Starting phenix.real_space_refine
on Wed Jun 11 22:23:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oks_20103/06_2025/6oks_20103.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oks_20103/06_2025/6oks_20103.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oks_20103/06_2025/6oks_20103.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oks_20103/06_2025/6oks_20103.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oks_20103/06_2025/6oks_20103.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oks_20103/06_2025/6oks_20103.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
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      56      5.16       5
     C    8428      2.51       5
     N    2184      2.21       5
     O    2576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 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: 13244
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 946
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 5, 'TRANS': 109}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L, N
  Time building chain proxies: 4.17, per 1000 atoms: 0.31
  Number of scatterers: 13244
  At special positions: 0
  Unit cell: (126.15, 121.8, 89.9, 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      56     16.00
     O    2576      8.00
     N    2184      7.00
     C    8428      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.28
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3024

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 28 sheets defined
      5.3% alpha, 32.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 758 through 764
      removed outlier: 3.539A  pdb=" N   MET A 762 " --> pdb=" O   ASP A 758 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 759 through 764
    Processing helix  chain 'C' and resid 759 through 764
    Processing helix  chain 'D' and resid 759 through 764
    Processing helix  chain 'E' and resid 759 through 764
    Processing helix  chain 'F' and resid 759 through 764
    Processing helix  chain 'G' and resid 759 through 764
    Processing helix  chain 'H' and resid 759 through 764
    Processing helix  chain 'I' and resid 759 through 764
    Processing helix  chain 'J' and resid 759 through 764
    Processing helix  chain 'K' and resid 759 through 764
    Processing helix  chain 'L' and resid 759 through 764
    Processing helix  chain 'M' and resid 759 through 764
    Processing helix  chain 'N' and resid 759 through 764
    Processing sheet with id=AA1, first strand: chain 'A' and resid 768 through 774
      removed outlier: 3.653A  pdb=" N   GLY A 785 " --> pdb=" O   ASP A 771 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASN A 773 " --> pdb=" O   ILE A 783 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ILE A 783 " --> pdb=" O   ASN A 773 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 815 through 822
      removed outlier: 6.521A  pdb=" N   ASP A 817 " --> pdb=" O   ALA A 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA A 808 " --> pdb=" O   ASP A 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY A 819 " --> pdb=" O   VAL A 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 806 " --> pdb=" O   GLY A 819 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU A 858 " --> pdb=" O   GLU A 869 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 768 through 774
      removed outlier: 3.652A  pdb=" N   GLY B 785 " --> pdb=" O   ASP B 771 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN B 773 " --> pdb=" O   ILE B 783 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE B 783 " --> pdb=" O   ASN B 773 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 815 through 822
      removed outlier: 6.522A  pdb=" N   ASP B 817 " --> pdb=" O   ALA B 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA B 808 " --> pdb=" O   ASP B 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY B 819 " --> pdb=" O   VAL B 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL B 806 " --> pdb=" O   GLY B 819 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU B 858 " --> pdb=" O   GLU B 869 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 768 through 774
      removed outlier: 3.653A  pdb=" N   GLY C 785 " --> pdb=" O   ASP C 771 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASN C 773 " --> pdb=" O   ILE C 783 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE C 783 " --> pdb=" O   ASN C 773 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 815 through 822
      removed outlier: 6.522A  pdb=" N   ASP C 817 " --> pdb=" O   ALA C 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA C 808 " --> pdb=" O   ASP C 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY C 819 " --> pdb=" O   VAL C 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL C 806 " --> pdb=" O   GLY C 819 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU C 858 " --> pdb=" O   GLU C 869 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 768 through 774
      removed outlier: 3.652A  pdb=" N   GLY D 785 " --> pdb=" O   ASP D 771 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN D 773 " --> pdb=" O   ILE D 783 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE D 783 " --> pdb=" O   ASN D 773 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 815 through 822
      removed outlier: 6.522A  pdb=" N   ASP D 817 " --> pdb=" O   ALA D 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA D 808 " --> pdb=" O   ASP D 817 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLY D 819 " --> pdb=" O   VAL D 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL D 806 " --> pdb=" O   GLY D 819 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   LEU D 858 " --> pdb=" O   GLU D 869 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 768 through 774
      removed outlier: 3.653A  pdb=" N   GLY E 785 " --> pdb=" O   ASP E 771 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN E 773 " --> pdb=" O   ILE E 783 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ILE E 783 " --> pdb=" O   ASN E 773 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 815 through 822
      removed outlier: 6.521A  pdb=" N   ASP E 817 " --> pdb=" O   ALA E 808 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ALA E 808 " --> pdb=" O   ASP E 817 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLY E 819 " --> pdb=" O   VAL E 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL E 806 " --> pdb=" O   GLY E 819 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   LEU E 858 " --> pdb=" O   GLU E 869 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 768 through 774
      removed outlier: 3.653A  pdb=" N   GLY F 785 " --> pdb=" O   ASP F 771 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASN F 773 " --> pdb=" O   ILE F 783 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ILE F 783 " --> pdb=" O   ASN F 773 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 815 through 822
      removed outlier: 6.521A  pdb=" N   ASP F 817 " --> pdb=" O   ALA F 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA F 808 " --> pdb=" O   ASP F 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY F 819 " --> pdb=" O   VAL F 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL F 806 " --> pdb=" O   GLY F 819 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU F 858 " --> pdb=" O   GLU F 869 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 768 through 774
      removed outlier: 3.652A  pdb=" N   GLY G 785 " --> pdb=" O   ASP G 771 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN G 773 " --> pdb=" O   ILE G 783 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ILE G 783 " --> pdb=" O   ASN G 773 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'G' and resid 815 through 822
      removed outlier: 6.521A  pdb=" N   ASP G 817 " --> pdb=" O   ALA G 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA G 808 " --> pdb=" O   ASP G 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY G 819 " --> pdb=" O   VAL G 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL G 806 " --> pdb=" O   GLY G 819 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   LEU G 858 " --> pdb=" O   GLU G 869 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 768 through 774
      removed outlier: 3.652A  pdb=" N   GLY H 785 " --> pdb=" O   ASP H 771 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN H 773 " --> pdb=" O   ILE H 783 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE H 783 " --> pdb=" O   ASN H 773 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 815 through 822
      removed outlier: 6.522A  pdb=" N   ASP H 817 " --> pdb=" O   ALA H 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA H 808 " --> pdb=" O   ASP H 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY H 819 " --> pdb=" O   VAL H 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL H 806 " --> pdb=" O   GLY H 819 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   LEU H 858 " --> pdb=" O   GLU H 869 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'I' and resid 768 through 774
      removed outlier: 3.653A  pdb=" N   GLY I 785 " --> pdb=" O   ASP I 771 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN I 773 " --> pdb=" O   ILE I 783 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ILE I 783 " --> pdb=" O   ASN I 773 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'I' and resid 815 through 822
      removed outlier: 6.521A  pdb=" N   ASP I 817 " --> pdb=" O   ALA I 808 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ALA I 808 " --> pdb=" O   ASP I 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY I 819 " --> pdb=" O   VAL I 806 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL I 806 " --> pdb=" O   GLY I 819 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU I 858 " --> pdb=" O   GLU I 869 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'J' and resid 768 through 774
      removed outlier: 3.653A  pdb=" N   GLY J 785 " --> pdb=" O   ASP J 771 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASN J 773 " --> pdb=" O   ILE J 783 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE J 783 " --> pdb=" O   ASN J 773 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'J' and resid 815 through 822
      removed outlier: 6.521A  pdb=" N   ASP J 817 " --> pdb=" O   ALA J 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA J 808 " --> pdb=" O   ASP J 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY J 819 " --> pdb=" O   VAL J 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL J 806 " --> pdb=" O   GLY J 819 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   LEU J 858 " --> pdb=" O   GLU J 869 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'K' and resid 768 through 774
      removed outlier: 3.653A  pdb=" N   GLY K 785 " --> pdb=" O   ASP K 771 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN K 773 " --> pdb=" O   ILE K 783 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ILE K 783 " --> pdb=" O   ASN K 773 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'K' and resid 815 through 822
      removed outlier: 6.522A  pdb=" N   ASP K 817 " --> pdb=" O   ALA K 808 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ALA K 808 " --> pdb=" O   ASP K 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY K 819 " --> pdb=" O   VAL K 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL K 806 " --> pdb=" O   GLY K 819 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU K 858 " --> pdb=" O   GLU K 869 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 768 through 774
      removed outlier: 3.652A  pdb=" N   GLY L 785 " --> pdb=" O   ASP L 771 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASN L 773 " --> pdb=" O   ILE L 783 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ILE L 783 " --> pdb=" O   ASN L 773 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 815 through 822
      removed outlier: 6.521A  pdb=" N   ASP L 817 " --> pdb=" O   ALA L 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA L 808 " --> pdb=" O   ASP L 817 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   GLY L 819 " --> pdb=" O   VAL L 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL L 806 " --> pdb=" O   GLY L 819 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU L 858 " --> pdb=" O   GLU L 869 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'M' and resid 768 through 774
      removed outlier: 3.652A  pdb=" N   GLY M 785 " --> pdb=" O   ASP M 771 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN M 773 " --> pdb=" O   ILE M 783 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE M 783 " --> pdb=" O   ASN M 773 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'M' and resid 815 through 822
      removed outlier: 6.521A  pdb=" N   ASP M 817 " --> pdb=" O   ALA M 808 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ALA M 808 " --> pdb=" O   ASP M 817 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY M 819 " --> pdb=" O   VAL M 806 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL M 806 " --> pdb=" O   GLY M 819 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU M 858 " --> pdb=" O   GLU M 869 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'N' and resid 768 through 774
      removed outlier: 3.653A  pdb=" N   GLY N 785 " --> pdb=" O   ASP N 771 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN N 773 " --> pdb=" O   ILE N 783 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE N 783 " --> pdb=" O   ASN N 773 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'N' and resid 815 through 822
      removed outlier: 6.522A  pdb=" N   ASP N 817 " --> pdb=" O   ALA N 808 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ALA N 808 " --> pdb=" O   ASP N 817 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLY N 819 " --> pdb=" O   VAL N 806 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL N 806 " --> pdb=" O   GLY N 819 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   LEU N 858 " --> pdb=" O   GLU N 869 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    714 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: 3.48

