRO C1021 "
           pdb=" CA  PRO C1021 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  129.10   50.90     0      5.00e+00 4.00e-02 1.04e+02
  dihedral pdb=" CA  GLN A1020 "
           pdb=" C   GLN A1020 "
           pdb=" N   PRO A1021 "
           pdb=" CA  PRO A1021 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  129.11   50.89     0      5.00e+00 4.00e-02 1.04e+02
  ... (remaining 8580 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1861
       0.070 -    0.140: 248
       0.140 -    0.209: 6
       0.209 -    0.279: 3
       0.279 -    0.349: 3
  Chirality restraints: 2121
  Sorted by residual:
  chirality pdb=" CA  GLU A 836 "
            pdb=" N   GLU A 836 "
            pdb=" C   GLU A 836 "
            pdb=" CB  GLU A 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.04e+00
  chirality pdb=" CA  GLU B 836 "
            pdb=" N   GLU B 836 "
            pdb=" C   GLU B 836 "
            pdb=" CB  GLU B 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.04e+00
  chirality pdb=" CA  GLU C 836 "
            pdb=" N   GLU C 836 "
            pdb=" C   GLU C 836 "
            pdb=" CB  GLU C 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.02e+00
  ... (remaining 2118 not shown)

  Planarity restraints: 2616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 464 "   -0.375 9.50e-02 1.11e+02   1.68e-01 1.74e+01
        pdb=" NE  ARG C 464 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 464 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 464 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 464 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 464 "   -0.375 9.50e-02 1.11e+02   1.68e-01 1.73e+01
        pdb=" NE  ARG B 464 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 464 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 464 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 464 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 464 "    0.375 9.50e-02 1.11e+02   1.68e-01 1.73e+01
        pdb=" NE  ARG A 464 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 464 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 464 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 464 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2613 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.19: 108
        2.19 -     2.87: 6251
        2.87 -     3.55: 23178
        3.55 -     4.22: 43683
        4.22 -     4.90: 71608
  Nonbonded interactions: 144828
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 723 "
            pdb=" ND2 ASN C 724 "
     model   vdw
     1.518 3.120
  nonbonded pdb=" ND2 ASN A 724 "
            pdb=" O   VAL C 723 "
     model   vdw
     1.518 3.120
  nonbonded pdb=" O   VAL A 723 "
            pdb=" ND2 ASN B 724 "
     model   vdw
     1.518 3.120
  nonbonded pdb=" NH2 ARG B 899 "
            pdb=" OE2 GLU C1071 "
     model   vdw
     1.583 3.120
  nonbonded pdb=" OE2 GLU A1071 "
            pdb=" NH2 ARG C 899 "
     model   vdw
     1.584 3.120
  ... (remaining 144823 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.130
  Set scattering table:                    0.150
  Process input model:                     40.400
  Find NCS groups from input model:        0.280
  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:             0.010
  Load rotamer database and sin/cos tables:11.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4632
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   0.417  14865  Z= 0.676
  Angle     :  0.891  15.457  20208  Z= 0.504
  Chirality :  0.047   0.349   2121
  Planarity :  0.008   0.168   2616
  Dihedral  : 14.868  83.546   5232
  Min Nonbonded Distance : 1.518

Molprobity Statistics.
  All-atom Clashscore : 75.36
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  3.85 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.84 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.33 %

