Starting phenix.real_space_refine
on Tue Jul 29 10:30:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6seg_10155/07_2025/6seg_10155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6seg_10155/07_2025/6seg_10155.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6seg_10155/07_2025/6seg_10155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6seg_10155/07_2025/6seg_10155.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6seg_10155/07_2025/6seg_10155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6seg_10155/07_2025/6seg_10155.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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     288      5.49       5
     S      10      5.16       5
     C    6471      2.51       5
     N    2175      2.21       5
     O    2745      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11689
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 618
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 739
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
    Chain: "D"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 618
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 799
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 4, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 7.04, per 1000 atoms: 0.60
  Number of scatterers: 11689
  At special positions: 0
  Unit cell: (74.24, 120.32, 113.92, 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      10     16.00
     P     288     15.00
     O    2745      8.00
     N    2175      7.00
     C    6471      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: 2.72
  Conformation dependent library (CDL) restraints added in 875.5 milliseconds
  

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1344

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 8 sheets defined
      72.9% alpha, 2.7% beta
      127 base pairs and 265 stacking pairs defined.
    Time for finding SS restraints: 5.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.819A  pdb=" N   LYS A  49 " --> pdb=" O   GLN A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 4.082A  pdb=" N   LYS A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.531A  pdb=" N   LEU A  91 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 133
      removed outlier: 3.869A  pdb=" N   VAL A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 50 through 76
      removed outlier: 3.890A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.780A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.164A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.613A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ASN C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 56 through 84
      removed outlier: 3.586A  pdb=" N   ASN D  67 " --> pdb=" O   ASN D  63 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.507A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.792A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 57
      removed outlier: 3.504A  pdb=" N   SER E  57 " --> pdb=" O   LYS E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.077A  pdb=" N   LYS E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.766A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 134
      removed outlier: 3.501A  pdb=" N   VAL E 126 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY E 134 " --> pdb=" O   ARG E 130 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.746A  pdb=" N   GLY F  28 " --> pdb=" O   ASN F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 50 through 76
      removed outlier: 3.556A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.616A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 36
      removed outlier: 3.656A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.259A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 88
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.599A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.570A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 105 through 122
      removed outlier: 3.617A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   VAL H 111 " --> pdb=" O   ALA H 107 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   THR H 119 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 6.700A  pdb=" N   ASN A  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.490A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.455A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.754A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86
      removed outlier: 6.871A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.583A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    357 hydrogen bonds defined for protein.
    1062 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      329 hydrogen bonds
      654 hydrogen bond angles
      0 basepair planarities
      127 basepair parallelities
      265 stacking parallelities
  Total time for adding SS restraints: 4.03

  Time building geometry restraints manager: 3.30 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: 1875
        1.33 -     1.45: 4394
        1.45 -     1.57: 5633
        1.57 -     1.68: 576
        1.68 -     1.80: 18
  Bond restraints: 12496
  Sorted by residual:
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.494 -0.072 3.00e-02 1.11e+03 5.70e+00
  bond pdb=" C   LEU A 121 "
       pdb=" N   PHE A 122 "
    ideal  model  delta    sigma   weight residual