  Time building geometry restraints manager: 3.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4256
        1.34 -     1.46: 2884
        1.46 -     1.57: 6272
        1.57 -     1.69: 14
        1.69 -     1.81: 112
  Bond restraints: 13538
  Sorted by residual:
  bond pdb=" C   ARG N 805 "
       pdb=" N   VAL N 806 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.56e-02 4.11e+03 4.50e+00
  bond pdb=" C   ARG K 805 "
       pdb=" N   VAL K 806 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.56e-02 4.11e+03 4.47e+00
  bond pdb=" C   ARG L 805 "
       pdb=" N   VAL L 806 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.033 1.56e-02 4.11e+03 4.42e+00
  bond pdb=" C   ARG G 805 "
       pdb=" N   VAL G 806 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.033 1.56e-02 4.11e+03 4.36e+00
  bond pdb=" C   ARG H 805 "
       pdb=" N   VAL H 806 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.56e-02 4.11e+03 4.33e+00
  ... (remaining 13533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 17071
        2.04 -     4.07: 967
        4.07 -     6.11: 204
        6.11 -     8.14: 14
        8.14 -    10.18: 42
  Bond angle restraints: 18298
  Sorted by residual:
  angle pdb=" CB  GLU L 824 "
        pdb=" CG  GLU L 824 "
        pdb=" CD  GLU L 824 "
      ideal   model   delta    sigma   weight residual
     112.60  121.58   -8.98 1.70e+00 3.46e-01 2.79e+01
  angle pdb=" CB  GLU C 824 "
        pdb=" CG  GLU C 824 "
        pdb=" CD  GLU C 824 "
      ideal   model   delta    sigma   weight residual
     112.60  121.56   -8.96 1.70e+00 3.46e-01 2.78e+01
  angle pdb=" CB  GLU A 824 "
        pdb=" CG  GLU A 824 "
        pdb=" CD  GLU A 824 "
      ideal   model   delta    sigma   weight residual
     112.60  121.56   -8.96 1.70e+00 3.46e-01 2.78e+01
  angle pdb=" CB  GLU N 824 "
        pdb=" CG  GLU N 824 "
        pdb=" CD  GLU N 824 "
      ideal   model   delta    sigma   weight residual
     112.60  121.56   -8.96 1.70e+00 3.46e-01 2.78e+01
  angle pdb=" CB  GLU I 824 "
        pdb=" CG  GLU I 824 "
        pdb=" CD  GLU I 824 "
      ideal   model   delta    sigma   weight residual
     112.60  121.56   -8.96 1.70e+00 3.46e-01 2.78e+01
  ... (remaining 18293 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.87: 6664
       13.87 -    27.75: 915
       27.75 -    41.62: 317
       41.62 -    55.49: 196
       55.49 -    69.36: 56
  Dihedral angle restraints: 8148
    sinusoidal: 3374
      harmonic: 4774
  Sorted by residual:
  dihedral pdb=" CA  TYR K 861 "
           pdb=" C   TYR K 861 "
           pdb=" N   ALA K 862 "
           pdb=" CA  ALA K 862 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.24   24.76     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  ASP F 758 "
           pdb=" C   ASP F 758 "
           pdb=" N   GLN F 759 "
           pdb=" CA  GLN F 759 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.26  -24.74     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  TYR D 861 "
           pdb=" C   TYR D 861 "
           pdb=" N   ALA D 862 "
           pdb=" CA  ALA D 862 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.26   24.74     0      5.00e+00 4.00e-02 2.45e+01
  ... (remaining 8145 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1061
       0.036 -    0.072: 526
       0.072 -    0.108: 192
       0.108 -    0.144: 125
       0.144 -    0.180: 14
  Chirality restraints: 1918
  Sorted by residual:
  chirality pdb=" CB  ILE D 801 "
            pdb=" CA  ILE D 801 "
            pdb=" CG1 ILE D 801 "
            pdb=" CG2 ILE D 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CB  ILE E 801 "
            pdb=" CA  ILE E 801 "
            pdb=" CG1 ILE E 801 "
            pdb=" CG2 ILE E 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.03e-01
  chirality pdb=" CB  ILE H 801 "
            pdb=" CA  ILE H 801 "
            pdb=" CG1 ILE H 801 "
            pdb=" CG2 ILE H 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.00e-01
  ... (remaining 1915 not shown)

  Planarity restraints: 2394
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 864 "   -0.053 5.00e-02 4.00e+02   7.92e-02 1.00e+01
        pdb=" N   PRO E 865 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO E 865 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO E 865 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR M 864 "   -0.052 5.00e-02 4.00e+02   7.92e-02 1.00e+01
        pdb=" N   PRO M 865 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO M 865 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO M 865 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F 864 "   -0.052 5.00e-02 4.00e+02   7.91e-02 1.00e+01
        pdb=" N   PRO F 865 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO F 865 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO F 865 "   -0.045 5.00e-02 4.00e+02
  ... (remaining 2391 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 4200
        2.82 -     3.34: 10897
        3.34 -     3.86: 21318
        3.86 -     4.38: 22480
        4.38 -     4.90: 38628
  Nonbonded interactions: 97523
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS M 765 "
            pdb=" OE2 GLU M 869 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" NE2 HIS G 765 "
            pdb=" OE2 GLU G 869 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" NE2 HIS A 765 "
            pdb=" OE2 GLU A 869 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" NE2 HIS K 765 "
            pdb=" OE2 GLU K 869 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" NE2 HIS B 765 "
            pdb=" OE2 GLU B 869 "
     model   vdw
     2.299 3.120
  ... (remaining 97518 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: 0.13
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'N'
}

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 group one per residue
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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.150
  Process input model:                     28.410
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
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   0.055  13538  Z= 0.382
  Angle     :  1.152  10.178  18298  Z= 0.655
  Chirality :  0.053   0.180   1918
  Planarity :  0.009   0.079   2394
  Dihedral  : 17.363  69.364   5124
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.33 %
    Favored  : 81.67 %
  Rotamer:
    Outliers :  9.80 %
    Allowed  :  6.86 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -5.50 (0.15), residues: 1582
  helix: -4.78 (0.17), residues: 182
  sheet: -2.21 (0.36), residues: 168
  loop : -4.08 (0.13), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.005   HIS H 765 
 PHE   0.015   0.002   PHE M 774 
 TYR   0.018   0.002   TYR I 855 
 ARG   0.009   0.001   ARG G 868 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19580 (  280)
  hydrogen bonds       : angle      11.88876 (  714)
  covalent geometry    : bond        0.00793 (13538)
  covalent geometry    : angle       1.15180 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  674 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 140
    poor density    : 534
  time to evaluate  : 1.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  759 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8565 (tm-30)
REVERT: A  762 MET cc_start: 0.6611 (mtt) cc_final: 0.6090 (mtt)
REVERT: A  780 ASN cc_start: 0.8567 (p0) cc_final: 0.8007 (p0)
REVERT: A  791 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8417 (p)
REVERT: B  759 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8548 (tm-30)
REVERT: B  762 MET cc_start: 0.6854 (mtt) cc_final: 0.6564 (mtt)
REVERT: B  780 ASN cc_start: 0.8224 (p0) cc_final: 0.7846 (p0)
REVERT: B  786 MET cc_start: 0.8440 (tpp) cc_final: 0.7776 (ttt)
REVERT: B  787 TYR cc_start: 0.8594 (m-10) cc_final: 0.8301 (m-80)
REVERT: B  791 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8398 (p)
REVERT: B  806 VAL cc_start: 0.9660 (OUTLIER) cc_final: 0.9301 (m)
REVERT: C  759 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: C  762 MET cc_start: 0.7033 (mtt) cc_final: 0.6508 (mtt)
REVERT: C  786 MET cc_start: 0.8143 (tpp) cc_final: 0.7636 (tpp)
REVERT: C  787 TYR cc_start: 0.8445 (m-10) cc_final: 0.8078 (m-80)
REVERT: C  791 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8556 (p)
REVERT: C  800 TYR cc_start: 0.8400 (t80) cc_final: 0.8142 (t80)
REVERT: C  868 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7577 (mmt90)
REVERT: D  759 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8349 (tm-30)
REVERT: D  762 MET cc_start: 0.7067 (mtt) cc_final: 0.6475 (mtt)
REVERT: D  780 ASN cc_start: 0.9094 (p0) cc_final: 0.8758 (p0)
REVERT: D  786 MET cc_start: 0.8292 (tpp) cc_final: 0.7923 (tpp)
REVERT: D  787 TYR cc_start: 0.8377 (m-10) cc_final: 0.7858 (m-80)
REVERT: D  791 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8623 (p)
REVERT: D  824 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8501 (tm-30)
REVERT: D  825 MET cc_start: 0.8144 (mtp) cc_final: 0.7780 (mtp)
REVERT: E  762 MET cc_start: 0.7253 (mtt) cc_final: 0.6834 (mtt)
REVERT: E  787 TYR cc_start: 0.8514 (m-10) cc_final: 0.8214 (m-10)
REVERT: E  791 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8231 (p)
REVERT: E  800 TYR cc_start: 0.8598 (t80) cc_final: 0.8358 (t80)
REVERT: E  806 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9204 (m)
REVERT: E  824 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7882 (tm-30)
REVERT: F  762 MET cc_start: 0.6846 (mtt) cc_final: 0.6603 (mtt)
REVERT: F  780 ASN cc_start: 0.8416 (p0) cc_final: 0.7943 (p0)
REVERT: F  787 TYR cc_start: 0.8728 (m-10) cc_final: 0.8203 (m-10)
REVERT: F  791 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8404 (p)
REVERT: G  759 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8679 (tm-30)
REVERT: G  762 MET cc_start: 0.7170 (mtt) cc_final: 0.6378 (mtt)
REVERT: G  780 ASN cc_start: 0.8335 (p0) cc_final: 0.8091 (p0)
REVERT: G  787 TYR cc_start: 0.8640 (m-10) cc_final: 0.8322 (m-10)
REVERT: G  791 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8734 (p)
REVERT: G  868 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7519 (mmt180)
REVERT: H  790 PRO cc_start: 0.6800 (Cg_endo) cc_final: 0.6541 (Cg_exo)
REVERT: H  791 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8230 (m)
REVERT: H  807 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6889 (mm-30)
REVERT: H  824 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7921 (tm-30)
REVERT: H  856 LYS cc_start: 0.8508 (tmmt) cc_final: 0.7903 (tmtt)
REVERT: H  870 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9039 (tt)
REVERT: I  762 MET cc_start: 0.6732 (mtt) cc_final: 0.6353 (mtt)
REVERT: I  803 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7777 (mtpp)
REVERT: I  824 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8108 (tm-30)
REVERT: I  852 ILE cc_start: 0.8398 (pt) cc_final: 0.8177 (tp)
REVERT: I  856 LYS cc_start: 0.8710 (tmmt) cc_final: 0.8107 (tmtt)
REVERT: I  870 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9028 (tt)
REVERT: J  762 MET cc_start: 0.7206 (mtt) cc_final: 0.6855 (mtt)
REVERT: J  786 MET cc_start: 0.8131 (tpp) cc_final: 0.7837 (mmm)
REVERT: J  807 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6544 (mm-30)
REVERT: J  870 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9105 (tt)
REVERT: K  791 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8547 (m)
REVERT: L  783 ILE cc_start: 0.9444 (mt) cc_final: 0.8902 (mt)
REVERT: L  786 MET cc_start: 0.7982 (tpp) cc_final: 0.7531 (mmm)
REVERT: L  824 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8265 (tm-30)
REVERT: L  856 LYS cc_start: 0.8010 (tmmt) cc_final: 0.7347 (tmtt)
REVERT: L  859 ARG cc_start: 0.7302 (mmm-85) cc_final: 0.6106 (mmm-85)
REVERT: L  866 ASP cc_start: 0.8868 (m-30) cc_final: 0.8365 (m-30)
REVERT: M  762 MET cc_start: 0.7227 (mtt) cc_final: 0.6853 (mtt)
REVERT: M  783 ILE cc_start: 0.9622 (mt) cc_final: 0.8744 (mp)
REVERT: M  786 MET cc_start: 0.8053 (tpp) cc_final: 0.7604 (mmm)
REVERT: M  807 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6815 (mm-30)
REVERT: M  852 ILE cc_start: 0.8282 (pt) cc_final: 0.7925 (tp)
REVERT: N  762 MET cc_start: 0.7389 (mtt) cc_final: 0.7166 (mtt)
REVERT: N  806 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8767 (t)
REVERT: N  807 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6161 (mm-30)
REVERT: N  824 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8248 (tm-30)
REVERT: N  856 LYS cc_start: 0.8201 (tmmt) cc_final: 0.7897 (ttpp)
  outliers start: 140
  outliers final: 25
  residues processed: 589
  average time/residue: 0.2638
  time to fit residues: 220.6191
Evaluate side-chains
  374 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 328
  time to evaluate  : 1.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    3.9990
   chunk 116 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 78 optimal weight:    8.9990
   chunk 62 optimal weight:    0.0370
   chunk 120 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0270
   chunk 89 optimal weight:    9.9990
   chunk 139 optimal weight:    5.9990
   overall best weight:    2.0122