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: -0.83 (0.19), residues: 1869
  helix: -0.33 (0.24), residues: 471
  sheet:  0.14 (0.26), residues: 402
  loop : -0.91 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 654 
 HIS   0.005   0.002   HIS C 676 
 PHE   0.010   0.002   PHE B 776 
 TYR   0.023   0.002   TYR C1028 
 ARG   0.006   0.001   ARG A 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19200 (  600)
  hydrogen bonds       : angle       8.26620 ( 1764)
  SS BOND              : bond        0.00391 (    3)
  SS BOND              : angle       1.06526 (    6)
  covalent geometry    : bond        0.00569 (14859)
  covalent geometry    : angle       0.89132 (20202)
  Misc. bond           : bond        0.41724 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 321
  time to evaluate  : 1.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8330 (mtp) cc_final: 0.7944 (mtm)
REVERT: A  501 MET cc_start: 0.7471 (mtt) cc_final: 0.6875 (mtt)
REVERT: A  579 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6791 (t80)
REVERT: A  595 ASN cc_start: 0.7708 (m110) cc_final: 0.7458 (m-40)
REVERT: B  462 THR cc_start: 0.5698 (OUTLIER) cc_final: 0.5182 (t)
REVERT: B  464 ARG cc_start: 0.3963 (OUTLIER) cc_final: 0.3306 (ttp-170)
REVERT: C  576 ILE cc_start: 0.5302 (mt) cc_final: 0.4584 (mm)
REVERT: C  663 MET cc_start: 0.2946 (tpt) cc_final: 0.1827 (tpt)
REVERT: C  672 VAL cc_start: 0.3201 (t) cc_final: 0.2973 (t)
  outliers start: 21
  outliers final: 5
  residues processed: 330
  average time/residue: 1.0148
  time to fit residues: 379.7856
Evaluate side-chains
  188 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 180
  time to evaluate  : 2.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  579 TYR
Chi-restraints excluded: chain A residue  733 MET
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  464 ARG
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain C residue  733 MET
Chi-restraints excluded: chain C residue  906 MET
Chi-restraints excluded: chain C residue  964 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 157 optimal weight:    2.9990
   chunk 140 optimal weight:    0.8980
   chunk 78 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   chunk 95 optimal weight:    0.2980
   chunk 75 optimal weight:    0.7980
   chunk 145 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 88 optimal weight:    0.1980
   chunk 108 optimal weight:    0.9980
   chunk 168 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 512 HIS
A 513 ASN
A 606 ASN
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 676 HIS
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 ASN
A 826 GLN
** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 593 ASN
B 595 ASN
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 724 ASN
** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 500 ASN
C 513 ASN
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 676 HIS
C 765 GLN
C 826 GLN
C 854 HIS
** C 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 902 HIS
C1020 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.105523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.093042 restraints weight = 26774.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.28
r_work: 0.3274 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.8988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.127  14865  Z= 0.392
  Angle     :  1.056  18.142  20208  Z= 0.563
  Chirality :  0.057   0.274   2121
  Planarity :  0.009   0.089   2616
  Dihedral  :  7.810  60.145   2083
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 25.80
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  5.51 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 15.93 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.39 %

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: -1.65 (0.18), residues: 1869
  helix: -1.06 (0.23), residues: 432
  sheet: -0.26 (0.24), residues: 426
  loop : -1.48 (0.18), residues: 1011

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B 487 
 HIS   0.017   0.004   HIS B 902 
 PHE   0.034   0.004   PHE B 821 
 TYR   0.028   0.003   TYR A 811 
 ARG   0.013   0.002   ARG C 641 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05816 (  600)
  hydrogen bonds       : angle       6.84742 ( 1764)
  SS BOND              : bond        0.00188 (    3)
  SS BOND              : angle       1.35179 (    6)
  covalent geometry    : bond        0.00710 (14859)
  covalent geometry    : angle       1.05616 (20202)
  Misc. bond           : bond        0.00173 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 297
  time to evaluate  : 1.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8302 (mtp) cc_final: 0.7866 (mtm)
REVERT: A  526 MET cc_start: 0.8591 (mmm) cc_final: 0.8341 (mmm)
REVERT: A  720 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7276 (mppt)
REVERT: B  663 MET cc_start: 0.7885 (tpt) cc_final: 0.7195 (tpt)
REVERT: B  681 ASN cc_start: 0.6879 (m-40) cc_final: 0.6653 (m110)
REVERT: B  709 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7829 (ttp)
REVERT: B  711 MET cc_start: 0.7596 (mtt) cc_final: 0.7379 (mtm)
REVERT: B  765 GLN cc_start: 0.8173 (tt0) cc_final: 0.7932 (pt0)
REVERT: B  781 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7500 (mm-30)
REVERT: C  589 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7525 (tt)
REVERT: C  679 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.4917 (ptm)
REVERT: C  803 TRP cc_start: 0.7254 (t60) cc_final: 0.6761 (t60)
REVERT: C  828 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8374 (t)
REVERT: C  847 ARG cc_start: 0.7394 (ptt180) cc_final: 0.7091 (ptt180)
REVERT: C  854 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6903 (t-90)
REVERT: C  856 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.7023 (pt)
REVERT: C  862 LEU cc_start: 0.7288 (mt) cc_final: 0.7028 (mm)
REVERT: C  886 THR cc_start: 0.3839 (t) cc_final: 0.3290 (p)
REVERT: C  889 MET cc_start: 0.7301 (ttp) cc_final: 0.7017 (ttm)
REVERT: C  934 LEU cc_start: 0.6222 (mt) cc_final: 0.5979 (mt)
  outliers start: 79
  outliers final: 15
  residues processed: 346
  average time/residue: 1.2714
  time to fit residues: 492.8830
Evaluate side-chains
  219 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 197
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  664 VAL
Chi-restraints excluded: chain B residue  683 HIS
Chi-restraints excluded: chain B residue  709 MET
Chi-restraints excluded: chain B residue  784 HIS
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  920 VAL
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  589 LEU
Chi-restraints excluded: chain C residue  679 MET
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  841 SER
Chi-restraints excluded: chain C residue  854 HIS
Chi-restraints excluded: chain C residue  856 ILE
Chi-restraints excluded: chain C residue  915 THR
Chi-restraints excluded: chain C residue 1041 THR
Chi-restraints excluded: chain C residue 1079 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 157 optimal weight:    0.7980
   chunk 126 optimal weight:    0.6980
   chunk 144 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 541 GLN
A 676 HIS
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 ASN
A 819 ASN
** A 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1020 GLN
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 HIS
** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 724 ASN
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 805 ASN
B 826 GLN
B 892 GLN
** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 676 HIS
C 683 HIS
C 765 GLN
C 829 ASN
** C 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 863 GLN
C 941 ASN
** C 987 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.078654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.066062 restraints weight = 26770.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 1.99
r_work: 0.2788 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2681 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          1.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.109  14865  Z= 0.284
  Angle     :  0.868  12.383  20208  Z= 0.455
  Chirality :  0.051   0.267   2121
  Planarity :  0.007   0.109   2616
  Dihedral  :  6.605  62.799   2064
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.75 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 17.54 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.33 %

