Starting phenix.real_space_refine
on Thu Sep 18 00:15:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mu4_48619/09_2025/9mu4_48619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mu4_48619/09_2025/9mu4_48619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mu4_48619/09_2025/9mu4_48619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mu4_48619/09_2025/9mu4_48619.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mu4_48619/09_2025/9mu4_48619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mu4_48619/09_2025/9mu4_48619.map"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.039
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: 5
    Type Number    sf(0)   Gaussians
     P     328      5.49       5
     S      14      5.16       5
     C    7024      2.51       5
     N    2384      2.21       5
     O    3044      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12794
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "c"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 812
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "g"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 812
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "d"
      Number of atoms: 753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 753
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "h"
      Number of atoms: 753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 753
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "a"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 817
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "e"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 817
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "b"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "f"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "T"
      Number of atoms: 3344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 3344
          Classifications: {'DNA': 164}
          Link IDs: {'rna3p': 163}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 3380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 3380
          Classifications: {'DNA': 164}
          Link IDs: {'rna3p': 163}
  Time building chain proxies: 3.30, per 1000 atoms: 0.26
  Number of scatterers: 12794
  At special positions: 0
  Unit cell: (118.841, 80.766, 159.224, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     328     15.00
     O    3044      8.00
     N    2384      7.00
     C    7024      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: 1.19
  Conformation dependent library (CDL) restraints added in 438.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      70.8% alpha, 3.1% beta
      163 base pairs and 298 stacking pairs defined.
    Time for finding SS restraints: 2.37
  Creating SS restraints...
    Processing helix  chain 'c' and resid 16 through 22
    Processing helix  chain 'c' and resid 26 through 36
      removed outlier: 3.620A  pdb=" N   ILE c  30 " --> pdb=" O   PRO c  26 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 45 through 73
      removed outlier: 4.525A  pdb=" N   VAL c  49 " --> pdb=" O   ALA c  45 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 79 through 90
      removed outlier: 3.575A  pdb=" N   ASP c  90 " --> pdb=" O   ALA c  86 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 91 through 97
    Processing helix  chain 'g' and resid 16 through 21
    Processing helix  chain 'g' and resid 26 through 36
      removed outlier: 3.797A  pdb=" N   ILE g  30 " --> pdb=" O   PRO g  26 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 45 through 73
      removed outlier: 4.412A  pdb=" N   VAL g  49 " --> pdb=" O   ALA g  45 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 79 through 90
      removed outlier: 3.576A  pdb=" N   LEU g  83 " --> pdb=" O   ILE g  79 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASP g  90 " --> pdb=" O   ALA g  86 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 91 through 97
    Processing helix  chain 'd' and resid 35 through 47
    Processing helix  chain 'd' and resid 53 through 82
      removed outlier: 3.668A  pdb=" N   ASN d  82 " --> pdb=" O   LEU d  78 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 88 through 100
      removed outlier: 3.746A  pdb=" N   ILE d  92 " --> pdb=" O   THR d  88 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 102 through 122
      removed outlier: 3.803A  pdb=" N   LYS d 106 " --> pdb=" O   GLY d 102 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 35 through 47
    Processing helix  chain 'h' and resid 53 through 82
      removed outlier: 3.566A  pdb=" N   ASN h  82 " --> pdb=" O   LEU h  78 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 88 through 100
      removed outlier: 3.598A  pdb=" N   ILE h  92 " --> pdb=" O   THR h  88 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 102 through 123
      removed outlier: 3.906A  pdb=" N   LYS h 106 " --> pdb=" O   GLY h 102 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 45 through 56
    Processing helix  chain 'a' and resid 64 through 80
      removed outlier: 3.545A  pdb=" N   PHE a  68 " --> pdb=" O   ARG a  64 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ASP a  78 " --> pdb=" O   GLU a  74 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE a  79 " --> pdb=" O   ILE a  75 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 86 through 115
    Processing helix  chain 'a' and resid 121 through 132