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

Flipped N/Q/H residues before XYZ refinement:
C 851 ASN
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 792 GLN
** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.076005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.069804 restraints weight = 52446.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.071520 restraints weight = 29013.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.072701 restraints weight = 18150.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13538  Z= 0.162
  Angle     :  0.718   6.336  18298  Z= 0.377
  Chirality :  0.043   0.163   1918
  Planarity :  0.007   0.068   2394
  Dihedral  :  6.795  23.961   1820
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.71 %
    Favored  : 87.29 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.01 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.52 (0.14), residues: 1582
  helix: -4.37 (0.21), residues: 168
  sheet: -2.03 (0.39), residues: 168
  loop : -4.22 (0.12), residues: 1246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS A 765 
 PHE   0.009   0.001   PHE B 774 
 TYR   0.017   0.001   TYR N 855 
 ARG   0.005   0.001   ARG B 805 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04909 (  280)
  hydrogen bonds       : angle      10.18142 (  714)
  covalent geometry    : bond        0.00362 (13538)
  covalent geometry    : angle       0.71751 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  446 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 445
  time to evaluate  : 1.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  759 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8409 (tm-30)
REVERT: A  780 ASN cc_start: 0.8107 (p0) cc_final: 0.7573 (p0)
REVERT: A  800 TYR cc_start: 0.7828 (t80) cc_final: 0.7384 (t80)
REVERT: B  759 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8219 (pm20)
REVERT: B  786 MET cc_start: 0.8232 (tpp) cc_final: 0.6982 (ttt)
REVERT: B  800 TYR cc_start: 0.8128 (t80) cc_final: 0.7915 (t80)
REVERT: C  762 MET cc_start: 0.6153 (mtt) cc_final: 0.5444 (mtt)
REVERT: C  791 THR cc_start: 0.8554 (p) cc_final: 0.8333 (p)
REVERT: C  858 LEU cc_start: 0.9047 (tp) cc_final: 0.8813 (tp)
REVERT: D  759 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8020 (tm-30)
REVERT: D  762 MET cc_start: 0.6206 (mtt) cc_final: 0.5541 (mtt)
REVERT: D  780 ASN cc_start: 0.8141 (p0) cc_final: 0.7768 (p0)
REVERT: D  800 TYR cc_start: 0.7775 (t80) cc_final: 0.7430 (t80)
REVERT: E  762 MET cc_start: 0.6841 (mtt) cc_final: 0.6544 (mtt)
REVERT: E  786 MET cc_start: 0.8125 (tpp) cc_final: 0.7906 (tpp)
REVERT: E  791 THR cc_start: 0.8255 (p) cc_final: 0.8039 (p)
REVERT: E  866 ASP cc_start: 0.8619 (m-30) cc_final: 0.7863 (t0)
REVERT: F  780 ASN cc_start: 0.7697 (p0) cc_final: 0.7360 (p0)
REVERT: F  791 THR cc_start: 0.8370 (p) cc_final: 0.8158 (p)
REVERT: G  759 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8467 (tm-30)
REVERT: G  762 MET cc_start: 0.5963 (mtt) cc_final: 0.5530 (mtt)
REVERT: G  780 ASN cc_start: 0.7887 (p0) cc_final: 0.7346 (p0)
REVERT: G  803 LYS cc_start: 0.8894 (mttt) cc_final: 0.8617 (mttm)
REVERT: H  771 ASP cc_start: 0.8540 (t0) cc_final: 0.7463 (p0)
REVERT: H  856 LYS cc_start: 0.8701 (tmmt) cc_final: 0.8399 (tmtt)
REVERT: I  762 MET cc_start: 0.6223 (mtt) cc_final: 0.5842 (mtt)
REVERT: I  807 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7044 (mm-30)
REVERT: I  856 LYS cc_start: 0.8837 (tmmt) cc_final: 0.8555 (tmtt)
REVERT: I  870 LEU cc_start: 0.9369 (tp) cc_final: 0.9096 (tt)
REVERT: J  762 MET cc_start: 0.6592 (mtt) cc_final: 0.5983 (mtt)
REVERT: J  807 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7050 (mm-30)
REVERT: J  844 SER cc_start: 0.9067 (p) cc_final: 0.8793 (p)
REVERT: J  870 LEU cc_start: 0.9193 (tp) cc_final: 0.8955 (tt)
REVERT: K  762 MET cc_start: 0.7581 (mtm) cc_final: 0.7372 (mtt)
REVERT: K  771 ASP cc_start: 0.8721 (t0) cc_final: 0.7681 (p0)
REVERT: K  772 LEU cc_start: 0.9172 (mp) cc_final: 0.8881 (mp)
REVERT: K  869 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6592 (tm-30)
REVERT: L  786 MET cc_start: 0.8496 (tpp) cc_final: 0.8185 (mmm)
REVERT: L  790 PRO cc_start: 0.6941 (Cg_exo) cc_final: 0.6727 (Cg_endo)
REVERT: L  858 LEU cc_start: 0.8727 (tp) cc_final: 0.8421 (tp)
REVERT: M  771 ASP cc_start: 0.8786 (t0) cc_final: 0.7568 (p0)
REVERT: M  807 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7043 (mm-30)
REVERT: M  825 MET cc_start: 0.7969 (pmm) cc_final: 0.7746 (ptp)
REVERT: N  762 MET cc_start: 0.6980 (mtt) cc_final: 0.6517 (mtt)
REVERT: N  771 ASP cc_start: 0.8670 (t0) cc_final: 0.7569 (p0)
REVERT: N  807 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6522 (mm-30)
REVERT: N  825 MET cc_start: 0.8139 (ptp) cc_final: 0.7902 (ptp)
  outliers start: 1
  outliers final: 0
  residues processed: 446
  average time/residue: 0.2471
  time to fit residues: 158.5553
Evaluate side-chains
  320 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 320
  time to evaluate  : 1.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 117 optimal weight:    0.5980
   chunk 133 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 99 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   chunk 140 optimal weight:    8.9990
   chunk 134 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
** B 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 759 GLN
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 794 ASN
** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 794 ASN
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.071376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.065440 restraints weight = 53935.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.067071 restraints weight = 29942.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.068162 restraints weight = 18808.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13538  Z= 0.237
  Angle     :  0.785   7.020  18298  Z= 0.411
  Chirality :  0.044   0.152   1918
  Planarity :  0.007   0.072   2394
  Dihedral  :  6.846  21.660   1820
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.94 %
    Favored  : 83.06 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.16 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.73 (0.15), residues: 1582
  helix: -4.22 (0.24), residues: 168
  sheet: -3.36 (0.26), residues: 308
  loop : -4.19 (0.13), residues: 1106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS A 765 
 PHE   0.016   0.002   PHE E 774 
 TYR   0.021   0.002   TYR N 855 
 ARG   0.007   0.001   ARG E 859 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05502 (  280)
  hydrogen bonds       : angle       9.99037 (  714)
  covalent geometry    : bond        0.00532 (13538)
  covalent geometry    : angle       0.78471 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 397
  time to evaluate  : 1.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  780 ASN cc_start: 0.8273 (p0) cc_final: 0.7764 (p0)
REVERT: A  824 GLU cc_start: 0.9006 (tp30) cc_final: 0.8285 (tm-30)
REVERT: B  780 ASN cc_start: 0.7836 (p0) cc_final: 0.7570 (p0)
REVERT: B  786 MET cc_start: 0.8243 (tpp) cc_final: 0.7347 (ttt)
REVERT: B  829 LEU cc_start: 0.9398 (mt) cc_final: 0.9017 (mt)
REVERT: C  762 MET cc_start: 0.6117 (mtt) cc_final: 0.5464 (mtt)
REVERT: C  791 THR cc_start: 0.8677 (p) cc_final: 0.8303 (p)
REVERT: C  851 ASN cc_start: 0.7746 (t0) cc_final: 0.7467 (t0)
REVERT: C  860 ILE cc_start: 0.8201 (mp) cc_final: 0.7457 (mp)
REVERT: D  759 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8163 (tm-30)
REVERT: D  762 MET cc_start: 0.6748 (mtt) cc_final: 0.6071 (mtt)
REVERT: D  780 ASN cc_start: 0.8188 (p0) cc_final: 0.7968 (p0)
REVERT: D  786 MET cc_start: 0.8173 (tpp) cc_final: 0.7798 (tpt)
REVERT: D  791 THR cc_start: 0.8450 (p) cc_final: 0.8243 (p)
REVERT: E  762 MET cc_start: 0.6896 (mtt) cc_final: 0.6571 (mtt)
REVERT: E  786 MET cc_start: 0.8088 (tpp) cc_final: 0.7841 (tpp)
REVERT: E  824 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: E  866 ASP cc_start: 0.8365 (m-30) cc_final: 0.7646 (t0)
REVERT: F  780 ASN cc_start: 0.8075 (p0) cc_final: 0.7693 (p0)
REVERT: F  791 THR cc_start: 0.8474 (p) cc_final: 0.8262 (p)
REVERT: G  759 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: G  762 MET cc_start: 0.6173 (mtt) cc_final: 0.5574 (mtt)
REVERT: G  780 ASN cc_start: 0.8008 (p0) cc_final: 0.7534 (p0)
REVERT: G  787 TYR cc_start: 0.8849 (m-80) cc_final: 0.8441 (m-80)
REVERT: G  803 LYS cc_start: 0.8905 (mttt) cc_final: 0.8616 (mttm)
REVERT: H  771 ASP cc_start: 0.8639 (t0) cc_final: 0.7301 (p0)
REVERT: H  772 LEU cc_start: 0.9240 (mp) cc_final: 0.8940 (mp)
REVERT: H  824 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: H  861 TYR cc_start: 0.5885 (t80) cc_final: 0.5653 (t80)
REVERT: I  762 MET cc_start: 0.6720 (mtt) cc_final: 0.6285 (mtt)
REVERT: I  771 ASP cc_start: 0.8641 (t0) cc_final: 0.7537 (p0)
REVERT: I  772 LEU cc_start: 0.9359 (mp) cc_final: 0.9061 (mp)
REVERT: I  807 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6707 (tm-30)
REVERT: I  824 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: I  856 LYS cc_start: 0.8891 (tmmt) cc_final: 0.8689 (tttm)
REVERT: I  870 LEU cc_start: 0.9386 (tp) cc_final: 0.9074 (tt)
REVERT: J  762 MET cc_start: 0.7074 (mtt) cc_final: 0.6742 (mtt)
REVERT: J  807 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7154 (mm-30)
REVERT: J  844 SER cc_start: 0.9105 (p) cc_final: 0.8896 (p)
REVERT: J  870 LEU cc_start: 0.9240 (tp) cc_final: 0.8834 (tt)
REVERT: K  771 ASP cc_start: 0.8819 (t0) cc_final: 0.7685 (p0)
REVERT: K  772 LEU cc_start: 0.9329 (mp) cc_final: 0.8949 (mp)
REVERT: L  771 ASP cc_start: 0.8608 (t70) cc_final: 0.7760 (p0)
REVERT: L  772 LEU cc_start: 0.9275 (mp) cc_final: 0.9043 (mp)
REVERT: L  786 MET cc_start: 0.8318 (tpp) cc_final: 0.8055 (mmm)
REVERT: L  807 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7312 (mm-30)
REVERT: L  844 SER cc_start: 0.9176 (p) cc_final: 0.8938 (p)
REVERT: M  771 ASP cc_start: 0.8958 (t0) cc_final: 0.7889 (p0)
REVERT: M  807 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6602 (mm-30)
REVERT: N  762 MET cc_start: 0.6950 (mtt) cc_final: 0.6549 (mtt)
REVERT: N  771 ASP cc_start: 0.8688 (t0) cc_final: 0.7335 (p0)
REVERT: N  824 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7578 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 399
  average time/residue: 0.2343
  time to fit residues: 136.2024
Evaluate side-chains
  298 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 1.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   chunk 142 optimal weight:    4.9990
   chunk 136 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0670
   overall best weight:    1.9324