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 (0.19), residues: 1869
  helix: -0.65 (0.24), residues: 435
  sheet: -0.61 (0.23), residues: 453
  loop : -1.05 (0.19), residues: 981

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 654 
 HIS   0.041   0.002   HIS C 854 
 PHE   0.030   0.003   PHE C 776 
 TYR   0.024   0.003   TYR C 801 
 ARG   0.009   0.001   ARG C 482 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05104 (  600)
  hydrogen bonds       : angle       6.13337 ( 1764)
  SS BOND              : bond        0.00119 (    3)
  SS BOND              : angle       0.96006 (    6)
  covalent geometry    : bond        0.00639 (14859)
  covalent geometry    : angle       0.86803 (20202)
  Misc. bond           : bond        0.00400 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 161
  time to evaluate  : 1.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.3749 (mtm180) cc_final: 0.3318 (mtm180)
REVERT: A  526 MET cc_start: 0.8767 (mmm) cc_final: 0.8562 (mmm)
REVERT: A  553 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8088 (p90)
REVERT: A  661 MET cc_start: 0.8967 (tmm) cc_final: 0.8760 (tmm)
REVERT: A  720 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7678 (mtpt)
REVERT: B  486 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7101 (mt0)
REVERT: B  765 GLN cc_start: 0.7996 (tt0) cc_final: 0.7745 (pt0)
REVERT: B  816 ASP cc_start: 0.7486 (m-30) cc_final: 0.7261 (m-30)
REVERT: B  967 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8063 (tt0)
REVERT: C  579 TYR cc_start: 0.5873 (m-10) cc_final: 0.5620 (m-10)
REVERT: C  620 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6283 (tpt)
REVERT: C  621 GLU cc_start: 0.7914 (tt0) cc_final: 0.7637 (tm-30)
REVERT: C  622 TYR cc_start: 0.7514 (m-80) cc_final: 0.7190 (m-80)
REVERT: C  856 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8193 (mt)
REVERT: C  862 LEU cc_start: 0.8021 (mt) cc_final: 0.7818 (mm)
REVERT: C  863 GLN cc_start: 0.8297 (mp10) cc_final: 0.7950 (mm-40)
  outliers start: 74
  outliers final: 23
  residues processed: 209
  average time/residue: 1.2819
  time to fit residues: 295.0736
Evaluate side-chains
  154 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  976 SER
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  920 VAL
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue  994 SER
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  598 ILE
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  805 ASN
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  856 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 134 optimal weight:    0.8980
   chunk 183 optimal weight:    0.9980
   chunk 123 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0980
   chunk 161 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 129 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 139 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 125 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 466 GLN
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 ASN
A 878 GLN
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
C 513 ASN
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 683 HIS
** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 941 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.070212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.057814 restraints weight = 26988.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.2717 rms_B_bonded: 1.99
r_work: 0.2612 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2504 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          1.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.089  14865  Z= 0.254
  Angle     :  0.779  13.622  20208  Z= 0.407
  Chirality :  0.048   0.249   2121
  Planarity :  0.007   0.136   2616
  Dihedral  :  6.482  60.056   2064
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.91 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.34 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.28 %