    1.335  1.277  0.058 3.04e-02 1.08e+03 3.64e+00
  bond pdb=" CB  MET G  51 "
       pdb=" CG  MET G  51 "
    ideal  model  delta    sigma   weight residual
    1.520  1.467  0.053 3.00e-02 1.11e+03 3.13e+00
  bond pdb=" CG  LEU D 101 "
       pdb=" CD1 LEU D 101 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.58e+00
  bond pdb=" CG  GLU C  92 "
       pdb=" CD  GLU C  92 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.42e+00
  ... (remaining 12491 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 17895
        2.75 -     5.49: 210
        5.49 -     8.24: 16
        8.24 -    10.98: 3
       10.98 -    13.73: 1
  Bond angle restraints: 18125
  Sorted by residual:
  angle pdb=" CA  ARG A  80 "
        pdb=" CB  ARG A  80 "
        pdb=" CG  ARG A  80 "
      ideal   model   delta    sigma   weight residual
     114.10  122.82   -8.72 2.00e+00 2.50e-01 1.90e+01
  angle pdb=" CA  LEU A 121 "
        pdb=" CB  LEU A 121 "
        pdb=" CG  LEU A 121 "
      ideal   model   delta    sigma   weight residual
     116.30  130.03  -13.73 3.50e+00 8.16e-02 1.54e+01
  angle pdb=" C3'  DG J  20 "
        pdb=" O3'  DG J  20 "
        pdb=" P    DG J  21 "
      ideal   model   delta    sigma   weight residual
     120.20  125.69   -5.49 1.50e+00 4.44e-01 1.34e+01
  angle pdb=" CB  MET G  51 "
        pdb=" CG  MET G  51 "
        pdb=" SD  MET G  51 "
      ideal   model   delta    sigma   weight residual
     112.70  101.94   10.76 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     112.50  116.53   -4.03 1.16e+00 7.43e-01 1.21e+01
  ... (remaining 18120 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.97: 5311
       34.97 -    69.95: 1378
       69.95 -   104.92: 18
      104.92 -   139.89: 0
      139.89 -   174.87: 1
  Dihedral angle restraints: 6708
    sinusoidal: 4618
      harmonic: 2090
  Sorted by residual:
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   45.13  174.87     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  ARG A  63 "
           pdb=" C   ARG A  63 "
           pdb=" N   LYS A  64 "
           pdb=" CA  LYS A  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  PRO D 103 "
           pdb=" C   PRO D 103 "
           pdb=" N   GLY D 104 "
           pdb=" CA  GLY D 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.53  -17.47     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 6705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 1944
       0.099 -    0.198: 106
       0.198 -    0.298: 7
       0.298 -    0.397: 1
       0.397 -    0.496: 1
  Chirality restraints: 2059
  Sorted by residual:
  chirality pdb=" CG  LEU D  45 "
            pdb=" CB  LEU D  45 "
            pdb=" CD1 LEU D  45 "
            pdb=" CD2 LEU D  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.09   -0.50 2.00e-01 2.50e+01 6.15e+00
  chirality pdb=" CB  ILE G 111 "
            pdb=" CA  ILE G 111 "
            pdb=" CG1 ILE G 111 "
            pdb=" CG2 ILE G 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CG  LEU E 112 "
            pdb=" CB  LEU E 112 "
            pdb=" CD1 LEU E 112 "
            pdb=" CD2 LEU E 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.13e+00
  ... (remaining 2056 not shown)

  Planarity restraints: 1283
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  69 "    0.035 2.00e-02 2.50e+03   2.01e-02 9.09e+00
        pdb=" N1   DC I  69 "   -0.044 2.00e-02 2.50e+03
        pdb=" C2   DC I  69 "    0.011 2.00e-02 2.50e+03
        pdb=" O2   DC I  69 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DC I  69 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DC I  69 "    0.005 2.00e-02 2.50e+03
        pdb=" N4   DC I  69 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DC I  69 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DC I  69 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  35 "    0.038 2.00e-02 2.50e+03   1.97e-02 8.70e+00
        pdb=" N1   DC I  35 "   -0.040 2.00e-02 2.50e+03
        pdb=" C2   DC I  35 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DC I  35 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DC I  35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DC I  35 "    0.008 2.00e-02 2.50e+03
        pdb=" N4   DC I  35 "    0.012 2.00e-02 2.50e+03
        pdb=" C5   DC I  35 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6   DC I  35 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I   5 "   -0.037 2.00e-02 2.50e+03   1.91e-02 8.24e+00
        pdb=" N1   DC I   5 "    0.039 2.00e-02 2.50e+03
        pdb=" C2   DC I   5 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2   DC I   5 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DC I   5 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DC I   5 "   -0.007 2.00e-02 2.50e+03
        pdb=" N4   DC I   5 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5   DC I   5 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DC I   5 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1280 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2588
        2.81 -     3.33: 9223
        3.33 -     3.85: 23485
        3.85 -     4.38: 27726
        4.38 -     4.90: 38845
  Nonbonded interactions: 101867
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 113 "
            pdb=" OD2 ASP E 125 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OG1 THR A 113 "
            pdb=" OD2 ASP A 125 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.345 2.496