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

Flipped N/Q/H residues before XYZ refinement:
** B 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 794 ASN
** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 794 ASN
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.075094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.069085 restraints weight = 51943.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.070745 restraints weight = 28768.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.071853 restraints weight = 17859.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13538  Z= 0.154
  Angle     :  0.709   7.558  18298  Z= 0.367
  Chirality :  0.043   0.131   1918
  Planarity :  0.006   0.067   2394
  Dihedral  :  6.428  23.900   1820
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.58 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.22 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.55 (0.16), residues: 1582
  helix: -3.97 (0.25), residues: 168
  sheet: -3.26 (0.26), residues: 308
  loop : -4.07 (0.13), residues: 1106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS A 765 
 PHE   0.008   0.001   PHE I 774 
 TYR   0.017   0.001   TYR D 800 
 ARG   0.009   0.001   ARG K 868 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04529 (  280)
  hydrogen bonds       : angle       9.52747 (  714)
  covalent geometry    : bond        0.00351 (13538)
  covalent geometry    : angle       0.70862 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  416 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 414
  time to evaluate  : 2.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  780 ASN cc_start: 0.8231 (p0) cc_final: 0.7708 (p0)
REVERT: A  824 GLU cc_start: 0.8882 (tp30) cc_final: 0.8227 (tm-30)
REVERT: A  866 ASP cc_start: 0.8580 (m-30) cc_final: 0.7803 (t0)
REVERT: B  780 ASN cc_start: 0.7795 (p0) cc_final: 0.7454 (p0)
REVERT: B  786 MET cc_start: 0.8224 (tpp) cc_final: 0.7293 (ttt)
REVERT: B  803 LYS cc_start: 0.9075 (mttt) cc_final: 0.8747 (mttm)
REVERT: B  824 GLU cc_start: 0.8818 (tp30) cc_final: 0.8147 (tm-30)
REVERT: C  762 MET cc_start: 0.6569 (mtt) cc_final: 0.5946 (mtt)
REVERT: C  791 THR cc_start: 0.8473 (p) cc_final: 0.8261 (p)
REVERT: D  759 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8060 (tm-30)
REVERT: D  762 MET cc_start: 0.6351 (mtt) cc_final: 0.5659 (mtt)
REVERT: D  780 ASN cc_start: 0.7982 (p0) cc_final: 0.7733 (p0)
REVERT: D  786 MET cc_start: 0.8637 (tpp) cc_final: 0.8361 (tpt)
REVERT: D  791 THR cc_start: 0.8369 (p) cc_final: 0.8153 (p)
REVERT: E  762 MET cc_start: 0.6721 (mtt) cc_final: 0.6374 (mtt)
REVERT: E  780 ASN cc_start: 0.7994 (p0) cc_final: 0.7637 (p0)
REVERT: E  786 MET cc_start: 0.8131 (tpp) cc_final: 0.7702 (ttt)
REVERT: E  866 ASP cc_start: 0.8451 (m-30) cc_final: 0.7911 (t0)
REVERT: F  783 ILE cc_start: 0.9308 (mp) cc_final: 0.8996 (mt)
REVERT: G  759 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8550 (tm-30)
REVERT: G  762 MET cc_start: 0.6085 (mtt) cc_final: 0.5490 (mtt)
REVERT: G  780 ASN cc_start: 0.7907 (p0) cc_final: 0.7137 (p0)
REVERT: G  803 LYS cc_start: 0.8917 (mttt) cc_final: 0.8552 (mttm)
REVERT: G  870 LEU cc_start: 0.9614 (tp) cc_final: 0.9352 (tt)
REVERT: H  771 ASP cc_start: 0.8570 (t0) cc_final: 0.7283 (p0)
REVERT: H  824 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8356 (tm-30)
REVERT: H  861 TYR cc_start: 0.5962 (t80) cc_final: 0.5749 (t80)
REVERT: I  762 MET cc_start: 0.6556 (mtt) cc_final: 0.6269 (mtt)
REVERT: I  771 ASP cc_start: 0.8616 (t0) cc_final: 0.7496 (p0)
REVERT: I  772 LEU cc_start: 0.9330 (mp) cc_final: 0.9049 (mp)
REVERT: I  803 LYS cc_start: 0.7794 (tptt) cc_final: 0.7400 (mmmt)
REVERT: I  807 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7078 (tm-30)
REVERT: I  824 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8146 (tm-30)
REVERT: I  869 GLU cc_start: 0.7978 (tp30) cc_final: 0.7137 (tm-30)
REVERT: I  870 LEU cc_start: 0.9399 (tp) cc_final: 0.8983 (tt)
REVERT: J  762 MET cc_start: 0.6987 (mtt) cc_final: 0.6689 (mtt)
REVERT: J  807 GLU cc_start: 0.7805 (mt-10) cc_final: 0.6841 (tm-30)
REVERT: J  824 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7752 (tm-30)
REVERT: J  870 LEU cc_start: 0.9065 (tp) cc_final: 0.8815 (tt)
REVERT: K  771 ASP cc_start: 0.8791 (t0) cc_final: 0.7668 (p0)
REVERT: K  772 LEU cc_start: 0.9230 (mp) cc_final: 0.8814 (mp)
REVERT: L  771 ASP cc_start: 0.8662 (t70) cc_final: 0.7979 (p0)
REVERT: L  786 MET cc_start: 0.8307 (tpp) cc_final: 0.7998 (mmm)
REVERT: L  807 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6243 (tm-30)
REVERT: L  824 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8163 (tm-30)
REVERT: M  771 ASP cc_start: 0.8969 (t0) cc_final: 0.7891 (p0)
REVERT: M  807 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6634 (tm-30)
REVERT: N  762 MET cc_start: 0.6817 (mtt) cc_final: 0.6387 (mtt)
REVERT: N  771 ASP cc_start: 0.8756 (t0) cc_final: 0.7355 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 416
  average time/residue: 0.2849
  time to fit residues: 168.7426
Evaluate side-chains
  331 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 331
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 147 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 133 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 53 optimal weight:    0.6980
   chunk 24 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 148 optimal weight:   10.0000
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** B 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 851 ASN
** G 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 794 ASN
** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 794 ASN
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.073414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.067446 restraints weight = 51837.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.069133 restraints weight = 28632.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.070156 restraints weight = 17692.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.4718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13538  Z= 0.192
  Angle     :  0.748   7.893  18298  Z= 0.387
  Chirality :  0.044   0.139   1918
  Planarity :  0.007   0.071   2394
  Dihedral  :  6.440  22.012   1820
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.75 %
    Favored  : 83.25 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.52 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.06 (0.16), residues: 1582
  helix: -3.67 (0.29), residues: 168
  sheet: -1.57 (0.40), residues: 168
  loop : -3.96 (0.13), residues: 1246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B 765 
 PHE   0.012   0.001   PHE J 774 
 TYR   0.016   0.001   TYR K 855 
 ARG   0.008   0.001   ARG C 859 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04837 (  280)
  hydrogen bonds       : angle       9.35913 (  714)
  covalent geometry    : bond        0.00433 (13538)
  covalent geometry    : angle       0.74777 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  408 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 405
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  824 GLU cc_start: 0.8840 (tp30) cc_final: 0.8422 (tm-30)
REVERT: A  866 ASP cc_start: 0.8366 (m-30) cc_final: 0.7711 (t0)
REVERT: B  780 ASN cc_start: 0.7898 (p0) cc_final: 0.7596 (p0)
REVERT: B  786 MET cc_start: 0.8267 (tpp) cc_final: 0.7566 (ttt)