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 (0.19), residues: 1869
  helix: -0.76 (0.23), residues: 459
  sheet: -0.64 (0.24), residues: 444
  loop : -0.95 (0.20), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 654 
 HIS   0.008   0.002   HIS C 854 
 PHE   0.026   0.002   PHE C 496 
 TYR   0.023   0.002   TYR B 553 
 ARG   0.019   0.001   ARG A 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04641 (  600)
  hydrogen bonds       : angle       5.87087 ( 1764)
  SS BOND              : bond        0.00074 (    3)
  SS BOND              : angle       0.91412 (    6)
  covalent geometry    : bond        0.00564 (14859)
  covalent geometry    : angle       0.77910 (20202)
  Misc. bond           : bond        0.00484 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 128
  time to evaluate  : 1.639 
Fit side-chains
REVERT: A  464 ARG cc_start: 0.3894 (mtm180) cc_final: 0.3531 (mtm180)
REVERT: A  475 MET cc_start: 0.8691 (mtm) cc_final: 0.8452 (mtp)
REVERT: A  482 ARG cc_start: 0.8406 (mtm110) cc_final: 0.8113 (mtm-85)
REVERT: A  602 MET cc_start: 0.9093 (ttp) cc_final: 0.8768 (ttp)
REVERT: A  661 MET cc_start: 0.8987 (tmm) cc_final: 0.8778 (OUTLIER)
REVERT: A  720 LYS cc_start: 0.8122 (tppt) cc_final: 0.7630 (mppt)
REVERT: A  781 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8458 (mm-30)
REVERT: B  486 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7405 (mt0)
REVERT: B  661 MET cc_start: 0.8983 (tmm) cc_final: 0.8717 (tmm)
REVERT: B  920 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8553 (m)
REVERT: B  967 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8450 (tt0)
REVERT: C  466 GLN cc_start: 0.6720 (mt0) cc_final: 0.6274 (mt0)
REVERT: C  553 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8708 (p90)
REVERT: C  582 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7685 (tptp)
REVERT: C  620 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7473 (tpp)
REVERT: C  622 TYR cc_start: 0.8191 (m-80) cc_final: 0.7978 (m-80)
REVERT: C  781 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8420 (mm-30)
  outliers start: 53
  outliers final: 20
  residues processed: 162
  average time/residue: 1.3472
  time to fit residues: 239.7417
Evaluate side-chains
  132 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  906 MET
Chi-restraints excluded: chain B residue  920 VAL
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  582 LYS
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 122 optimal weight:    0.0980
   chunk 62 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 175 optimal weight:    0.7980
   chunk 120 optimal weight:    0.5980
   chunk 158 optimal weight:    0.9990
   chunk 123 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 146 optimal weight:    0.6980
   chunk 181 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 662 GLN
** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
C 799 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.068579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.056439 restraints weight = 27356.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 1.98
r_work: 0.2604 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2496 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          1.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.093  14865  Z= 0.223
  Angle     :  0.733  12.833  20208  Z= 0.383
  Chirality :  0.047   0.228   2121
  Planarity :  0.008   0.227   2616
  Dihedral  :  6.327  58.169   2064
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.07 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.47 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