      removed outlier: 3.507A  pdb=" N   ILE a 125 " --> pdb=" O   MET a 121 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 45 through 56
    Processing helix  chain 'e' and resid 64 through 80
      removed outlier: 3.526A  pdb=" N   PHE e  68 " --> pdb=" O   ARG e  64 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ASP e  78 " --> pdb=" O   GLU e  74 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   PHE e  79 " --> pdb=" O   ILE e  75 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LYS e  80 " --> pdb=" O   ALA e  76 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 86 through 115
    Processing helix  chain 'e' and resid 121 through 132
      removed outlier: 3.686A  pdb=" N   ILE e 125 " --> pdb=" O   MET e 121 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 26 through 30
    Processing helix  chain 'b' and resid 31 through 43
    Processing helix  chain 'b' and resid 50 through 77
      removed outlier: 3.966A  pdb=" N   GLU b  54 " --> pdb=" O   LEU b  50 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG b  68 " --> pdb=" O   GLU b  64 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA b  77 " --> pdb=" O   TYR b  73 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 83 through 94
      removed outlier: 3.713A  pdb=" N   VAL b  87 " --> pdb=" O   THR b  83 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 25 through 30
      removed outlier: 4.004A  pdb=" N   GLN f  28 " --> pdb=" O   ASP f  25 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 31 through 43
    Processing helix  chain 'f' and resid 50 through 77
      removed outlier: 3.915A  pdb=" N   GLU f  54 " --> pdb=" O   LEU f  50 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG f  68 " --> pdb=" O   GLU f  64 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 83 through 94
      removed outlier: 3.604A  pdb=" N   VAL f  87 " --> pdb=" O   THR f  83 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN f  94 " --> pdb=" O   ALA f  90 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'c' and resid 42 through 43
      removed outlier: 7.333A  pdb=" N   ARG c  42 " --> pdb=" O   ILE d  87 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'c' and resid 77 through 78
    Processing sheet with id=AA3, first strand: chain 'c' and resid 100 through 102
    Processing sheet with id=AA4, first strand: chain 'g' and resid 42 through 43
      removed outlier: 7.549A  pdb=" N   ARG g  42 " --> pdb=" O   ILE h  87 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'g' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'g' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'a' and resid 84 through 85
      removed outlier: 7.153A  pdb=" N   ARG a  84 " --> pdb=" O   VAL b  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'a' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'e' and resid 84 through 85
      removed outlier: 6.973A  pdb=" N   ARG e  84 " --> pdb=" O   VAL f  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'e' and resid 119 through 120

    388 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      406 hydrogen bonds
      812 hydrogen bond angles
      0 basepair planarities
      163 basepair parallelities
      298 stacking parallelities
  Total time for adding SS restraints: 2.83

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2495
        1.33 -     1.46: 4769
        1.46 -     1.58: 5748
        1.58 -     1.70: 652
        1.70 -     1.82: 26
  Bond restraints: 13690
  Sorted by residual:
  bond pdb=" C3'  DT N -17 "
       pdb=" O3'  DT N -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.499 -0.077 3.00e-02 1.11e+03 6.55e+00
  bond pdb=" C3'  DA N  75 "
       pdb=" O3'  DA N  75 "
    ideal  model  delta    sigma   weight residual
    1.422  1.493 -0.071 3.00e-02 1.11e+03 5.61e+00
  bond pdb=" C3'  DC T   4 "
       pdb=" O3'  DC T   4 "
    ideal  model  delta    sigma   weight residual
    1.422  1.484 -0.062 3.00e-02 1.11e+03 4.27e+00
  bond pdb=" C3'  DT T  43 "
       pdb=" O3'  DT T  43 "
    ideal  model  delta    sigma   weight residual
    1.422  1.481 -0.059 3.00e-02 1.11e+03 3.90e+00
  bond pdb=" C3'  DG T -30 "
       pdb=" O3'  DG T -30 "
    ideal  model  delta    sigma   weight residual
    1.422  1.479 -0.057 3.00e-02 1.11e+03 3.67e+00
  ... (remaining 13685 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 19471
        2.34 -     4.67: 387
        4.67 -     7.01: 31
        7.01 -     9.35: 7
        9.35 -    11.68: 4
  Bond angle restraints: 19900
  Sorted by residual:
  angle pdb=" C   GLY c  37 "
        pdb=" N   ASN c  38 "
        pdb=" CA  ASN c  38 "
      ideal   model   delta    sigma   weight residual
     121.54  131.40   -9.86 1.91e+00 2.74e-01 2.67e+01
  angle pdb=" C   GLY g  37 "
        pdb=" N   ASN g  38 "
        pdb=" CA  ASN g  38 "
      ideal   model   delta    sigma   weight residual
     122.46  129.39   -6.93 1.41e+00 5.03e-01 2.41e+01
  angle pdb=" CB  MET b  85 "
        pdb=" CG  MET b  85 "
        pdb=" SD  MET b  85 "
      ideal   model   delta    sigma   weight residual
     112.70  124.38  -11.68 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" CA  GLU f  75 "
        pdb=" CB  GLU f  75 "
        pdb=" CG  GLU f  75 "
      ideal   model   delta    sigma   weight residual
     114.10  121.88   -7.78 2.00e+00 2.50e-01 1.51e+01
  angle pdb=" C3'  DA N  75 "
        pdb=" O3'  DA N  75 "
        pdb=" P    DT N  76 "
      ideal   model   delta    sigma   weight residual
