Starting phenix.real_space_refine
on Wed Mar  4 04:22:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mxl_24073/03_2026/7mxl_24073.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mxl_24073/03_2026/7mxl_24073.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mxl_24073/03_2026/7mxl_24073.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mxl_24073/03_2026/7mxl_24073.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mxl_24073/03_2026/7mxl_24073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mxl_24073/03_2026/7mxl_24073.map"
  }
  resolution = 3.2
  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=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    6850      2.51       5
     N    1817      2.21       5
     O    2162      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10866
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1553
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 193}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1554
          Classifications: {'peptide': 200}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 186}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1233
          Classifications: {'peptide': 159}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 150}
    Chain: "J"
      Number of atoms: 1618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1618
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201}
          Chain breaks: 2
    Chain: "K"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1650
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202}
    Chain: "L"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1632
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201}
    Chain: "H"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1626
          Classifications: {'peptide': 217}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 206}
  Time building chain proxies: 2.19, per 1000 atoms: 0.20
  Number of scatterers: 10866
  At special positions: 0
  Unit cell: (114.4, 148.72, 144.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    2162      8.00
     N    1817      7.00
     C    6850      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 144 " - pdb=" SG  CYS A 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 134 " - pdb=" SG  CYS K 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 147 " - pdb=" SG  CYS J 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 135 " - pdb=" SG  CYS K 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 146 " - pdb=" SG  CYS H 202 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 539.0 milliseconds
  