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: -1.23 (0.19), residues: 1869
  helix: -0.56 (0.24), residues: 453
  sheet: -0.79 (0.24), residues: 453
  loop : -0.86 (0.20), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 654 
 HIS   0.006   0.001   HIS B 702 
 PHE   0.020   0.002   PHE C 496 
 TYR   0.023   0.002   TYR C 553 
 ARG   0.036   0.001   ARG A 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04486 (  600)
  hydrogen bonds       : angle       5.75069 ( 1764)
  SS BOND              : bond        0.00122 (    3)
  SS BOND              : angle       1.17167 (    6)
  covalent geometry    : bond        0.00497 (14859)
  covalent geometry    : angle       0.73305 (20202)
  Misc. bond           : bond        0.00833 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 108
  time to evaluate  : 1.635 
Fit side-chains
   revert: symmetry clash
REVERT: A  482 ARG cc_start: 0.8358 (mtm110) cc_final: 0.7997 (mtm-85)
REVERT: A  661 MET cc_start: 0.9049 (tmm) cc_final: 0.8704 (tmm)
REVERT: A  720 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7653 (mppt)
REVERT: A  781 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8418 (mm-30)
REVERT: B  486 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7690 (mt0)
REVERT: B  621 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8559 (pp20)
REVERT: B  661 MET cc_start: 0.8981 (tmm) cc_final: 0.8741 (tmm)
REVERT: B  816 ASP cc_start: 0.7943 (m-30) cc_final: 0.7502 (m-30)
REVERT: C  487 TRP cc_start: 0.4687 (m100) cc_final: 0.4352 (m100)
REVERT: C  553 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8538 (p90)
REVERT: C  582 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7731 (tptp)
REVERT: C  781 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8463 (mm-30)
  outliers start: 48
  outliers final: 23
  residues processed: 140
  average time/residue: 1.4765
  time to fit residues: 226.5584
Evaluate side-chains
  125 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 1.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  621 GLU
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue  959 TYR
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  582 LYS
Chi-restraints excluded: chain C residue  618 LEU
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 169 optimal weight:    0.0670
   chunk 108 optimal weight:    0.9990
   chunk 178 optimal weight:    0.3980
   chunk 101 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 171 optimal weight:    0.6980
   chunk 159 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 512 HIS
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.069401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.057262 restraints weight = 27213.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.2723 rms_B_bonded: 1.99
r_work: 0.2618 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2510 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          1.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  14865  Z= 0.190
  Angle     :  0.719  12.610  20208  Z= 0.375
  Chirality :  0.046   0.228   2121
  Planarity :  0.008   0.238   2616
  Dihedral  :  7.122 157.319   2064
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.33 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.47 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

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: -1.24 (0.19), residues: 1869
  helix: -0.59 (0.24), residues: 459
  sheet: -0.78 (0.24), residues: 447
  loop : -0.85 (0.20), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 654 
 HIS   0.004   0.001   HIS B 702 
 PHE   0.035   0.002   PHE C 496 
 TYR   0.022   0.002   TYR C 553 
 ARG   0.036   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04309 (  600)
  hydrogen bonds       : angle       5.68788 ( 1764)
  SS BOND              : bond        0.00105 (    3)
  SS BOND              : angle       1.13305 (    6)
  covalent geometry    : bond        0.00418 (14859)
  covalent geometry    : angle       0.71851 (20202)
  Misc. bond           : bond        0.00847 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 107
  time to evaluate  : 1.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.4438 (mtm180) cc_final: 0.3526 (mtm180)
REVERT: A  482 ARG cc_start: 0.8345 (mtm110) cc_final: 0.7939 (mtm-85)
REVERT: A  661 MET cc_start: 0.9001 (tmm) cc_final: 0.8762 (tmm)
REVERT: A  717 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8320 (p0)
REVERT: A  720 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7612 (mppt)
REVERT: A  781 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8410 (mm-30)
REVERT: A 1011 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8723 (p)
REVERT: B  486 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7845 (mt0)
REVERT: B  621 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8596 (pp20)
REVERT: B  661 MET cc_start: 0.8967 (tmm) cc_final: 0.8690 (tmm)
REVERT: B  765 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8530 (mt0)
REVERT: B  816 ASP cc_start: 0.7884 (m-30) cc_final: 0.7449 (m-30)
REVERT: C  482 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7695 (ptt-90)
REVERT: C  499 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8444 (ttmt)
REVERT: C  553 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8537 (p90)
REVERT: C  582 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7873 (tptp)
REVERT: C  662 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8266 (pt0)
REVERT: C  781 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8452 (mm-30)
REVERT: C  869 ASP cc_start: 0.8495 (m-30) cc_final: 0.8253 (m-30)
  outliers start: 44
  outliers final: 20
  residues processed: 139
  average time/residue: 1.4663
  time to fit residues: 222.9303
Evaluate side-chains
  132 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 1.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  621 GLU
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  765 GLN
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  499 LYS
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  582 LYS
Chi-restraints excluded: chain C residue  662 GLN
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 96 optimal weight:    0.0470
   chunk 85 optimal weight:    0.0770
   chunk 4 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   chunk 160 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 152 optimal weight:    1.9990
   chunk 182 optimal weight:    0.5980
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 583 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.068983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.056782 restraints weight = 27081.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.2693 rms_B_bonded: 1.98
r_work: 0.2593 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2487 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          1.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14865  Z= 0.191
  Angle     :  0.715  13.359  20208  Z= 0.373
  Chirality :  0.046   0.228   2121
  Planarity :  0.006   0.082   2616
  Dihedral  :  7.154 169.382   2064
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.39 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 19.01 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