     120.20  125.67   -5.47 1.50e+00 4.44e-01 1.33e+01
  ... (remaining 19895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.50: 5730
       34.50 -    69.00: 1666
       69.00 -   103.51: 22
      103.51 -   138.01: 8
      138.01 -   172.51: 2
  Dihedral angle restraints: 7428
    sinusoidal: 5192
      harmonic: 2236
  Sorted by residual:
  dihedral pdb=" CA  ILE b  30 "
           pdb=" C   ILE b  30 "
           pdb=" N   THR b  31 "
           pdb=" CA  THR b  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.82  -24.18     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" C4'  DA N  75 "
           pdb=" C3'  DA N  75 "
           pdb=" O3'  DA N  75 "
           pdb=" P    DT N  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.49  172.51     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT N -17 "
           pdb=" C3'  DT N -17 "
           pdb=" O3'  DT N -17 "
           pdb=" P    DT N -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   50.33  169.67     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 7425 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 2085
       0.081 -    0.162: 168
       0.162 -    0.243: 8
       0.243 -    0.324: 2
       0.324 -    0.405: 1
  Chirality restraints: 2264
  Sorted by residual:
  chirality pdb=" CG  LEU g  63 "
            pdb=" CB  LEU g  63 "
            pdb=" CD1 LEU g  63 "
            pdb=" CD2 LEU g  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.18   -0.41 2.00e-01 2.50e+01 4.10e+00
  chirality pdb=" CB  ILE h  52 "
            pdb=" CA  ILE h  52 "
            pdb=" CG1 ILE h  52 "
            pdb=" CG2 ILE h  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CB  ILE d  52 "
            pdb=" CA  ILE d  52 "
            pdb=" CG1 ILE d  52 "
            pdb=" CG2 ILE d  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.69e+00
  ... (remaining 2261 not shown)

  Planarity restraints: 1388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE g  79 "    0.048 5.00e-02 4.00e+02   7.22e-02 8.33e+00
        pdb=" N   PRO g  80 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO g  80 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO g  80 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET e 121 "   -0.041 5.00e-02 4.00e+02   6.16e-02 6.07e+00
        pdb=" N   PRO e 122 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO e 122 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO e 122 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR d 119 "   -0.010 2.00e-02 2.50e+03   1.61e-02 5.16e+00
        pdb=" CG  TYR d 119 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR d 119 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR d 119 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR d 119 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR d 119 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR d 119 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR d 119 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1385 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2891
        2.82 -     3.34: 10658
        3.34 -     3.86: 25488
        3.86 -     4.38: 29416
        4.38 -     4.90: 40972
  Nonbonded interactions: 109425
  Sorted by model distance:
  nonbonded pdb=" O   TYR g  39 "
            pdb=" OG  SER h  76 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   TYR c  39 "
            pdb=" OG  SER d  76 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" NH1 ARG c  32 "
            pdb=" OP1  DA T -44 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" NH2 ARG c  71 "
            pdb=" OG1 THR d  50 "
     model   vdw
     2.360 3.120
  nonbonded pdb=" NE2 GLN g  24 "
            pdb=" OE1 GLN h  45 "
     model   vdw
     2.378 3.120
  ... (remaining 109420 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'a'
  selection = chain 'e'
}
ncs_group {
  reference = chain 'b'
  selection = chain 'f'
}
ncs_group {
  reference = chain 'c'
  selection = chain 'g'
}
ncs_group {
  reference = chain 'd'
  selection = chain 'h'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.350
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.150
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
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      :  0.006   0.077  13690  Z= 0.263
  Angle     :  0.838  11.683  19900  Z= 0.481
  Chirality :  0.047   0.405   2264
  Planarity :  0.007   0.072   1388
  Dihedral  : 28.803 172.510   5984
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.86 (0.25), residues: 754
  helix: -0.72 (0.18), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.25 (0.36), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG d  77 
 TYR   0.039   0.003   TYR d 119 
 PHE   0.019   0.002   PHE c  25 
 HIS   0.006   0.001   HIS c  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 (13690)
  covalent geometry    : angle       0.83771 (19900)
  hydrogen bonds       : bond        0.09654 (  794)
  hydrogen bonds       : angle       3.89937 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.333 
Fit side-chains
REVERT: g   90 ASP cc_start: 0.8303 (t0) cc_final: 0.8009 (t0)
REVERT: g   92 GLU cc_start: 0.8709 (mp0) cc_final: 0.8430 (mp0)
REVERT: g  100 VAL cc_start: 0.9141 (t) cc_final: 0.8491 (t)
REVERT: d   32 LYS cc_start: 0.8972 (tppt) cc_final: 0.8684 (mmmm)
REVERT: d   74 GLU cc_start: 0.9133 (tp30) cc_final: 0.8933 (tp30)
REVERT: h   81 TYR cc_start: 0.8667 (m-10) cc_final: 0.8439 (m-10)