REVERT: B  803 LYS cc_start: 0.9120 (mttt) cc_final: 0.8778 (mttm)
REVERT: B  829 LEU cc_start: 0.9330 (mt) cc_final: 0.9128 (mt)
REVERT: C  762 MET cc_start: 0.6738 (mtt) cc_final: 0.5915 (mtt)
REVERT: C  791 THR cc_start: 0.8489 (p) cc_final: 0.8255 (p)
REVERT: D  762 MET cc_start: 0.6470 (mtt) cc_final: 0.5780 (mtt)
REVERT: D  780 ASN cc_start: 0.8374 (p0) cc_final: 0.8083 (p0)
REVERT: D  786 MET cc_start: 0.8439 (tpp) cc_final: 0.7626 (tpt)
REVERT: D  791 THR cc_start: 0.8308 (p) cc_final: 0.8091 (p)
REVERT: E  762 MET cc_start: 0.6901 (mtt) cc_final: 0.6475 (mtt)
REVERT: E  780 ASN cc_start: 0.8119 (p0) cc_final: 0.7871 (p0)
REVERT: E  786 MET cc_start: 0.7913 (tpp) cc_final: 0.7618 (tpp)
REVERT: E  800 TYR cc_start: 0.7812 (t80) cc_final: 0.7607 (t80)
REVERT: E  803 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8280 (mttm)
REVERT: E  866 ASP cc_start: 0.8426 (m-30) cc_final: 0.7686 (t0)
REVERT: F  791 THR cc_start: 0.8640 (p) cc_final: 0.8433 (p)
REVERT: G  759 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8610 (tm-30)
REVERT: G  762 MET cc_start: 0.6119 (mtt) cc_final: 0.5397 (mtt)
REVERT: G  780 ASN cc_start: 0.8087 (p0) cc_final: 0.7690 (p0)
REVERT: G  803 LYS cc_start: 0.8940 (mttt) cc_final: 0.8552 (mttm)
REVERT: G  870 LEU cc_start: 0.9698 (tp) cc_final: 0.9469 (tp)
REVERT: H  771 ASP cc_start: 0.8713 (t0) cc_final: 0.7366 (p0)
REVERT: H  772 LEU cc_start: 0.9422 (mt) cc_final: 0.8967 (mp)
REVERT: H  824 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8427 (tm-30)
REVERT: I  762 MET cc_start: 0.6680 (mtt) cc_final: 0.6409 (mtt)
REVERT: I  807 GLU cc_start: 0.7721 (mt-10) cc_final: 0.6937 (tm-30)
REVERT: I  824 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8191 (tm-30)
REVERT: I  856 LYS cc_start: 0.8709 (tmmt) cc_final: 0.8198 (tmtt)
REVERT: I  869 GLU cc_start: 0.7883 (tp30) cc_final: 0.7149 (tm-30)
REVERT: I  870 LEU cc_start: 0.9319 (tp) cc_final: 0.8843 (tt)
REVERT: J  762 MET cc_start: 0.7047 (mtt) cc_final: 0.6619 (mtt)
REVERT: J  807 GLU cc_start: 0.7885 (mt-10) cc_final: 0.6723 (tm-30)
REVERT: J  824 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7854 (tm-30)
REVERT: J  844 SER cc_start: 0.9056 (p) cc_final: 0.8811 (p)
REVERT: J  870 LEU cc_start: 0.9107 (tp) cc_final: 0.8836 (tt)
REVERT: K  762 MET cc_start: 0.7714 (mtm) cc_final: 0.7501 (mtt)
REVERT: K  771 ASP cc_start: 0.8815 (t0) cc_final: 0.7656 (p0)
REVERT: K  783 ILE cc_start: 0.9532 (mp) cc_final: 0.9320 (mt)
REVERT: L  786 MET cc_start: 0.8112 (tpp) cc_final: 0.7908 (mmm)
REVERT: L  807 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6647 (tm-30)
REVERT: L  824 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8157 (tm-30)
REVERT: L  844 SER cc_start: 0.9146 (p) cc_final: 0.8910 (p)
REVERT: L  868 ARG cc_start: 0.8286 (mmt180) cc_final: 0.7705 (mmm-85)
REVERT: M  807 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6756 (tm-30)
REVERT: M  824 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8208 (tm-30)
REVERT: N  762 MET cc_start: 0.6897 (mtt) cc_final: 0.6415 (mtt)
REVERT: N  771 ASP cc_start: 0.8751 (t0) cc_final: 0.7240 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 408
  average time/residue: 0.2527
  time to fit residues: 146.3270
Evaluate side-chains
  311 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 106 optimal weight:    0.1980
   chunk 119 optimal weight:    4.9990
   chunk 115 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 68 optimal weight:    9.9990
   chunk 152 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 42 optimal weight:    8.9990
   chunk 150 optimal weight:    4.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
** E 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 794 ASN
** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 794 ASN
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.074027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.067902 restraints weight = 51815.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.069589 restraints weight = 28813.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.070743 restraints weight = 17938.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.5030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13538  Z= 0.162
  Angle     :  0.721   8.452  18298  Z= 0.373
  Chirality :  0.044   0.216   1918
  Planarity :  0.006   0.065   2394
  Dihedral  :  6.299  23.553   1820
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.41 %
    Favored  : 85.59 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.26 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.18 (0.17), residues: 1582
  helix: -3.55 (0.30), residues: 168
  sheet: -3.09 (0.26), residues: 308
  loop : -3.81 (0.15), residues: 1106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS A 765 
 PHE   0.009   0.001   PHE J 774 
 TYR   0.017   0.001   TYR B 861 
 ARG   0.009   0.001   ARG C 859 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04449 (  280)
  hydrogen bonds       : angle       9.16222 (  714)
  covalent geometry    : bond        0.00368 (13538)
  covalent geometry    : angle       0.72147 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  393 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 391
  time to evaluate  : 1.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  762 MET cc_start: 0.7507 (mtm) cc_final: 0.7302 (mtt)
REVERT: A  824 GLU cc_start: 0.8827 (tp30) cc_final: 0.8499 (tm-30)
REVERT: A  866 ASP cc_start: 0.8381 (m-30) cc_final: 0.7848 (t0)
REVERT: B  780 ASN cc_start: 0.7688 (p0) cc_final: 0.7412 (p0)
REVERT: B  803 LYS cc_start: 0.9025 (mttt) cc_final: 0.8650 (mttm)
REVERT: B  824 GLU cc_start: 0.8821 (tp30) cc_final: 0.8207 (tm-30)
REVERT: C  759 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7745 (tm-30)
REVERT: C  762 MET cc_start: 0.6676 (mtt) cc_final: 0.5781 (mtt)
REVERT: C  791 THR cc_start: 0.8420 (p) cc_final: 0.8155 (p)
REVERT: D  762 MET cc_start: 0.6365 (mtt) cc_final: 0.5737 (mtt)
REVERT: D  780 ASN cc_start: 0.8028 (p0) cc_final: 0.7739 (p0)
REVERT: D  786 MET cc_start: 0.8576 (tpp) cc_final: 0.8362 (tpt)
REVERT: D  787 TYR cc_start: 0.8929 (m-80) cc_final: 0.8220 (m-80)
REVERT: D  791 THR cc_start: 0.8234 (p) cc_final: 0.7982 (p)
REVERT: D  800 TYR cc_start: 0.7456 (t80) cc_final: 0.7235 (t80)
REVERT: E  762 MET cc_start: 0.7002 (mtt) cc_final: 0.6541 (mtt)
REVERT: E  786 MET cc_start: 0.8094 (tpp) cc_final: 0.7624 (ttt)
REVERT: E  791 THR cc_start: 0.8223 (p) cc_final: 0.8003 (p)
REVERT: E  800 TYR cc_start: 0.7808 (t80) cc_final: 0.7597 (t80)
REVERT: E  803 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8345 (mttm)
REVERT: E  866 ASP cc_start: 0.8533 (m-30) cc_final: 0.8049 (t0)
REVERT: F  783 ILE cc_start: 0.9201 (mp) cc_final: 0.8922 (mt)
REVERT: G  759 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8538 (tm-30)
REVERT: G  762 MET cc_start: 0.5992 (mtt) cc_final: 0.5400 (mtt)
REVERT: G  780 ASN cc_start: 0.7959 (p0) cc_final: 0.7664 (p0)
REVERT: G  803 LYS cc_start: 0.8907 (mttt) cc_final: 0.8615 (mttm)
REVERT: G  853 MET cc_start: 0.7896 (ppp) cc_final: 0.7434 (ppp)
REVERT: G  870 LEU cc_start: 0.9630 (tp) cc_final: 0.9430 (tt)
REVERT: H  762 MET cc_start: 0.8172 (mtm) cc_final: 0.7860 (mtt)
REVERT: H  771 ASP cc_start: 0.8664 (t0) cc_final: 0.7342 (p0)
REVERT: H  772 LEU cc_start: 0.9472 (mt) cc_final: 0.9015 (mp)
REVERT: H  824 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8371 (tm-30)