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2634

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 34 sheets defined
      9.6% alpha, 47.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 66
      No H-bonds generated for 'chain 'A' and resid 64 through 66'
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.677A  pdb=" N   THR A  91 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.573A  pdb=" N   ASP B  82 " --> pdb=" O   GLU B  79 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   PHE B  83 " --> pdb=" O   SER B  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 79 through 83'
    Processing helix  chain 'B' and resid 121 through 128
    Processing helix  chain 'C' and resid 15 through 24
    Processing helix  chain 'C' and resid 25 through 28
      removed outlier: 4.588A  pdb=" N   ASP C  28 " --> pdb=" O   LEU C  25 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 25 through 28'
    Processing helix  chain 'C' and resid 30 through 35
    Processing helix  chain 'C' and resid 130 through 155
    Processing helix  chain 'J' and resid 28 through 32
      removed outlier: 3.624A  pdb=" N   TYR J  32 " --> pdb=" O   PHE J  29 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 87 through 91
      removed outlier: 4.028A  pdb=" N   THR J  91 " --> pdb=" O   SER J  88 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 29 through 32
    Processing helix  chain 'K' and resid 80 through 84
      removed outlier: 3.980A  pdb=" N   PHE K  84 " --> pdb=" O   PRO K  81 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 122 through 129
    Processing helix  chain 'K' and resid 184 through 188
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.547A  pdb=" N   ASP L  82 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   PHE L  83 " --> pdb=" O   SER L  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 79 through 83'
    Processing helix  chain 'L' and resid 121 through 128
      removed outlier: 3.532A  pdb=" N   LEU L 125 " --> pdb=" O   SER L 121 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS L 126 " --> pdb=" O   ASP L 122 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 183 through 188
      removed outlier: 3.512A  pdb=" N   LYS L 188 " --> pdb=" O   ALA L 184 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.862A  pdb=" N   SER H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.793A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 162 through 164
      No H-bonds generated for 'chain 'H' and resid 162 through 164'
    Processing helix  chain 'H' and resid 191 through 195
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.592A  pdb=" N   TRP A  37 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TYR A  51 " --> pdb=" O   TRP A  35 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP A  35 " --> pdb=" O   TYR A  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.592A  pdb=" N   TRP A  37 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TYR A  51 " --> pdb=" O   TRP A  35 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP A  35 " --> pdb=" O   TYR A  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 127
      removed outlier: 6.036A  pdb=" N   TYR A 180 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 124 through 127
      removed outlier: 6.036A  pdb=" N   TYR A 180 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 155 through 158
      removed outlier: 3.542A  pdb=" N   THR A 155 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13
      removed outlier: 7.009A  pdb=" N   LEU B  11 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118
    Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 196
    Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 12
      removed outlier: 3.875A  pdb=" N   LYS C  98 " --> pdb=" O   HIS C 122 " (cutoff:3.500A)
      removed outlier: 9.832A  pdb=" N   GLU C  97 " --> pdb=" O   GLU C  88 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   GLU C  88 " --> pdb=" O   GLU C  97 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   LYS C  69 " --> pdb=" O   ILE C  87 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   GLY C  89 " --> pdb=" O   TYR C  67 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   TYR C  67 " --> pdb=" O   GLY C  89 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE C  54 " --> pdb=" O   ILE C  45 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 12
      removed outlier: 3.875A  pdb=" N   LYS C  98 " --> pdb=" O   HIS C 122 " (cutoff:3.500A)
      removed outlier: 9.832A  pdb=" N   GLU C  97 " --> pdb=" O   GLU C  88 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   GLU C  88 " --> pdb=" O   GLU C  97 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 3 through 6
    Processing sheet with id=AB5, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.470A  pdb=" N   ILE J  34 " --> pdb=" O   TRP J  50 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   TRP J  50 " --> pdb=" O   ILE J  34 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   TRP J  36 " --> pdb=" O   MET J  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'J' and resid 10 through 12
      removed outlier: 4.276A  pdb=" N   TYR J 109 " --> pdb=" O   ARG J  98 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'J' and resid 127 through 131
      removed outlier: 6.198A  pdb=" N   TYR J 183 " --> pdb=" O   ASP J 151 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'J' and resid 127 through 131
      removed outlier: 6.198A  pdb=" N   TYR J 183 " --> pdb=" O   ASP J 151 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'J' and resid 158 through 161
    Processing sheet with id=AC1, first strand: chain 'K' and resid 4 through 7
    Processing sheet with id=AC2, first strand: chain 'K' and resid 12 through 13
      removed outlier: 3.773A  pdb=" N   LEU K  13 " --> pdb=" O   GLU K 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'K' and resid 54 through 55
      removed outlier: 6.428A  pdb=" N   TRP K  36 " --> pdb=" O   LEU K  48 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   TYR K  50 " --> pdb=" O   LEU K  34 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU K  34 " --> pdb=" O   TYR K  50 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'K' and resid 118 through 119
      removed outlier: 3.676A  pdb=" N   VAL K 134 " --> pdb=" O   PHE K 119 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   TYR K 174 " --> pdb=" O   ASN K 139 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'K' and resid 145 through 151
      removed outlier: 4.020A  pdb=" N   LYS K 146 " --> pdb=" O   THR K 198 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   TYR K 193 " --> pdb=" O   PHE K 210 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.231A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.231A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'L' and resid 19 through 24
    Processing sheet with id=AC9, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.573A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   SER L 131 " --> pdb=" O   LEU L 181 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   LEU L 181 " --> pdb=" O   SER L 131 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 179 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   LEU L 179 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 177 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   SER L 177 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   ASN L 137 " --> pdb=" O   LEU L 175 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   LEU L 175 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'L' and resid 153 through 154
      removed outlier: 3.630A  pdb=" N   LYS L 207 " --> pdb=" O   CYS L 194 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.844A  pdb=" N   MET H  34 " --> pdb=" O   PHE H  50 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   PHE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.724A  pdb=" N   ASN H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'H' and resid 126 through 130
      removed outlier: 5.883A  pdb=" N   TYR H 182 " --> pdb=" O   ASP H 150 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'H' and resid 126 through 130
      removed outlier: 5.883A  pdb=" N   TYR H 182 " --> pdb=" O   ASP H 150 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'H' and resid 157 through 160

    512 hydrogen bonds defined for protein.
    1281 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.86