REVERT: h   83 LYS cc_start: 0.9350 (mptt) cc_final: 0.9078 (mttp)
REVERT: h  103 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7898 (mm-30)
REVERT: a   60 GLU cc_start: 0.8588 (pm20) cc_final: 0.8353 (pm20)
REVERT: a   74 GLU cc_start: 0.8485 (tt0) cc_final: 0.8213 (tt0)
REVERT: a   82 ASP cc_start: 0.8563 (t0) cc_final: 0.8225 (t0)
REVERT: a   91 MET cc_start: 0.8948 (mpp) cc_final: 0.8577 (mmm)
REVERT: a   94 GLN cc_start: 0.8962 (tt0) cc_final: 0.8668 (tt0)
REVERT: a  108 THR cc_start: 0.9347 (m) cc_final: 0.9136 (t)
REVERT: b   26 ASN cc_start: 0.9113 (m110) cc_final: 0.8815 (m110)
REVERT: b   68 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8241 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1608
  time to fit residues: 37.7883
Evaluate side-chains
  145 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0370
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
** c  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  76 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 = 0.3949 r_free = 0.3949 target = 0.095986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.067054 restraints weight = 39990.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.89
r_work: 0.3140 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13690  Z= 0.169
  Angle     :  0.578   5.659  19900  Z= 0.351
  Chirality :  0.033   0.157   2264
  Planarity :  0.004   0.051   1388
  Dihedral  : 31.435 171.770   4484
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.12 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.29), residues: 754
  helix:  1.29 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.88 (0.38), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c  35 
 TYR   0.025   0.001   TYR b  99 
 PHE   0.004   0.001   PHE b 101 
 HIS   0.003   0.001   HIS b  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (13690)
  covalent geometry    : angle       0.57813 (19900)
  hydrogen bonds       : bond        0.03693 (  794)
  hydrogen bonds       : angle       2.68145 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 164
  time to evaluate  : 0.331 
Fit side-chains
REVERT: c   72 ASP cc_start: 0.8603 (t0) cc_final: 0.8008 (m-30)
REVERT: d   32 LYS cc_start: 0.8751 (tppt) cc_final: 0.8446 (mmmm)
REVERT: h   49 ASP cc_start: 0.8545 (m-30) cc_final: 0.8132 (t0)
REVERT: h   81 TYR cc_start: 0.8660 (m-10) cc_final: 0.8309 (m-10)
REVERT: h   83 LYS cc_start: 0.9278 (mptt) cc_final: 0.9021 (mttp)
REVERT: a   57 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8686 (ttmt)
REVERT: a   60 GLU cc_start: 0.8695 (pm20) cc_final: 0.8479 (pm20)
REVERT: a   74 GLU cc_start: 0.8369 (tt0) cc_final: 0.8036 (tt0)
REVERT: a   82 ASP cc_start: 0.8544 (t0) cc_final: 0.8238 (t0)
REVERT: a   91 MET cc_start: 0.8737 (mpp) cc_final: 0.8426 (mmm)
REVERT: e   91 MET cc_start: 0.8817 (mmt) cc_final: 0.8602 (mmt)
REVERT: b   26 ASN cc_start: 0.8964 (m110) cc_final: 0.8701 (m-40)
  outliers start: 9
  outliers final: 3
  residues processed: 164
  average time/residue: 0.1535
  time to fit residues: 34.0734
Evaluate side-chains
  147 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   45 GLN
Chi-restraints excluded: chain h residue   67 ILE
Chi-restraints excluded: chain f residue   50 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 86 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
** c  24 GLN ** 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 = 0.3927 r_free = 0.3927 target = 0.095032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.065922 restraints weight = 40312.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.88
r_work: 0.3109 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13690  Z= 0.204
  Angle     :  0.587   5.505  19900  Z= 0.353
  Chirality :  0.034   0.147   2264
  Planarity :  0.004   0.046   1388
  Dihedral  : 31.604 173.682   4484
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 10.99 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.30), residues: 754
  helix:  1.97 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.64 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG f  93 
 TYR   0.019   0.002   TYR b  89 
 PHE   0.007   0.001   PHE g  25 
 HIS   0.003   0.001   HIS g  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (13690)
  covalent geometry    : angle       0.58669 (19900)
  hydrogen bonds       : bond        0.03772 (  794)
  hydrogen bonds       : angle       2.60717 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.333 
Fit side-chains
REVERT: c   72 ASP cc_start: 0.8626 (t0) cc_final: 0.7991 (m-30)
REVERT: d   32 LYS cc_start: 0.8768 (tppt) cc_final: 0.8463 (mmmm)
REVERT: h   49 ASP cc_start: 0.8639 (m-30) cc_final: 0.8221 (t0)
REVERT: h   81 TYR cc_start: 0.8771 (m-10) cc_final: 0.8393 (m-10)
REVERT: h   83 LYS cc_start: 0.9258 (mptt) cc_final: 0.8989 (mttp)
REVERT: a   57 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8809 (ttmt)
REVERT: a   60 GLU cc_start: 0.8692 (pm20) cc_final: 0.8422 (pm20)
REVERT: a   74 GLU cc_start: 0.8407 (tt0) cc_final: 0.8080 (tt0)
REVERT: a   82 ASP cc_start: 0.8551 (t0) cc_final: 0.8256 (t0)
REVERT: a   88 SER cc_start: 0.9070 (p) cc_final: 0.8754 (t)
REVERT: e   91 MET cc_start: 0.8784 (mmt) cc_final: 0.8525 (mmt)
REVERT: b   26 ASN cc_start: 0.9002 (m110) cc_final: 0.8555 (m110)
REVERT: b   89 TYR cc_start: 0.8433 (m-10) cc_final: 0.7879 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 155
  average time/residue: 0.1567
  time to fit residues: 32.7964