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: -1.17 (0.19), residues: 1869
  helix: -0.48 (0.24), residues: 453
  sheet: -0.82 (0.24), residues: 447
  loop : -0.79 (0.20), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 654 
 HIS   0.004   0.001   HIS B 702 
 PHE   0.032   0.002   PHE C 496 
 TYR   0.022   0.002   TYR C 553 
 ARG   0.018   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04318 (  600)
  hydrogen bonds       : angle       5.66523 ( 1764)
  SS BOND              : bond        0.00109 (    3)
  SS BOND              : angle       1.13124 (    6)
  covalent geometry    : bond        0.00421 (14859)
  covalent geometry    : angle       0.71513 (20202)
  Misc. bond           : bond        0.00865 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 104
  time to evaluate  : 1.524 
Fit side-chains
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.4498 (mtm180) cc_final: 0.3554 (mtm180)
REVERT: A  482 ARG cc_start: 0.8327 (mtm110) cc_final: 0.7832 (mtm-85)
REVERT: A  526 MET cc_start: 0.8962 (mmm) cc_final: 0.8720 (mmm)
REVERT: A  661 MET cc_start: 0.8996 (tmm) cc_final: 0.8767 (tmm)
REVERT: A  720 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7635 (mppt)
REVERT: A  781 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8436 (mm-30)
REVERT: A 1011 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8765 (p)
REVERT: B  591 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8360 (mm110)
REVERT: B  661 MET cc_start: 0.8967 (tmm) cc_final: 0.8667 (tmm)
REVERT: B  765 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8494 (mt0)
REVERT: B  926 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8229 (pt0)
REVERT: C  553 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8492 (p90)
REVERT: C  582 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7438 (tptp)
REVERT: C  586 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8025 (mt-10)
REVERT: C  662 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8283 (pt0)
REVERT: C  781 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8520 (mm-30)
REVERT: C  869 ASP cc_start: 0.8460 (m-30) cc_final: 0.8222 (m-30)
  outliers start: 39
  outliers final: 21
  residues processed: 133
  average time/residue: 1.4062
  time to fit residues: 204.9372
Evaluate side-chains
  127 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  621 GLU
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  765 GLN
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  582 LYS
Chi-restraints excluded: chain C residue  662 GLN
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 168 optimal weight:    0.9990
   chunk 182 optimal weight:    1.9990
   chunk 161 optimal weight:    0.3980
   chunk 95 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 174 optimal weight:    0.5980
   chunk 141 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 110 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 583 GLN
** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.067435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.055398 restraints weight = 27157.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.2683 rms_B_bonded: 1.98
r_work: 0.2579 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2470 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          1.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082  14865  Z= 0.222
  Angle     :  0.736  16.687  20208  Z= 0.386
  Chirality :  0.047   0.222   2121
  Planarity :  0.008   0.238   2616
  Dihedral  :  7.320 172.753   2064
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.44 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.81 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

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: -1.21 (0.19), residues: 1869
  helix: -0.55 (0.24), residues: 459
  sheet: -0.93 (0.24), residues: 453
  loop : -0.74 (0.20), residues: 957