  ... (remaining 101862 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' and resid 16 through 111)
}
ncs_group {
  reference = (chain 'D' and resid 35 through 124)
  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:             0.210
  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:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     31.220
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.050
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
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   0.072  12496  Z= 0.279
  Angle     :  0.857  13.727  18125  Z= 0.510
  Chirality :  0.054   0.496   2059
  Planarity :  0.007   0.063   1283
  Dihedral  : 27.752 174.868   5364
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  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: -3.47 (0.23), residues: 712
  helix: -2.21 (0.17), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.95 (0.34), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  47 
 HIS   0.007   0.002   HIS B  75 
 PHE   0.015   0.003   PHE A  84 
 TYR   0.022   0.003   TYR F  98 
 ARG   0.019   0.001   ARG C  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10465 (  686)
  hydrogen bonds       : angle       4.48599 ( 1716)
  covalent geometry    : bond        0.00631 (12496)
  covalent geometry    : angle       0.85651 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8330 (tmmt) cc_final: 0.8125 (tmmt)
REVERT: B   44 LYS cc_start: 0.8659 (tttt) cc_final: 0.8039 (mptt)
REVERT: B   79 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7485 (mtpp)
REVERT: C   73 ASN cc_start: 0.8222 (t0) cc_final: 0.7834 (t0)
REVERT: C   74 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7454 (mttp)
REVERT: C   95 LYS cc_start: 0.7845 (mtmt) cc_final: 0.7536 (ttmm)
REVERT: D   37 TYR cc_start: 0.8839 (m-80) cc_final: 0.8451 (m-80)
REVERT: D   59 MET cc_start: 0.7932 (tpp) cc_final: 0.7606 (tpt)
REVERT: E   62 ILE cc_start: 0.8163 (mt) cc_final: 0.7951 (mt)
REVERT: G   36 LYS cc_start: 0.8438 (mptt) cc_final: 0.8155 (mptt)
REVERT: G   90 ASP cc_start: 0.7445 (t0) cc_final: 0.7196 (t0)
REVERT: H   99 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7768 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.3954
  time to fit residues: 55.8977
Evaluate side-chains
  91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 73 optimal weight:    9.9990
   chunk 40 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 88 optimal weight:    8.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
G 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.181798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137527 restraints weight = 13456.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 0.87
r_work: 0.3357 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.0760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12496  Z= 0.176
  Angle     :  0.628   5.964  18125  Z= 0.375
  Chirality :  0.036   0.153   2059
  Planarity :  0.005   0.053   1283
  Dihedral  : 30.782 170.942   3964
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.38 %
    Favored  : 90.62 %
  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: -0.98 (0.28), residues: 712
  helix: -0.17 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.69 (0.36), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  86 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.015   0.002   TYR F  98 
 ARG   0.004   0.001   ARG F  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05332 (  686)
  hydrogen bonds       : angle       3.29534 ( 1716)
  covalent geometry    : bond        0.00375 (12496)
  covalent geometry    : angle       0.62830 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A  122 PHE cc_start: 0.8819 (m-80) cc_final: 0.8508 (m-80)
REVERT: B   44 LYS cc_start: 0.8888 (tttt) cc_final: 0.8013 (mptt)
REVERT: C   95 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7703 (ttmm)
REVERT: D   59 MET cc_start: 0.8172 (tpp) cc_final: 0.7928 (tpt)
REVERT: E   62 ILE cc_start: 0.8528 (mt) cc_final: 0.8283 (mt)
REVERT: G   24 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7995 (mm-40)
REVERT: G   36 LYS cc_start: 0.8590 (mptt) cc_final: 0.8364 (mptt)
  outliers start: 6
  outliers final: 4
  residues processed: 105
  average time/residue: 0.3498
  time to fit residues: 46.9980
Evaluate side-chains
  99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 53 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.182500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.137932 restraints weight = 13572.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 0.89
r_work: 0.3353 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12496  Z= 0.164
  Angle     :  0.585   5.906  18125  Z= 0.354
  Chirality :  0.035   0.144   2059
  Planarity :  0.004   0.042   1283
  Dihedral  : 30.745 170.557   3964
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.39 %
    Favored  : 88.78 %
  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:  0.02 (0.30), residues: 712
  helix:  0.57 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.45 (0.38), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  86 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.006   0.001   PHE E  67 
 TYR   0.010   0.001   TYR E 110 
 ARG   0.006   0.000   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04993 (  686)
  hydrogen bonds       : angle       2.99884 ( 1716)