Evaluate side-chains
  148 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain d residue   69 GLU
Chi-restraints excluded: chain h residue   45 GLN
Chi-restraints excluded: chain h residue   67 ILE
Chi-restraints excluded: chain a residue   87 SER
Chi-restraints excluded: chain e residue   61 LEU
Chi-restraints excluded: chain b residue   31 THR
Chi-restraints excluded: chain b residue   51 ILE
Chi-restraints excluded: chain f residue   50 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 9 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0980
   chunk 93 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.5582

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

Flipped N/Q/H residues before XYZ refinement:
c  24 GLN
d  82 ASN
a  94 GLN
** f  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.096019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.067040 restraints weight = 40334.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.86
r_work: 0.3134 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13690  Z= 0.166
  Angle     :  0.562   5.512  19900  Z= 0.341
  Chirality :  0.033   0.140   2264
  Planarity :  0.004   0.042   1388
  Dihedral  : 31.445 173.877   4484
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.62 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.31), residues: 754
  helix:  2.35 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.40 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG c  35 
 TYR   0.032   0.001   TYR d  81 
 PHE   0.005   0.001   PHE g  25 
 HIS   0.002   0.001   HIS g  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (13690)
  covalent geometry    : angle       0.56183 (19900)
  hydrogen bonds       : bond        0.03432 (  794)
  hydrogen bonds       : angle       2.47318 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.240 
Fit side-chains
REVERT: c   72 ASP cc_start: 0.8627 (t0) cc_final: 0.8033 (m-30)
REVERT: g  110 ASN cc_start: 0.9115 (t0) cc_final: 0.8858 (p0)
REVERT: d   32 LYS cc_start: 0.8746 (tppt) cc_final: 0.8445 (mmmm)
REVERT: h   49 ASP cc_start: 0.8634 (m-30) cc_final: 0.8229 (t0)
REVERT: h   81 TYR cc_start: 0.8792 (m-10) cc_final: 0.8504 (m-10)
REVERT: h   83 LYS cc_start: 0.9255 (mptt) cc_final: 0.8979 (mttp)
REVERT: a   57 LYS cc_start: 0.8992 (ttmm) cc_final: 0.8673 (ttmt)
REVERT: a   60 GLU cc_start: 0.8694 (pm20) cc_final: 0.8445 (pm20)
REVERT: a   82 ASP cc_start: 0.8542 (t0) cc_final: 0.8251 (t0)
REVERT: a   88 SER cc_start: 0.9032 (p) cc_final: 0.8703 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 160
  average time/residue: 0.1563
  time to fit residues: 33.7540
Evaluate side-chains
  152 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain d residue   69 GLU
Chi-restraints excluded: chain h residue   67 ILE
Chi-restraints excluded: chain a residue   87 SER
Chi-restraints excluded: chain e residue   61 LEU
Chi-restraints excluded: chain e residue  113 ILE
Chi-restraints excluded: chain b residue   31 THR
Chi-restraints excluded: chain b residue   51 ILE
Chi-restraints excluded: chain b residue   97 THR
Chi-restraints excluded: chain f residue   50 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 6 optimal weight:    0.2980
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** f  76 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 = 0.3938 r_free = 0.3938 target = 0.095572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.066485 restraints weight = 40160.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.87
r_work: 0.3121 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13690  Z= 0.189
  Angle     :  0.573   5.726  19900  Z= 0.346
  Chirality :  0.034   0.142   2264
  Planarity :  0.004   0.041   1388
  Dihedral  : 31.517 174.683   4484
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.54 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.31), residues: 754
  helix:  2.41 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.37 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG a 130 
 TYR   0.031   0.002   TYR b  89 
 PHE   0.007   0.001   PHE c  25 
 HIS   0.003   0.001   HIS b  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (13690)
  covalent geometry    : angle       0.57346 (19900)
  hydrogen bonds       : bond        0.03623 (  794)
  hydrogen bonds       : angle       2.50990 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: c   72 ASP cc_start: 0.8634 (t0) cc_final: 0.8083 (m-30)
REVERT: g  110 ASN cc_start: 0.9122 (t0) cc_final: 0.8839 (p0)
REVERT: d   32 LYS cc_start: 0.8751 (tppt) cc_final: 0.8460 (mmmm)
REVERT: d  106 LYS cc_start: 0.8473 (pttp) cc_final: 0.8251 (pttm)
REVERT: h   49 ASP cc_start: 0.8672 (m-30) cc_final: 0.8269 (t0)
REVERT: h   81 TYR cc_start: 0.8845 (m-10) cc_final: 0.8546 (m-10)
REVERT: h   83 LYS cc_start: 0.9242 (mptt) cc_final: 0.8956 (mttp)
REVERT: a   57 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8766 (ttmt)
REVERT: a   60 GLU cc_start: 0.8697 (pm20) cc_final: 0.8408 (pm20)
REVERT: a   82 ASP cc_start: 0.8588 (t0) cc_final: 0.8278 (t0)
REVERT: a   88 SER cc_start: 0.9051 (p) cc_final: 0.8725 (t)
REVERT: e   91 MET cc_start: 0.8769 (mmt) cc_final: 0.8510 (mmt)
  outliers start: 16
  outliers final: 12
  residues processed: 155
  average time/residue: 0.1485
  time to fit residues: 31.2354
Evaluate side-chains
  154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue   63 LEU
Chi-restraints excluded: chain g residue  100 VAL
Chi-restraints excluded: chain d residue   69 GLU