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 654 
 HIS   0.005   0.001   HIS B 702 
 PHE   0.031   0.002   PHE C 496 
 TYR   0.023   0.002   TYR B 622 
 ARG   0.047   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04476 (  600)
  hydrogen bonds       : angle       5.70159 ( 1764)
  SS BOND              : bond        0.00123 (    3)
  SS BOND              : angle       1.09463 (    6)
  covalent geometry    : bond        0.00492 (14859)
  covalent geometry    : angle       0.73610 (20202)
  Misc. bond           : bond        0.00965 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 100
  time to evaluate  : 1.684 
Fit side-chains
   revert: symmetry clash
REVERT: A  482 ARG cc_start: 0.8317 (mtm110) cc_final: 0.7853 (mtm-85)
REVERT: A  526 MET cc_start: 0.8978 (mmm) cc_final: 0.8688 (mmm)
REVERT: A  661 MET cc_start: 0.9014 (tmm) cc_final: 0.8724 (tmm)
REVERT: A  720 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7610 (mppt)
REVERT: A  781 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8423 (mm-30)
REVERT: A 1011 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8815 (p)
REVERT: B  591 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8381 (mm110)
REVERT: B  661 MET cc_start: 0.8949 (tmm) cc_final: 0.8627 (tmm)
REVERT: B  765 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8481 (mt0)
REVERT: B  816 ASP cc_start: 0.8002 (m-30) cc_final: 0.7483 (m-30)
REVERT: C  553 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8491 (p90)
REVERT: C  582 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7602 (tptm)
REVERT: C  662 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8300 (pt0)
REVERT: C  781 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8575 (mm-30)
REVERT: C  869 ASP cc_start: 0.8465 (m-30) cc_final: 0.8228 (m-30)
  outliers start: 39
  outliers final: 22
  residues processed: 129
  average time/residue: 1.4549
  time to fit residues: 205.9758
Evaluate side-chains
  125 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 1.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  621 GLU
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  765 GLN
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  582 LYS
Chi-restraints excluded: chain C residue  662 GLN
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 153 optimal weight:    0.0570
   chunk 82 optimal weight:    0.8980
   chunk 168 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 145 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0970
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.069151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.057049 restraints weight = 27051.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.2721 rms_B_bonded: 1.99
r_work: 0.2617 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2511 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          1.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096  14865  Z= 0.178
  Angle     :  0.735  24.645  20208  Z= 0.384
  Chirality :  0.046   0.224   2121
  Planarity :  0.007   0.178   2616
  Dihedral  :  7.205 174.067   2064
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.60 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.08 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

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 (0.19), residues: 1869
  helix: -0.66 (0.23), residues: 477
  sheet: -0.99 (0.23), residues: 480
  loop : -0.80 (0.21), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 654 
 HIS   0.004   0.001   HIS A 736 
 PHE   0.028   0.002   PHE C 496 
 TYR   0.022   0.002   TYR C 553 
 ARG   0.027   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04380 (  600)
  hydrogen bonds       : angle       5.66734 ( 1764)
  SS BOND              : bond        0.00183 (    3)
  SS BOND              : angle       1.13631 (    6)
  covalent geometry    : bond        0.00392 (14859)
  covalent geometry    : angle       0.73509 (20202)
  Misc. bond           : bond        0.00823 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 3.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  482 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7963 (mtm-85)
REVERT: A  602 MET cc_start: 0.9030 (ttp) cc_final: 0.8666 (ttp)
REVERT: A  661 MET cc_start: 0.9007 (tmm) cc_final: 0.8777 (tmm)
REVERT: A  720 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7625 (mppt)
REVERT: A  781 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8366 (mm-30)
REVERT: B  482 ARG cc_start: 0.7493 (ttp-170) cc_final: 0.6970 (ttp-110)
REVERT: B  490 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7069 (pt0)
REVERT: B  591 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8386 (mm110)
REVERT: B  621 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8660 (pp20)
REVERT: B  661 MET cc_start: 0.8951 (tmm) cc_final: 0.8648 (tmm)
REVERT: B  765 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8495 (mt0)
REVERT: B  816 ASP cc_start: 0.7999 (m-30) cc_final: 0.7483 (m-30)
REVERT: B  842 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8429 (ttm170)
REVERT: B  926 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (pt0)
REVERT: C  553 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8492 (p90)
REVERT: C  662 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8296 (pt0)
REVERT: C  781 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8554 (mm-30)
REVERT: C  869 ASP cc_start: 0.8431 (m-30) cc_final: 0.8209 (m-30)
  outliers start: 33
  outliers final: 19
  residues processed: 124
  average time/residue: 1.8575
  time to fit residues: 254.5274
Evaluate side-chains
  120 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 3.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  621 GLU
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  765 GLN
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  842 ARG
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  662 GLN
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 107 optimal weight:    0.2980
   chunk 179 optimal weight:    0.0000
   chunk 34 optimal weight:    0.7980
   chunk 152 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0870
   chunk 135 optimal weight:    0.9990
   chunk 131 optimal weight:    0.2980
   chunk 137 optimal weight:    0.3980
   chunk 115 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.2162