REVERT: I  762 MET cc_start: 0.6544 (mtt) cc_final: 0.6267 (mtt)
REVERT: I  807 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7074 (tm-30)
REVERT: I  824 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8245 (tm-30)
REVERT: I  856 LYS cc_start: 0.8719 (tmmt) cc_final: 0.8301 (tmtt)
REVERT: I  870 LEU cc_start: 0.9361 (tp) cc_final: 0.8965 (tt)
REVERT: J  762 MET cc_start: 0.7178 (mtt) cc_final: 0.6711 (mtt)
REVERT: J  807 GLU cc_start: 0.7805 (mt-10) cc_final: 0.6827 (tm-30)
REVERT: J  844 SER cc_start: 0.9042 (p) cc_final: 0.8812 (p)
REVERT: J  870 LEU cc_start: 0.9155 (tp) cc_final: 0.8932 (tt)
REVERT: K  762 MET cc_start: 0.7992 (mtm) cc_final: 0.7775 (mtt)
REVERT: K  771 ASP cc_start: 0.8728 (t0) cc_final: 0.7660 (p0)
REVERT: K  786 MET cc_start: 0.8923 (tpp) cc_final: 0.8674 (tpp)
REVERT: L  771 ASP cc_start: 0.8910 (t0) cc_final: 0.7720 (p0)
REVERT: L  772 LEU cc_start: 0.9313 (mp) cc_final: 0.8932 (mp)
REVERT: L  807 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7520 (mm-30)
REVERT: L  824 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8419 (tm-30)
REVERT: L  844 SER cc_start: 0.9065 (p) cc_final: 0.8809 (p)
REVERT: M  807 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6548 (tm-30)
REVERT: M  824 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8369 (tm-30)
REVERT: N  762 MET cc_start: 0.6732 (mtt) cc_final: 0.6194 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 393
  average time/residue: 0.2822
  time to fit residues: 158.5314
Evaluate side-chains
  323 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 323
  time to evaluate  : 1.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 91 optimal weight:    9.9990
   chunk 67 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 121 optimal weight:   10.0000
   chunk 124 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** F 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 759 GLN
H 759 GLN
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 759 GLN
** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 759 GLN
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 759 GLN
** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 794 ASN
N 759 GLN
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.067664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.061974 restraints weight = 54710.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.063565 restraints weight = 29743.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.064648 restraints weight = 18344.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.5319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.041  13538  Z= 0.378
  Angle     :  0.966   9.867  18298  Z= 0.505
  Chirality :  0.050   0.163   1918
  Planarity :  0.008   0.071   2394
  Dihedral  :  7.344  22.812   1820
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 21.87 %
    Favored  : 78.07 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.87 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.86 (0.17), residues: 1582
  helix: -3.28 (0.35), residues: 182
  sheet: -1.70 (0.38), residues: 168
  loop : -3.81 (0.14), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.004   HIS D 765 
 PHE   0.026   0.003   PHE J 774 
 TYR   0.023   0.003   TYR K 787 
 ARG   0.009   0.001   ARG E 868 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06723 (  280)
  hydrogen bonds       : angle       9.84459 (  714)
  covalent geometry    : bond        0.00838 (13538)
  covalent geometry    : angle       0.96591 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 368
  time to evaluate  : 2.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  786 MET cc_start: 0.8275 (tpp) cc_final: 0.7844 (ttt)
REVERT: A  866 ASP cc_start: 0.8588 (m-30) cc_final: 0.7910 (t0)
REVERT: B  780 ASN cc_start: 0.8088 (p0) cc_final: 0.7748 (p0)
REVERT: B  803 LYS cc_start: 0.9079 (mttt) cc_final: 0.8759 (mttm)
REVERT: B  824 GLU cc_start: 0.8865 (tp30) cc_final: 0.8339 (tm-30)
REVERT: B  829 LEU cc_start: 0.9424 (mt) cc_final: 0.9048 (mt)
REVERT: C  762 MET cc_start: 0.7120 (mtt) cc_final: 0.6104 (mtt)
REVERT: D  759 GLN cc_start: 0.8480 (pm20) cc_final: 0.8254 (pm20)
REVERT: D  762 MET cc_start: 0.6939 (mtt) cc_final: 0.6208 (mtt)
REVERT: D  780 ASN cc_start: 0.8484 (p0) cc_final: 0.8116 (p0)
REVERT: D  786 MET cc_start: 0.8466 (tpp) cc_final: 0.8150 (tpp)
REVERT: D  787 TYR cc_start: 0.8910 (m-80) cc_final: 0.8128 (m-80)
REVERT: D  800 TYR cc_start: 0.8218 (t80) cc_final: 0.8008 (t80)
REVERT: D  824 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: E  762 MET cc_start: 0.7613 (mtt) cc_final: 0.7157 (mtt)
REVERT: E  786 MET cc_start: 0.7995 (tpp) cc_final: 0.7677 (ttt)
REVERT: E  824 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8010 (tm-30)
REVERT: E  825 MET cc_start: 0.8862 (tpt) cc_final: 0.7770 (tpp)
REVERT: E  860 ILE cc_start: 0.7940 (mm) cc_final: 0.7534 (mm)
REVERT: E  861 TYR cc_start: 0.6416 (t80) cc_final: 0.6214 (t80)
REVERT: E  866 ASP cc_start: 0.8739 (m-30) cc_final: 0.8091 (t0)
REVERT: F  780 ASN cc_start: 0.8410 (p0) cc_final: 0.8197 (p0)
REVERT: F  824 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8035 (tm-30)
REVERT: G  759 GLN cc_start: 0.8934 (tm130) cc_final: 0.8644 (tm-30)
REVERT: G  762 MET cc_start: 0.7334 (mtt) cc_final: 0.6380 (mtt)
REVERT: G  803 LYS cc_start: 0.9022 (mttt) cc_final: 0.8703 (mttm)
REVERT: G  807 GLU cc_start: 0.8574 (mp0) cc_final: 0.8294 (mt-10)
REVERT: H  762 MET cc_start: 0.8201 (mtm) cc_final: 0.7834 (mtt)
REVERT: H  771 ASP cc_start: 0.8843 (t0) cc_final: 0.7386 (p0)
REVERT: H  772 LEU cc_start: 0.9581 (mt) cc_final: 0.8993 (mp)
REVERT: H  824 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: I  762 MET cc_start: 0.7214 (mtt) cc_final: 0.6712 (mtt)
REVERT: I  807 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6908 (tm-30)
REVERT: I  824 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: I  856 LYS cc_start: 0.8906 (tmmt) cc_final: 0.8600 (tmtt)
REVERT: I  870 LEU cc_start: 0.9314 (tp) cc_final: 0.8934 (tt)
REVERT: J  762 MET cc_start: 0.7618 (mtt) cc_final: 0.7031 (mtt)
REVERT: J  844 SER cc_start: 0.9040 (p) cc_final: 0.8814 (p)
REVERT: J  870 LEU cc_start: 0.9245 (tp) cc_final: 0.9011 (tt)
REVERT: K  786 MET cc_start: 0.8896 (tpp) cc_final: 0.8644 (mmm)
REVERT: K  791 THR cc_start: 0.8167 (m) cc_final: 0.7838 (p)
REVERT: L  807 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7584 (mm-30)
REVERT: L  824 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8435 (tm-30)
REVERT: L  868 ARG cc_start: 0.8630 (mmt180) cc_final: 0.8273 (mmm-85)
REVERT: M  807 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6372 (tm-30)
REVERT: M  824 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8524 (tm-30)
REVERT: N  762 MET cc_start: 0.7182 (mtt) cc_final: 0.6505 (mtt)
REVERT: N  807 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7046 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 369
  average time/residue: 0.2844
  time to fit residues: 150.3342
Evaluate side-chains
  289 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 3.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 133 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0170
   chunk 2 optimal weight:    4.9990
   chunk 97 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 136 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 90 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.7824