Chi-restraints excluded: chain h residue   45 GLN
Chi-restraints excluded: chain h residue   67 ILE
Chi-restraints excluded: chain a residue   87 SER
Chi-restraints excluded: chain e residue   61 LEU
Chi-restraints excluded: chain e residue  113 ILE
Chi-restraints excluded: chain b residue   31 THR
Chi-restraints excluded: chain b residue   51 ILE
Chi-restraints excluded: chain b residue   97 THR
Chi-restraints excluded: chain f residue   50 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.5188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.093049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.063621 restraints weight = 39669.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.85
r_work: 0.3059 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  13690  Z= 0.283
  Angle     :  0.643   8.526  19900  Z= 0.378
  Chirality :  0.038   0.156   2264
  Planarity :  0.005   0.042   1388
  Dihedral  : 32.128 179.500   4484
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.38 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.31), residues: 754
  helix:  2.24 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.47 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG f  93 
 TYR   0.025   0.002   TYR d  81 
 PHE   0.015   0.001   PHE c  25 
 HIS   0.003   0.001   HIS c  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00640 (13690)
  covalent geometry    : angle       0.64303 (19900)
  hydrogen bonds       : bond        0.04459 (  794)
  hydrogen bonds       : angle       2.74991 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: c   61 GLU cc_start: 0.8077 (tp30) cc_final: 0.7608 (tp30)
REVERT: c   72 ASP cc_start: 0.8616 (t0) cc_final: 0.8217 (m-30)
REVERT: d   32 LYS cc_start: 0.8791 (tppt) cc_final: 0.8489 (mmmm)
REVERT: d   66 ASP cc_start: 0.8674 (t70) cc_final: 0.8371 (t0)
REVERT: h   38 TYR cc_start: 0.8975 (m-80) cc_final: 0.8657 (m-80)
REVERT: h   49 ASP cc_start: 0.8584 (m-30) cc_final: 0.8274 (t0)
REVERT: h   81 TYR cc_start: 0.8894 (m-10) cc_final: 0.8579 (m-10)
REVERT: h   83 LYS cc_start: 0.9260 (mptt) cc_final: 0.8991 (mttp)
REVERT: a   57 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8814 (ttmt)
REVERT: a   82 ASP cc_start: 0.8575 (t0) cc_final: 0.8287 (t0)
REVERT: a   88 SER cc_start: 0.9110 (p) cc_final: 0.8851 (t)
REVERT: e   91 MET cc_start: 0.8825 (mmt) cc_final: 0.8584 (mmt)
REVERT: b   89 TYR cc_start: 0.8331 (m-10) cc_final: 0.8123 (m-80)
  outliers start: 16
  outliers final: 11
  residues processed: 157
  average time/residue: 0.1444
  time to fit residues: 31.1596
Evaluate side-chains
  156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue   63 LEU
Chi-restraints excluded: chain d residue   45 GLN
Chi-restraints excluded: chain d residue   69 GLU
Chi-restraints excluded: chain h residue   45 GLN
Chi-restraints excluded: chain h residue   67 ILE
Chi-restraints excluded: chain a residue   87 SER
Chi-restraints excluded: chain e residue   61 LEU
Chi-restraints excluded: chain e residue  113 ILE
Chi-restraints excluded: chain b residue   31 THR
Chi-restraints excluded: chain b residue   97 THR
Chi-restraints excluded: chain f residue   50 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 53 optimal weight:    0.0570
   chunk 90 optimal weight:   10.0000
   chunk 99 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
a  94 GLN
** f  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.095709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.066752 restraints weight = 40025.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.93
r_work: 0.3120 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13690  Z= 0.164
  Angle     :  0.579   8.421  19900  Z= 0.348
  Chirality :  0.033   0.194   2264
  Planarity :  0.004   0.041   1388
  Dihedral  : 31.491 179.595   4484
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.17 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.31), residues: 754
  helix:  2.57 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.32 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG c  35 
 TYR   0.021   0.001   TYR d  81 
 PHE   0.007   0.001   PHE c  25 
 HIS   0.002   0.001   HIS f  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (13690)
  covalent geometry    : angle       0.57871 (19900)
  hydrogen bonds       : bond        0.03448 (  794)
  hydrogen bonds       : angle       2.47479 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: c   72 ASP cc_start: 0.8643 (t0) cc_final: 0.8248 (m-30)
REVERT: g  110 ASN cc_start: 0.9128 (t0) cc_final: 0.8888 (p0)
REVERT: d   32 LYS cc_start: 0.8766 (tppt) cc_final: 0.8449 (mmmm)
REVERT: h   49 ASP cc_start: 0.8572 (m-30) cc_final: 0.8341 (t0)
REVERT: h   81 TYR cc_start: 0.8846 (m-10) cc_final: 0.8542 (m-10)
REVERT: h   83 LYS cc_start: 0.9285 (mptt) cc_final: 0.9017 (mttp)
REVERT: a   57 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8723 (ttmt)
REVERT: a   60 GLU cc_start: 0.8610 (pm20) cc_final: 0.8316 (pm20)
REVERT: a   82 ASP cc_start: 0.8529 (t0) cc_final: 0.8232 (t0)
REVERT: a   88 SER cc_start: 0.8993 (p) cc_final: 0.8664 (t)
REVERT: a   91 MET cc_start: 0.8929 (mpp) cc_final: 0.8673 (mmp)
REVERT: e   51 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8429 (mt-10)
REVERT: f   85 MET cc_start: 0.8989 (mmm) cc_final: 0.8454 (mmm)
  outliers start: 14
  outliers final: 12
  residues processed: 159
  average time/residue: 0.1506
  time to fit residues: 32.4206
Evaluate side-chains