  covalent geometry    : bond        0.00354 (12496)
  covalent geometry    : angle       0.58519 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A   79 THR cc_start: 0.8503 (p) cc_final: 0.8281 (p)
REVERT: B   44 LYS cc_start: 0.8872 (tttt) cc_final: 0.7961 (mptt)
REVERT: B   79 LYS cc_start: 0.7970 (mttp) cc_final: 0.7217 (mtpp)
REVERT: C   95 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7681 (ttmm)
REVERT: D   59 MET cc_start: 0.8145 (tpp) cc_final: 0.7907 (tpt)
REVERT: E   62 ILE cc_start: 0.8541 (mt) cc_final: 0.8273 (mt)
REVERT: F   91 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8564 (ttmt)
REVERT: G   24 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7985 (mm-40)
REVERT: G   36 LYS cc_start: 0.8610 (mptt) cc_final: 0.8345 (mptt)
  outliers start: 5
  outliers final: 3
  residues processed: 93
  average time/residue: 0.3363
  time to fit residues: 40.9593
Evaluate side-chains
  92 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 94 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
B  93 GLN
F  75 HIS
G 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.174718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.129587 restraints weight = 13659.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 0.97
r_work: 0.3251 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.061  12496  Z= 0.405
  Angle     :  0.752   6.945  18125  Z= 0.429
  Chirality :  0.046   0.179   2059
  Planarity :  0.007   0.085   1283
  Dihedral  : 31.919 166.750   3964
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 10.89 %
    Favored  : 86.77 %
  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: -0.35 (0.29), residues: 712
  helix:  0.35 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.71 (0.38), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  86 
 HIS   0.006   0.002   HIS E 115 
 PHE   0.015   0.002   PHE A  67 
 TYR   0.020   0.003   TYR H  42 
 ARG   0.008   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05693 (  686)
  hydrogen bonds       : angle       3.25984 ( 1716)
  covalent geometry    : bond        0.00943 (12496)
  covalent geometry    : angle       0.75183 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.865 
Fit side-chains
REVERT: A   79 THR cc_start: 0.8493 (p) cc_final: 0.8242 (p)
REVERT: A  114 LEU cc_start: 0.8491 (mt) cc_final: 0.8159 (mp)
REVERT: B   44 LYS cc_start: 0.8884 (tttt) cc_final: 0.7959 (mttt)
REVERT: B   79 LYS cc_start: 0.8184 (mttp) cc_final: 0.7450 (mtpp)
REVERT: C   35 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7859 (mtm-85)
REVERT: D   86 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.7765 (tpp-160)
REVERT: D  120 LYS cc_start: 0.8408 (tttt) cc_final: 0.8047 (tttp)
REVERT: E   53 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8386 (ttpt)
REVERT: E   62 ILE cc_start: 0.8663 (mt) cc_final: 0.8427 (mt)
REVERT: F   91 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8711 (ttpp)
REVERT: G   35 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8206 (ttm-80)
REVERT: G  112 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.5457 (pt0)
REVERT: H   48 VAL cc_start: 0.7965 (t) cc_final: 0.7585 (p)
  outliers start: 14
  outliers final: 10
  residues processed: 109
  average time/residue: 0.3739
  time to fit residues: 51.8268
Evaluate side-chains
  108 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  120 THR
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  112 GLN
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 79 optimal weight:    7.9990
   chunk 87 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.182949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.138792 restraints weight = 13536.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 0.85
r_work: 0.3423 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12496  Z= 0.161
  Angle     :  0.554   5.802  18125  Z= 0.337
  Chirality :  0.034   0.142   2059
  Planarity :  0.004   0.039   1283
  Dihedral  : 31.058 172.102   3964
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.74 %
    Favored  : 84.76 %
  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:  0.64 (0.30), residues: 712
  helix:  1.11 (0.22), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.45 (0.38), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  86 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.010   0.001   TYR E 110 
 ARG   0.008   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  686)
  hydrogen bonds       : angle       2.76598 ( 1716)
  covalent geometry    : bond        0.00350 (12496)
  covalent geometry    : angle       0.55391 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A   79 THR cc_start: 0.8051 (p) cc_final: 0.7686 (p)
REVERT: B   44 LYS cc_start: 0.8904 (tttt) cc_final: 0.8053 (mttt)
REVERT: C   35 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7825 (mtm-85)
REVERT: E   62 ILE cc_start: 0.8528 (mt) cc_final: 0.8275 (mt)
REVERT: F   91 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8539 (ttpp)
REVERT: G  107 VAL cc_start: 0.8706 (p) cc_final: 0.8331 (m)
REVERT: G  112 GLN cc_start: 0.6062 (OUTLIER) cc_final: 0.5464 (pt0)
  outliers start: 9
  outliers final: 6
  residues processed: 101
  average time/residue: 0.3555
  time to fit residues: 46.3561
Evaluate side-chains
  93 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  112 GLN