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.073338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.060935 restraints weight = 26854.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 2.06
r_work: 0.2684 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          1.4403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084  14865  Z= 0.142
  Angle     :  0.705  23.511  20208  Z= 0.367
  Chirality :  0.045   0.225   2121
  Planarity :  0.007   0.163   2616
  Dihedral  :  6.980 171.941   2064
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.17 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.54 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

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: -1.28 (0.19), residues: 1869
  helix: -0.62 (0.24), residues: 477
  sheet: -0.92 (0.23), residues: 480
  loop : -0.81 (0.21), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 968 
 HIS   0.004   0.001   HIS A 736 
 PHE   0.024   0.002   PHE C 496 
 TYR   0.022   0.002   TYR C 553 
 ARG   0.024   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04120 (  600)
  hydrogen bonds       : angle       5.56235 ( 1764)
  SS BOND              : bond        0.00192 (    3)
  SS BOND              : angle       1.32432 (    6)
  covalent geometry    : bond        0.00313 (14859)
  covalent geometry    : angle       0.70455 (20202)
  Misc. bond           : bond        0.00773 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 1.623 
Fit side-chains
   revert: symmetry clash
REVERT: A  482 ARG cc_start: 0.8339 (mtm110) cc_final: 0.7940 (mtm-85)
REVERT: A  602 MET cc_start: 0.9015 (ttp) cc_final: 0.8758 (ttp)
REVERT: A  720 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7733 (mppt)
REVERT: A  759 LYS cc_start: 0.8343 (mttt) cc_final: 0.8079 (mtpt)
REVERT: A  781 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8210 (mm-30)
REVERT: B  486 GLN cc_start: 0.8428 (mt0) cc_final: 0.7895 (pt0)
REVERT: B  490 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7609 (mm-40)
REVERT: B  591 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8437 (mm110)
REVERT: B  621 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8559 (pp20)
REVERT: B  816 ASP cc_start: 0.7952 (m-30) cc_final: 0.7434 (m-30)
REVERT: B  842 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8448 (ttt180)
REVERT: B  926 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8179 (pt0)
REVERT: C  553 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8557 (p90)
REVERT: C  662 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8313 (pt0)
REVERT: C  781 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8513 (mm-30)
REVERT: C  868 LYS cc_start: 0.9084 (mttt) cc_final: 0.8545 (mtmm)
REVERT: C  869 ASP cc_start: 0.8206 (m-30) cc_final: 0.7872 (m-30)
REVERT: C  940 THR cc_start: 0.8593 (m) cc_final: 0.8238 (p)
  outliers start: 29
  outliers final: 12
  residues processed: 136
  average time/residue: 1.6322
  time to fit residues: 243.6987
Evaluate side-chains
  117 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 2.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  621 GLU
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  842 ARG
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  662 GLN
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 185 optimal weight:    0.0570
   chunk 56 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9990
   chunk 93 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 146 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0010
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.2704

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 541 GLN
B 799 ASN
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 745 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.072262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.059848 restraints weight = 27006.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.2769 rms_B_bonded: 2.05
r_work: 0.2665 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2557 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          1.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  14865  Z= 0.152
  Angle     :  0.705  22.742  20208  Z= 0.369
  Chirality :  0.045   0.230   2121
  Planarity :  0.007   0.167   2616
  Dihedral  :  6.968 171.454   2064
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.17 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 20.15 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

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: -1.23 (0.19), residues: 1869
  helix: -0.56 (0.24), residues: 477
  sheet: -0.89 (0.23), residues: 480
  loop : -0.78 (0.21), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 654 
 HIS   0.003   0.001   HIS A 736 
 PHE   0.024   0.002   PHE C 496 
 TYR   0.022   0.002   TYR C 553 
 ARG   0.025   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04160 (  600)
  hydrogen bonds       : angle       5.54713 ( 1764)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       1.24940 (    6)
  covalent geometry    : bond        0.00337 (14859)
  covalent geometry    : angle       0.70477 (20202)
  Misc. bond           : bond        0.00770 (    3)

===============================================================================
Job complete
usr+sys time: 11097.38 seconds
wall clock time: 196 minutes 12.26 seconds (11772.26 seconds total)