  156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain g residue   63 LEU
Chi-restraints excluded: chain d residue   45 GLN
Chi-restraints excluded: chain d residue   69 GLU
Chi-restraints excluded: chain h residue   45 GLN
Chi-restraints excluded: chain h residue   67 ILE
Chi-restraints excluded: chain a residue   87 SER
Chi-restraints excluded: chain e residue   61 LEU
Chi-restraints excluded: chain e residue  113 ILE
Chi-restraints excluded: chain b residue   31 THR
Chi-restraints excluded: chain b residue   97 THR
Chi-restraints excluded: chain f residue   50 LEU
Chi-restraints excluded: chain f residue   51 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   chunk 64 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** f  76 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 = 0.3937 r_free = 0.3937 target = 0.095291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.066356 restraints weight = 39243.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.89
r_work: 0.3114 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13690  Z= 0.187
  Angle     :  0.594   9.363  19900  Z= 0.354
  Chirality :  0.034   0.179   2264
  Planarity :  0.004   0.040   1388
  Dihedral  : 31.533 179.379   4484
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.13 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.31), residues: 754
  helix:  2.53 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.34 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG c  35 
 TYR   0.042   0.002   TYR d  81 
 PHE   0.008   0.001   PHE c  25 
 HIS   0.003   0.001   HIS d  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (13690)
  covalent geometry    : angle       0.59388 (19900)
  hydrogen bonds       : bond        0.03564 (  794)
  hydrogen bonds       : angle       2.50175 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: c   64 GLU cc_start: 0.8461 (tp30) cc_final: 0.8217 (tp30)
REVERT: c   72 ASP cc_start: 0.8667 (t0) cc_final: 0.8253 (m-30)
REVERT: g  110 ASN cc_start: 0.9135 (t0) cc_final: 0.8877 (p0)
REVERT: d   32 LYS cc_start: 0.8757 (tppt) cc_final: 0.8446 (mmmm)
REVERT: h   49 ASP cc_start: 0.8600 (m-30) cc_final: 0.8351 (t0)
REVERT: h   81 TYR cc_start: 0.8852 (m-10) cc_final: 0.8558 (m-10)
REVERT: h   83 LYS cc_start: 0.9249 (mptt) cc_final: 0.8982 (mttp)
REVERT: a   57 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8784 (ttmt)
REVERT: a   60 GLU cc_start: 0.8659 (pm20) cc_final: 0.8399 (pm20)
REVERT: a   61 LEU cc_start: 0.8594 (tp) cc_final: 0.8183 (tp)
REVERT: a   82 ASP cc_start: 0.8532 (t0) cc_final: 0.8242 (t0)
REVERT: a   88 SER cc_start: 0.9014 (p) cc_final: 0.8687 (t)
REVERT: a   91 MET cc_start: 0.8917 (mpp) cc_final: 0.8692 (mmp)
REVERT: a   94 GLN cc_start: 0.8895 (tt0) cc_final: 0.8523 (tt0)
REVERT: a   98 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7647 (mt-10)
  outliers start: 16
  outliers final: 13
  residues processed: 156
  average time/residue: 0.1360
  time to fit residues: 28.8474
Evaluate side-chains
  157 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain d residue   45 GLN
Chi-restraints excluded: chain d residue   69 GLU
Chi-restraints excluded: chain h residue   45 GLN
Chi-restraints excluded: chain h residue   67 ILE
Chi-restraints excluded: chain a residue   87 SER
Chi-restraints excluded: chain e residue   61 LEU
Chi-restraints excluded: chain e residue  113 ILE
Chi-restraints excluded: chain e residue  116 LYS
Chi-restraints excluded: chain b residue   31 THR
Chi-restraints excluded: chain b residue   51 ILE
Chi-restraints excluded: chain b residue   97 THR
Chi-restraints excluded: chain f residue   50 LEU
Chi-restraints excluded: chain f residue   51 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 59 optimal weight:    0.2980
   chunk 62 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** f  76 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 = 0.3940 r_free = 0.3940 target = 0.095622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.066571 restraints weight = 39897.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.89
r_work: 0.3120 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13690  Z= 0.176
  Angle     :  0.598   9.503  19900  Z= 0.354
  Chirality :  0.034   0.232   2264
  Planarity :  0.004   0.039   1388
  Dihedral  : 31.537 178.819   4484
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.29 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.31), residues: 754
  helix:  2.56 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.44 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG c  35 
 TYR   0.040   0.002   TYR d  81 
 PHE   0.007   0.001   PHE c  25 
 HIS   0.002   0.001   HIS d  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (13690)
  covalent geometry    : angle       0.59777 (19900)
  hydrogen bonds       : bond        0.03558 (  794)
  hydrogen bonds       : angle       2.49629 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: c   35 ARG cc_start: 0.8814 (mtm-85) cc_final: 0.8174 (mtm-85)
REVERT: c   64 GLU cc_start: 0.8474 (tp30) cc_final: 0.8243 (tp30)
REVERT: c   72 ASP cc_start: 0.8657 (t0) cc_final: 0.8247 (m-30)
REVERT: g   90 ASP cc_start: 0.8072 (t0) cc_final: 0.7712 (t0)
REVERT: d   32 LYS cc_start: 0.8758 (tppt) cc_final: 0.8444 (mmmm)
REVERT: h   49 ASP cc_start: 0.8580 (m-30) cc_final: 0.8337 (t0)
REVERT: h   81 TYR cc_start: 0.8852 (m-10) cc_final: 0.8566 (m-10)
REVERT: h   83 LYS cc_start: 0.9252 (mptt) cc_final: 0.8983 (mttp)