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

Flipped N/Q/H residues before XYZ refinement:
** F 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.073930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.068059 restraints weight = 52538.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.069729 restraints weight = 28754.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.070857 restraints weight = 17668.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.5444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13538  Z= 0.155
  Angle     :  0.774  10.012  18298  Z= 0.399
  Chirality :  0.046   0.201   1918
  Planarity :  0.006   0.063   2394
  Dihedral  :  6.525  23.611   1820
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.22 %
    Favored  : 85.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.09 (0.17), residues: 1582
  helix: -3.62 (0.29), residues: 168
  sheet: -3.07 (0.26), residues: 308
  loop : -3.71 (0.15), residues: 1106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.004   HIS B 765 
 PHE   0.024   0.001   PHE B 788 
 TYR   0.023   0.001   TYR D 861 
 ARG   0.008   0.001   ARG C 859 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04474 (  280)
  hydrogen bonds       : angle       9.34343 (  714)
  covalent geometry    : bond        0.00354 (13538)
  covalent geometry    : angle       0.77356 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  406 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 406
  time to evaluate  : 1.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  762 MET cc_start: 0.7747 (mtm) cc_final: 0.7484 (mtt)
REVERT: A  866 ASP cc_start: 0.8288 (m-30) cc_final: 0.7982 (t0)
REVERT: A  868 ARG cc_start: 0.8001 (mmt90) cc_final: 0.7633 (mmm-85)
REVERT: B  762 MET cc_start: 0.7547 (mpp) cc_final: 0.7291 (mpp)
REVERT: B  780 ASN cc_start: 0.7830 (p0) cc_final: 0.7563 (p0)
REVERT: B  803 LYS cc_start: 0.8989 (mttt) cc_final: 0.8620 (mttm)
REVERT: B  824 GLU cc_start: 0.8918 (tp30) cc_final: 0.8108 (tm-30)
REVERT: B  866 ASP cc_start: 0.8782 (m-30) cc_final: 0.8515 (t0)
REVERT: B  868 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7428 (mmm-85)
REVERT: C  759 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7793 (tm-30)
REVERT: C  762 MET cc_start: 0.6604 (mtt) cc_final: 0.5672 (mtt)
REVERT: C  829 LEU cc_start: 0.9502 (mt) cc_final: 0.9168 (mt)
REVERT: D  759 GLN cc_start: 0.8346 (pm20) cc_final: 0.8045 (pm20)
REVERT: D  762 MET cc_start: 0.6218 (mtt) cc_final: 0.5696 (mtt)
REVERT: D  780 ASN cc_start: 0.8174 (p0) cc_final: 0.7751 (p0)
REVERT: D  786 MET cc_start: 0.8256 (tpp) cc_final: 0.7885 (tpp)
REVERT: D  787 TYR cc_start: 0.8759 (m-80) cc_final: 0.8439 (m-80)
REVERT: D  791 THR cc_start: 0.8342 (p) cc_final: 0.8094 (p)
REVERT: D  824 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: E  762 MET cc_start: 0.7168 (mtt) cc_final: 0.6703 (mtt)
REVERT: E  800 TYR cc_start: 0.7647 (t80) cc_final: 0.7440 (t80)
REVERT: E  803 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8396 (mttm)
REVERT: E  825 MET cc_start: 0.8684 (tpt) cc_final: 0.8468 (tpp)
REVERT: E  860 ILE cc_start: 0.7682 (mm) cc_final: 0.6375 (mp)
REVERT: E  866 ASP cc_start: 0.8533 (m-30) cc_final: 0.8075 (t0)
REVERT: E  870 LEU cc_start: 0.9660 (tp) cc_final: 0.9456 (tt)
REVERT: F  824 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: F  868 ARG cc_start: 0.7813 (mmt90) cc_final: 0.7521 (mmm-85)
REVERT: G  759 GLN cc_start: 0.8637 (pp30) cc_final: 0.8426 (tm-30)
REVERT: G  762 MET cc_start: 0.6552 (mtt) cc_final: 0.5652 (mtt)
REVERT: G  787 TYR cc_start: 0.8882 (m-10) cc_final: 0.8551 (m-80)
REVERT: G  803 LYS cc_start: 0.8927 (mttt) cc_final: 0.8618 (mttm)
REVERT: G  853 MET cc_start: 0.7600 (ppp) cc_final: 0.7343 (ppp)
REVERT: G  866 ASP cc_start: 0.8938 (t0) cc_final: 0.8426 (t0)
REVERT: G  868 ARG cc_start: 0.7476 (mmm-85) cc_final: 0.7216 (mmm-85)
REVERT: H  762 MET cc_start: 0.8288 (mtm) cc_final: 0.7766 (mtt)
REVERT: H  771 ASP cc_start: 0.8586 (t0) cc_final: 0.7412 (p0)
REVERT: H  772 LEU cc_start: 0.9485 (mt) cc_final: 0.9058 (mp)
REVERT: H  824 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: I  762 MET cc_start: 0.6641 (mtt) cc_final: 0.6330 (mtt)
REVERT: I  771 ASP cc_start: 0.8736 (t0) cc_final: 0.7277 (p0)
REVERT: I  807 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7115 (tp30)
REVERT: I  824 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8246 (tm-30)
REVERT: I  856 LYS cc_start: 0.8792 (tmmt) cc_final: 0.8369 (tmtt)
REVERT: I  870 LEU cc_start: 0.9268 (tp) cc_final: 0.8960 (tt)
REVERT: J  762 MET cc_start: 0.7133 (mtt) cc_final: 0.6580 (mtt)
REVERT: J  807 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7039 (tm-30)
REVERT: J  817 ASP cc_start: 0.8699 (t70) cc_final: 0.8260 (t0)
REVERT: J  844 SER cc_start: 0.8978 (p) cc_final: 0.8771 (p)
REVERT: J  870 LEU cc_start: 0.9276 (tp) cc_final: 0.8630 (tt)
REVERT: K  762 MET cc_start: 0.8023 (mtm) cc_final: 0.7727 (mtt)
REVERT: K  771 ASP cc_start: 0.8793 (t0) cc_final: 0.7442 (p0)
REVERT: K  786 MET cc_start: 0.9127 (tpp) cc_final: 0.8907 (mmm)
REVERT: K  791 THR cc_start: 0.7927 (m) cc_final: 0.7556 (p)
REVERT: L  762 MET cc_start: 0.8106 (mtm) cc_final: 0.7672 (mtt)
REVERT: L  807 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7303 (mm-30)
REVERT: L  824 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8371 (tm-30)
REVERT: L  844 SER cc_start: 0.9062 (p) cc_final: 0.8800 (p)
REVERT: M  762 MET cc_start: 0.7608 (mtm) cc_final: 0.7404 (mtt)
REVERT: M  807 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6547 (tm-30)
REVERT: N  762 MET cc_start: 0.6593 (mtt) cc_final: 0.6071 (mtt)
REVERT: N  807 GLU cc_start: 0.7781 (mt-10) cc_final: 0.6930 (tm-30)
REVERT: N  824 GLU cc_start: 0.8659 (tm-30) cc_final: 0.7690 (tm-30)
REVERT: N  858 LEU cc_start: 0.8113 (tt) cc_final: 0.7271 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 406
  average time/residue: 0.4006
  time to fit residues: 235.1047
Evaluate side-chains
  329 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 329
  time to evaluate  : 2.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   chunk 121 optimal weight:   10.0000
   chunk 50 optimal weight:    9.9990
   chunk 69 optimal weight:    8.9990
   chunk 133 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 151 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** H 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.069972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.064280 restraints weight = 53123.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.065868 restraints weight = 29143.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.066946 restraints weight = 18094.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.5552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  13538  Z= 0.267
  Angle     :  0.874   8.615  18298  Z= 0.456
  Chirality :  0.048   0.182   1918
  Planarity :  0.007   0.069   2394
  Dihedral  :  6.803  22.873   1820
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.11 %
    Favored  : 78.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.13 (0.17), residues: 1582
  helix: -3.45 (0.32), residues: 168
  sheet: -2.97 (0.26), residues: 308
  loop : -3.81 (0.15), residues: 1106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS B 765 
 PHE   0.021   0.002   PHE J 774 
 TYR   0.027   0.002   TYR C 861 
 ARG   0.008   0.001   ARG B 859 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05647 (  280)
  hydrogen bonds       : angle       9.40594 (  714)
  covalent geometry    : bond        0.00601 (13538)
  covalent geometry    : angle       0.87385 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 365
  time to evaluate  : 2.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  866 ASP cc_start: 0.8461 (m-30) cc_final: 0.7969 (t0)
REVERT: A  870 LEU cc_start: 0.9591 (tp) cc_final: 0.9338 (tp)
REVERT: B  759 GLN cc_start: 0.8741 (pm20) cc_final: 0.8452 (pm20)
REVERT: B  762 MET cc_start: 0.7973 (mpp) cc_final: 0.7492 (mpp)
REVERT: B  780 ASN cc_start: 0.8083 (p0) cc_final: 0.7774 (p0)
REVERT: B  803 LYS cc_start: 0.9026 (mttt) cc_final: 0.8679 (mttm)
REVERT: B  824 GLU cc_start: 0.8880 (tp30) cc_final: 0.8303 (tm-30)
REVERT: B  829 LEU cc_start: 0.9349 (mt) cc_final: 0.9064 (mt)
REVERT: B  866 ASP cc_start: 0.8797 (m-30) cc_final: 0.8451 (t0)
REVERT: B  868 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7287 (mmm-85)
REVERT: C  762 MET cc_start: 0.7070 (mtt) cc_final: 0.6196 (mtt)
REVERT: C  825 MET cc_start: 0.8658 (tpt) cc_final: 0.7925 (tpt)
REVERT: D  759 GLN cc_start: 0.8380 (pm20) cc_final: 0.8081 (pm20)
REVERT: D  780 ASN cc_start: 0.8534 (p0) cc_final: 0.8266 (p0)
REVERT: D  786 MET cc_start: 0.8291 (tpp) cc_final: 0.7920 (tpp)
REVERT: D  787 TYR cc_start: 0.8915 (m-80) cc_final: 0.8320 (m-80)
REVERT: D  791 THR cc_start: 0.8351 (p) cc_final: 0.8142 (p)
REVERT: D  824 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7697 (tm-30)
REVERT: E  762 MET cc_start: 0.7371 (mtt) cc_final: 0.6859 (mtt)
REVERT: E  787 TYR cc_start: 0.8899 (m-10) cc_final: 0.8474 (m-10)
REVERT: E  825 MET cc_start: 0.8696 (tpt) cc_final: 0.8081 (tpt)
REVERT: E  866 ASP cc_start: 0.8662 (m-30) cc_final: 0.8197 (t0)
REVERT: F  824 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7927 (tm-30)
REVERT: F  870 LEU cc_start: 0.9585 (tp) cc_final: 0.9302 (tp)
REVERT: G  759 GLN cc_start: 0.8646 (pp30) cc_final: 0.8285 (pp30)
REVERT: G  762 MET cc_start: 0.6854 (mtt) cc_final: 0.5890 (mtt)
REVERT: G  787 TYR cc_start: 0.9012 (m-10) cc_final: 0.8472 (m-80)
REVERT: G  803 LYS cc_start: 0.8994 (mttt) cc_final: 0.8679 (mttm)
REVERT: G  853 MET cc_start: 0.7780 (ppp) cc_final: 0.7404 (ppp)
REVERT: G  866 ASP cc_start: 0.8833 (t0) cc_final: 0.8389 (t0)
REVERT: H  762 MET cc_start: 0.8398 (mtm) cc_final: 0.8153 (mtt)
REVERT: H  771 ASP cc_start: 0.8714 (t0) cc_final: 0.7482 (p0)
REVERT: H  772 LEU cc_start: 0.9568 (mt) cc_final: 0.9080 (mp)
REVERT: H  859 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7648 (mmm-85)
REVERT: I  762 MET cc_start: 0.7168 (mtt) cc_final: 0.6668 (mtt)
REVERT: I  771 ASP cc_start: 0.8783 (t0) cc_final: 0.7410 (p0)
REVERT: I  807 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6951 (tm-30)
REVERT: I  824 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: I  856 LYS cc_start: 0.8856 (tmmt) cc_final: 0.8530 (tttm)
REVERT: J  762 MET cc_start: 0.7349 (mtt) cc_final: 0.6755 (mtt)
REVERT: J  844 SER cc_start: 0.9030 (p) cc_final: 0.8799 (p)
REVERT: J  868 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7641 (mmm-85)
REVERT: J  870 LEU cc_start: 0.9315 (tp) cc_final: 0.8919 (tt)
REVERT: K  762 MET cc_start: 0.8049 (mtm) cc_final: 0.7635 (mtt)
REVERT: K  771 ASP cc_start: 0.8916 (t0) cc_final: 0.7441 (p0)
REVERT: K  786 MET cc_start: 0.8931 (tpp) cc_final: 0.8655 (mmm)
REVERT: L  762 MET cc_start: 0.8088 (mtm) cc_final: 0.7650 (mtt)
REVERT: L  787 TYR cc_start: 0.8029 (m-80) cc_final: 0.7774 (m-80)
REVERT: L  807 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7308 (mm-30)
REVERT: L  824 GLU cc_start: 0.8763 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: M  762 MET cc_start: 0.7659 (mtm) cc_final: 0.7451 (mtt)
REVERT: M  807 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6361 (tm-30)
REVERT: N  762 MET cc_start: 0.6750 (mtt) cc_final: 0.6225 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 365
  average time/residue: 0.3601
  time to fit residues: 187.5077
Evaluate side-chains
  301 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 301
  time to evaluate  : 2.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0020
   chunk 53 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 26 optimal weight:    0.6980
   chunk 93 optimal weight:    8.9990
   chunk 96 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.1192