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   chunk 95 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.177036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.130418 restraints weight = 13640.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.11
r_work: 0.3285 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12496  Z= 0.189
  Angle     :  0.570   6.197  18125  Z= 0.342
  Chirality :  0.035   0.139   2059
  Planarity :  0.004   0.039   1283
  Dihedral  : 31.147 171.458   3964
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.40 %
    Favored  : 84.59 %
  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:  0.90 (0.30), residues: 712
  helix:  1.29 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.39 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  86 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.012   0.002   TYR D  40 
 ARG   0.008   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  686)
  hydrogen bonds       : angle       2.76101 ( 1716)
  covalent geometry    : bond        0.00425 (12496)
  covalent geometry    : angle       0.57040 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A   79 THR cc_start: 0.8111 (p) cc_final: 0.7751 (p)
REVERT: B   44 LYS cc_start: 0.8927 (tttt) cc_final: 0.8052 (mttt)
REVERT: C   35 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7898 (mtm-85)
REVERT: F   91 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8576 (ttpp)
REVERT: G  107 VAL cc_start: 0.8647 (p) cc_final: 0.8262 (m)
REVERT: G  112 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5647 (pt0)
  outliers start: 12
  outliers final: 9
  residues processed: 99
  average time/residue: 0.3469
  time to fit residues: 44.7475
Evaluate side-chains
  96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  120 THR
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  112 GLN
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 91 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.174297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.129058 restraints weight = 13725.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 0.97
r_work: 0.3245 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.065  12496  Z= 0.393
  Angle     :  0.732   8.129  18125  Z= 0.418
  Chirality :  0.045   0.154   2059
  Planarity :  0.006   0.070   1283
  Dihedral  : 31.963 167.367   3964
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.24 %
    Favored  : 83.58 %
  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:  0.07 (0.30), residues: 712
  helix:  0.71 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.70 (0.38), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  86 
 HIS   0.007   0.002   HIS F  75 
 PHE   0.014   0.002   PHE A  78 
 TYR   0.017   0.003   TYR H  42 
 ARG   0.008   0.001   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05524 (  686)
  hydrogen bonds       : angle       3.16327 ( 1716)
  covalent geometry    : bond        0.00913 (12496)
  covalent geometry    : angle       0.73201 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.783 
Fit side-chains
REVERT: A   91 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8754 (mm)
REVERT: B   44 LYS cc_start: 0.8895 (tttt) cc_final: 0.8005 (mttt)
REVERT: C   35 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7672 (mtm-85)
REVERT: D  120 LYS cc_start: 0.8435 (tttt) cc_final: 0.8055 (tttp)
REVERT: E   53 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8490 (ttpt)
REVERT: F   91 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8731 (ttpp)
REVERT: G  112 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.5556 (pt0)
REVERT: H   40 TYR cc_start: 0.9105 (m-80) cc_final: 0.8786 (m-80)
REVERT: H   48 VAL cc_start: 0.8068 (t) cc_final: 0.7695 (p)
REVERT: H   85 LYS cc_start: 0.8661 (mttt) cc_final: 0.8227 (mtpp)
  outliers start: 13
  outliers final: 11
  residues processed: 102
  average time/residue: 0.3676
  time to fit residues: 48.3213
Evaluate side-chains
  102 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  120 THR
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  112 GLN
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 92 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.180870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.136492 restraints weight = 13584.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 0.87
r_work: 0.3330 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12496  Z= 0.148
  Angle     :  0.553   6.382  18125  Z= 0.336
  Chirality :  0.034   0.141   2059
  Planarity :  0.004   0.045   1283
  Dihedral  : 31.195 171.371   3964
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.91 %
    Favored  : 83.42 %
  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:  0.96 (0.30), residues: 712
  helix:  1.39 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.53 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  86 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.015   0.001   TYR D  40 
 ARG   0.007   0.000   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  686)
  hydrogen bonds       : angle       2.72151 ( 1716)
  covalent geometry    : bond        0.00318 (12496)
  covalent geometry    : angle       0.55278 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.745 
Fit side-chains
REVERT: B   44 LYS cc_start: 0.8885 (tttt) cc_final: 0.7914 (mttt)
REVERT: B   91 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8272 (ttmt)
REVERT: C   35 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7752 (mtm-85)