REVERT: a   57 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8804 (ttmt)
REVERT: a   60 GLU cc_start: 0.8652 (pm20) cc_final: 0.8284 (pm20)
REVERT: a   82 ASP cc_start: 0.8527 (t0) cc_final: 0.8243 (t0)
REVERT: a   88 SER cc_start: 0.9002 (p) cc_final: 0.8698 (t)
REVERT: a   91 MET cc_start: 0.8918 (mpp) cc_final: 0.8684 (mmp)
REVERT: a   94 GLN cc_start: 0.8869 (tt0) cc_final: 0.8412 (tt0)
REVERT: a   98 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7646 (mt-10)
REVERT: f   85 MET cc_start: 0.8974 (mmm) cc_final: 0.8457 (mmm)
  outliers start: 16
  outliers final: 13
  residues processed: 155
  average time/residue: 0.1434
  time to fit residues: 29.9794
Evaluate side-chains
  156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain g residue   63 LEU
Chi-restraints excluded: chain d residue   45 GLN
Chi-restraints excluded: chain d residue   69 GLU
Chi-restraints excluded: chain h residue   45 GLN
Chi-restraints excluded: chain h residue   67 ILE
Chi-restraints excluded: chain a residue   87 SER
Chi-restraints excluded: chain e residue   61 LEU
Chi-restraints excluded: chain e residue  113 ILE
Chi-restraints excluded: chain e residue  116 LYS
Chi-restraints excluded: chain b residue   31 THR
Chi-restraints excluded: chain b residue   51 ILE
Chi-restraints excluded: chain b residue   97 THR
Chi-restraints excluded: chain f residue   50 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** f  76 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 = 0.3918 r_free = 0.3918 target = 0.094455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.065119 restraints weight = 40209.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 1.91
r_work: 0.3089 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13690  Z= 0.231
  Angle     :  0.629  10.250  19900  Z= 0.368
  Chirality :  0.036   0.237   2264
  Planarity :  0.004   0.040   1388
  Dihedral  : 31.705 177.414   4484
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.92 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.31), residues: 754
  helix:  2.45 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.44 (0.41), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG f  93 
 TYR   0.041   0.002   TYR b  89 
 PHE   0.012   0.001   PHE c  25 
 HIS   0.003   0.001   HIS a  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (13690)
  covalent geometry    : angle       0.62933 (19900)
  hydrogen bonds       : bond        0.04035 (  794)
  hydrogen bonds       : angle       2.61812 ( 1964)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: c   72 ASP cc_start: 0.8679 (t0) cc_final: 0.8248 (m-30)
REVERT: d   32 LYS cc_start: 0.8788 (tppt) cc_final: 0.8468 (mmmm)
REVERT: h   49 ASP cc_start: 0.8602 (m-30) cc_final: 0.8363 (t0)
REVERT: h   81 TYR cc_start: 0.8885 (m-10) cc_final: 0.8582 (m-10)
REVERT: h   83 LYS cc_start: 0.9261 (mptt) cc_final: 0.8995 (mttp)
REVERT: a   57 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8794 (ttmt)
REVERT: a   82 ASP cc_start: 0.8575 (t0) cc_final: 0.8273 (t0)
REVERT: a   88 SER cc_start: 0.9083 (p) cc_final: 0.8781 (t)
REVERT: a   91 MET cc_start: 0.8961 (mpp) cc_final: 0.8701 (mmp)
REVERT: a   94 GLN cc_start: 0.8918 (tt0) cc_final: 0.8559 (tt0)
REVERT: f   85 MET cc_start: 0.8962 (mmm) cc_final: 0.8446 (mmm)
  outliers start: 13
  outliers final: 13
  residues processed: 150
  average time/residue: 0.1449
  time to fit residues: 29.5653
Evaluate side-chains
  154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain g residue   63 LEU
Chi-restraints excluded: chain d residue   45 GLN
Chi-restraints excluded: chain d residue   69 GLU
Chi-restraints excluded: chain d residue   88 THR
Chi-restraints excluded: chain h residue   45 GLN
Chi-restraints excluded: chain h residue   67 ILE
Chi-restraints excluded: chain a residue   87 SER
Chi-restraints excluded: chain e residue   61 LEU
Chi-restraints excluded: chain e residue  113 ILE
Chi-restraints excluded: chain b residue   31 THR
Chi-restraints excluded: chain b residue   51 ILE
Chi-restraints excluded: chain b residue   97 THR
Chi-restraints excluded: chain f residue   50 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 75 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0870
   chunk 28 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** f  76 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 = 0.3946 r_free = 0.3946 target = 0.096003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.066899 restraints weight = 39841.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.79
r_work: 0.3138 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13690  Z= 0.167
  Angle     :  0.601  10.013  19900  Z= 0.354
  Chirality :  0.034   0.246   2264
  Planarity :  0.004   0.039   1388
  Dihedral  : 31.434 175.274   4484
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.08 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.31), residues: 754
  helix:  2.59 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.42 (0.41), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG c  35 
 TYR   0.039   0.002   TYR d  81 
 PHE   0.006   0.001   PHE c  25 
 HIS   0.003   0.001   HIS d  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (13690)
  covalent geometry    : angle       0.60132 (19900)
  hydrogen bonds       : bond        0.03490 (  794)
  hydrogen bonds       : angle       2.52685 ( 1964)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3180.60 seconds
wall clock time: 55 minutes 8.21 seconds (3308.21 seconds total)