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

Flipped N/Q/H residues before XYZ refinement:
** C 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.075303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.069340 restraints weight = 51454.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.070982 restraints weight = 28487.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.072107 restraints weight = 17800.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.5757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13538  Z= 0.140
  Angle     :  0.784   9.046  18298  Z= 0.401
  Chirality :  0.046   0.190   1918
  Planarity :  0.006   0.065   2394
  Dihedral  :  6.291  24.472   1820
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.65 %
    Favored  : 86.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.01 (0.17), residues: 1582
  helix: -3.68 (0.30), residues: 168
  sheet: -2.90 (0.27), residues: 308
  loop : -3.66 (0.15), residues: 1106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS B 765 
 PHE   0.011   0.001   PHE I 788 
 TYR   0.022   0.001   TYR E 861 
 ARG   0.008   0.001   ARG B 859 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04163 (  280)
  hydrogen bonds       : angle       9.08369 (  714)
  covalent geometry    : bond        0.00325 (13538)
  covalent geometry    : angle       0.78417 (18298)

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

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

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3164 Ramachandran restraints generated.
    1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  402 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 402
  time to evaluate  : 1.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  866 ASP cc_start: 0.8320 (m-30) cc_final: 0.8042 (t0)
REVERT: A  868 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7637 (mmm-85)
REVERT: B  759 GLN cc_start: 0.8614 (pm20) cc_final: 0.8355 (pm20)
REVERT: B  762 MET cc_start: 0.7906 (mpp) cc_final: 0.7487 (mpp)
REVERT: B  780 ASN cc_start: 0.7830 (p0) cc_final: 0.7571 (p0)
REVERT: B  787 TYR cc_start: 0.8813 (m-10) cc_final: 0.8517 (m-10)
REVERT: B  803 LYS cc_start: 0.8820 (mttt) cc_final: 0.8576 (mmtp)
REVERT: B  824 GLU cc_start: 0.8874 (tp30) cc_final: 0.8462 (tm-30)
REVERT: B  825 MET cc_start: 0.7779 (mmt) cc_final: 0.7115 (mmt)
REVERT: B  858 LEU cc_start: 0.8973 (tp) cc_final: 0.8763 (tp)
REVERT: B  870 LEU cc_start: 0.9601 (tt) cc_final: 0.9266 (tp)
REVERT: C  759 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7994 (tm-30)
REVERT: C  762 MET cc_start: 0.7021 (mtt) cc_final: 0.5926 (mtt)
REVERT: C  825 MET cc_start: 0.8522 (tpt) cc_final: 0.8066 (tpt)
REVERT: C  829 LEU cc_start: 0.9444 (mt) cc_final: 0.9120 (mt)
REVERT: C  866 ASP cc_start: 0.8555 (t0) cc_final: 0.8082 (t0)
REVERT: C  868 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.6574 (mmm-85)
REVERT: D  762 MET cc_start: 0.7803 (mtm) cc_final: 0.7504 (mtt)
REVERT: D  780 ASN cc_start: 0.8277 (p0) cc_final: 0.7912 (p0)
REVERT: D  786 MET cc_start: 0.8179 (tpp) cc_final: 0.7795 (tpt)
REVERT: D  787 TYR cc_start: 0.8832 (m-80) cc_final: 0.8601 (m-80)
REVERT: D  868 ARG cc_start: 0.7794 (mmt90) cc_final: 0.7353 (mmm-85)
REVERT: E  762 MET cc_start: 0.7030 (mtt) cc_final: 0.6550 (mtt)
REVERT: E  800 TYR cc_start: 0.7603 (t80) cc_final: 0.7395 (t80)
REVERT: E  866 ASP cc_start: 0.8414 (m-30) cc_final: 0.8154 (t0)
REVERT: F  868 ARG cc_start: 0.7706 (mmt90) cc_final: 0.7450 (mmm-85)
REVERT: F  870 LEU cc_start: 0.9468 (tp) cc_final: 0.9124 (tt)
REVERT: G  759 GLN cc_start: 0.8644 (pp30) cc_final: 0.8319 (tm-30)
REVERT: G  762 MET cc_start: 0.6502 (mtt) cc_final: 0.5622 (mtt)
REVERT: G  787 TYR cc_start: 0.8864 (m-10) cc_final: 0.8543 (m-80)
REVERT: G  803 LYS cc_start: 0.8990 (mttt) cc_final: 0.8618 (mmtp)
REVERT: G  853 MET cc_start: 0.7210 (ppp) cc_final: 0.6994 (ppp)
REVERT: G  866 ASP cc_start: 0.8835 (t0) cc_final: 0.8497 (t0)
REVERT: H  762 MET cc_start: 0.8255 (mtm) cc_final: 0.8033 (mtt)
REVERT: H  771 ASP cc_start: 0.8562 (t0) cc_final: 0.7537 (p0)
REVERT: H  772 LEU cc_start: 0.9500 (mt) cc_final: 0.9129 (mp)
REVERT: H  856 LYS cc_start: 0.8452 (ttpp) cc_final: 0.8180 (tmtt)
REVERT: I  762 MET cc_start: 0.6765 (mtt) cc_final: 0.6166 (mtt)
REVERT: I  771 ASP cc_start: 0.8653 (t0) cc_final: 0.7395 (p0)
REVERT: I  807 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7004 (tm-30)
REVERT: I  824 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: I  868 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7906 (mmm-85)
REVERT: J  762 MET cc_start: 0.7050 (mtt) cc_final: 0.6424 (mtt)
REVERT: J  783 ILE cc_start: 0.9606 (tt) cc_final: 0.9260 (mp)
REVERT: J  807 GLU cc_start: 0.7799 (mt-10) cc_final: 0.6703 (tm-30)
REVERT: J  870 LEU cc_start: 0.9235 (tp) cc_final: 0.8706 (tt)
REVERT: K  762 MET cc_start: 0.8004 (mtm) cc_final: 0.7661 (mtt)
REVERT: K  771 ASP cc_start: 0.8907 (t0) cc_final: 0.7647 (p0)
REVERT: K  842 LEU cc_start: 0.9297 (mm) cc_final: 0.9045 (mm)
REVERT: L  762 MET cc_start: 0.7936 (mtm) cc_final: 0.7427 (mtt)
REVERT: L  807 GLU cc_start: 0.7817 (mt-10) cc_final: 0.6968 (tm-30)
REVERT: L  824 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8406 (tm-30)
REVERT: L  844 SER cc_start: 0.9081 (p) cc_final: 0.8815 (p)
REVERT: M  759 GLN cc_start: 0.7945 (pp30) cc_final: 0.7544 (pp30)
REVERT: M  762 MET cc_start: 0.7833 (mtm) cc_final: 0.7375 (mtt)
REVERT: M  807 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6507 (tm-30)
REVERT: N  762 MET cc_start: 0.6333 (mtt) cc_final: 0.5699 (mtt)
REVERT: N  824 GLU cc_start: 0.8626 (tm-30) cc_final: 0.7680 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 402
  average time/residue: 0.2541
  time to fit residues: 146.3398
Evaluate side-chains
  328 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 328
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 75 optimal weight:    0.7980
   chunk 135 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 153 optimal weight:    8.9990
   chunk 143 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 132 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
** H 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.069498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.063902 restraints weight = 54064.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.065448 restraints weight = 29962.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.066513 restraints weight = 18645.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.5795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055  13538  Z= 0.295
  Angle     :  0.905   9.115  18298  Z= 0.472
  Chirality :  0.048   0.168   1918
  Planarity :  0.007   0.068   2394
  Dihedral  :  6.749  22.170   1820
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.18 %
    Favored  : 78.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.13 (0.17), residues: 1582
  helix: -3.57 (0.31), residues: 168
  sheet: -2.91 (0.27), residues: 308
  loop : -3.82 (0.15), residues: 1106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS E 765 
 PHE   0.023   0.003   PHE J 774 
 TYR   0.039   0.002   TYR B 861 
 ARG   0.011   0.001   ARG M 868 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05891 (  280)
  hydrogen bonds       : angle       9.27972 (  714)
  covalent geometry    : bond        0.00662 (13538)
  covalent geometry    : angle       0.90527 (18298)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4562.30 seconds
wall clock time: 83 minutes 39.19 seconds (5019.19 seconds total)