REVERT: F   91 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8580 (ttpp)
REVERT: G  112 GLN cc_start: 0.6031 (OUTLIER) cc_final: 0.5471 (pt0)
  outliers start: 10
  outliers final: 7
  residues processed: 96
  average time/residue: 0.3446
  time to fit residues: 42.7203
Evaluate side-chains
  95 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  120 THR
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  112 GLN
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 75 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.178133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.133080 restraints weight = 13638.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 0.88
r_work: 0.3299 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12496  Z= 0.218
  Angle     :  0.594   8.337  18125  Z= 0.352
  Chirality :  0.036   0.138   2059
  Planarity :  0.004   0.042   1283
  Dihedral  : 31.313 170.355   3964
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.08 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.30), residues: 712
  helix:  1.32 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.54 (0.38), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  86 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.010   0.001   PHE A  78 
 TYR   0.011   0.002   TYR D  40 
 ARG   0.007   0.001   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04294 (  686)
  hydrogen bonds       : angle       2.80794 ( 1716)
  covalent geometry    : bond        0.00497 (12496)
  covalent geometry    : angle       0.59441 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A   79 THR cc_start: 0.8220 (p) cc_final: 0.7904 (p)
REVERT: B   44 LYS cc_start: 0.8880 (tttt) cc_final: 0.7913 (mttt)
REVERT: B   91 LYS cc_start: 0.8653 (ttmm) cc_final: 0.7956 (mtpp)
REVERT: C   35 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7742 (mtm-85)
REVERT: F   91 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8534 (ttpp)
REVERT: G   35 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8105 (ttm-80)
REVERT: G  112 GLN cc_start: 0.6178 (OUTLIER) cc_final: 0.5657 (pt0)
  outliers start: 11
  outliers final: 8
  residues processed: 92
  average time/residue: 0.3666
  time to fit residues: 43.6608
Evaluate side-chains
  93 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  120 THR
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  112 GLN
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 2 optimal weight:    0.6980
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.177458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.130839 restraints weight = 13390.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.15
r_work: 0.3283 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12496  Z= 0.150
  Angle     :  0.573  13.139  18125  Z= 0.343
  Chirality :  0.034   0.140   2059
  Planarity :  0.004   0.040   1283
  Dihedral  : 31.300 170.491   3964
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.08 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.31), residues: 712
  helix:  1.51 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.43 (0.39), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  86 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.013   0.002   TYR E 110 
 ARG   0.007   0.000   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  686)
  hydrogen bonds       : angle       2.73050 ( 1716)
  covalent geometry    : bond        0.00324 (12496)
  covalent geometry    : angle       0.57316 (18125)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.825 
Fit side-chains
REVERT: A   79 THR cc_start: 0.8167 (p) cc_final: 0.7841 (p)
REVERT: B   44 LYS cc_start: 0.8908 (tttt) cc_final: 0.7988 (mttt)
REVERT: B   91 LYS cc_start: 0.8647 (ttmm) cc_final: 0.7967 (mtpp)
REVERT: C   35 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.7787 (mtm-85)
REVERT: F   91 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8562 (ttpp)
REVERT: G  112 GLN cc_start: 0.6088 (OUTLIER) cc_final: 0.5525 (pt0)
  outliers start: 11
  outliers final: 10
  residues processed: 93
  average time/residue: 0.4082
  time to fit residues: 48.6468
Evaluate side-chains
  96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  120 THR
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  112 GLN
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.179652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.134825 restraints weight = 13462.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 0.87
r_work: 0.3319 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.131  12496  Z= 0.199
  Angle     :  0.801  59.200  18125  Z= 0.485
  Chirality :  0.038   0.742   2059
  Planarity :  0.004   0.068   1283
  Dihedral  : 31.299 170.554   3964
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.74 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.31), residues: 712
  helix:  1.51 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.42 (0.39), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  86 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.013   0.001   TYR D  40 
 ARG   0.006   0.000   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04103 (  686)
  hydrogen bonds       : angle       2.72887 ( 1716)
  covalent geometry    : bond        0.00401 (12496)
  covalent geometry    : angle       0.80084 (18125)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6289.92 seconds
wall clock time: 110 minutes 1.40 seconds (6601.40 seconds total)