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3469
        1.34 -     1.46: 2735
        1.46 -     1.58: 4872
        1.58 -     1.70: 0
        1.70 -     1.82: 45
  Bond restraints: 11121
  Sorted by residual:
  bond pdb=" CG1 ILE H 101 "
       pdb=" CD1 ILE H 101 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.79e-01
  bond pdb=" CA  ASN A 208 "
       pdb=" CB  ASN A 208 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.69e-02 3.50e+03 9.65e-01
  bond pdb=" CG1 ILE C  92 "
       pdb=" CD1 ILE C  92 "
    ideal  model  delta    sigma   weight residual
    1.513  1.476  0.037 3.90e-02 6.57e+02 8.86e-01
  bond pdb=" CB  ASN A 208 "
       pdb=" CG  ASN A 208 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.50e-02 1.60e+03 8.42e-01
  bond pdb=" CB  LYS A 205 "
       pdb=" CG  LYS A 205 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.96e-01
  ... (remaining 11116 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 14654
        1.52 -     3.05: 402
        3.05 -     4.57: 52
        4.57 -     6.10: 12
        6.10 -     7.62: 4
  Bond angle restraints: 15124
  Sorted by residual:
  angle pdb=" C   GLU J 155 "
        pdb=" N   PRO J 156 "
        pdb=" CD  PRO J 156 "
      ideal   model   delta    sigma   weight residual
     120.60  114.33    6.27 2.20e+00 2.07e-01 8.13e+00
  angle pdb=" N   ILE J  30 "
        pdb=" CA  ILE J  30 "
        pdb=" C   ILE J  30 "
      ideal   model   delta    sigma   weight residual
     113.00  109.36    3.64 1.30e+00 5.92e-01 7.85e+00
  angle pdb=" N   LYS A 121 "
        pdb=" CA  LYS A 121 "
        pdb=" C   LYS A 121 "
      ideal   model   delta    sigma   weight residual
     108.34  111.90   -3.56 1.31e+00 5.83e-01 7.39e+00
  angle pdb=" C   SER A 207 "
        pdb=" N   ASN A 208 "
        pdb=" CA  ASN A 208 "
      ideal   model   delta    sigma   weight residual
     121.54  126.44   -4.90 1.91e+00 2.74e-01 6.57e+00
  angle pdb=" C   GLN J 178 "
        pdb=" N   SER J 179 "
        pdb=" CA  SER J 179 "
      ideal   model   delta    sigma   weight residual
     120.60  124.62   -4.02 1.60e+00 3.91e-01 6.30e+00
  ... (remaining 15119 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 6067
       17.58 -    35.16: 464
       35.16 -    52.74: 83
       52.74 -    70.31: 16
       70.31 -    87.89: 10
  Dihedral angle restraints: 6640
    sinusoidal: 2530
      harmonic: 4110
  Sorted by residual:
  dihedral pdb=" CB  CYS A  23 "
           pdb=" SG  CYS A  23 "
           pdb=" SG  CYS A  96 "
           pdb=" CB  CYS A  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.38   43.62     1      1.00e+01 1.00e-02 2.65e+01
  dihedral pdb=" CA  GLN J 178 "
           pdb=" C   GLN J 178 "
           pdb=" N   SER J 179 "
           pdb=" CA  SER J 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.50  -25.50     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CB  CYS K 135 "
           pdb=" SG  CYS K 135 "
           pdb=" SG  CYS K 195 "
           pdb=" CB  CYS K 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.90  -41.90     1      1.00e+01 1.00e-02 2.46e+01
  ... (remaining 6637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1048
       0.034 -    0.067: 428
       0.067 -    0.101: 158
       0.101 -    0.135: 58
       0.135 -    0.168: 8
  Chirality restraints: 1700
  Sorted by residual:
  chirality pdb=" CB  THR K  10 "
            pdb=" CA  THR K  10 "
            pdb=" OG1 THR K  10 "
            pdb=" CG2 THR K  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CG  LEU A  19 "
            pdb=" CB  LEU A  19 "
            pdb=" CD1 LEU A  19 "
            pdb=" CD2 LEU A  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.53e-01
  chirality pdb=" CA  ILE B  48 "
            pdb=" N   ILE B  48 "
            pdb=" C   ILE B  48 "
            pdb=" CB  ILE B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.94e-01
  ... (remaining 1697 not shown)

  Planarity restraints: 1933
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU J 155 "    0.064 5.00e-02 4.00e+02   9.74e-02 1.52e+01
        pdb=" N   PRO J 156 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO J 156 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO J 156 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN H  13 "    0.027 5.00e-02 4.00e+02   4.01e-02 2.58e+00
        pdb=" N   PRO H  14 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 152 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO H 153 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO H 153 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 153 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1930 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 239
        2.67 -     3.22: 10207
        3.22 -     3.78: 16757
        3.78 -     4.34: 23800
        4.34 -     4.90: 39668
  Nonbonded interactions: 90671
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 105 "
            pdb=" OH  TYR B 173 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OE2 GLU C 102 "
            pdb=" OH  TYR L  49 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" NE2 GLN J 178 "
            pdb=" OG  SER J 180 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" O   TYR K 187 "
            pdb=" OH  TYR K 193 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" NH1 ARG H  98 "
            pdb=" OD1 ASN H 108 "
     model   vdw
     2.204 3.120
  ... (remaining 90666 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 'B' and (resid 2 through 3 or resid 5 through 8 or resid 10 through 12 or \ 
 resid 14 through 28 or resid 31 or resid 33 through 36 or resid 38 through 45 o \ 
r resid 47 through 49 or resid 51 through 52 or resid 54 or resid 56 through 59  \ 
or resid 61 through 69 or resid 71 through 75 or resid 78 or resid 81 through 84 \ 
 or resid 86 or resid 88 or resid 90 or resid 95 or resid 97 through 99 or resid \ 
 101 through 104 or resid 106 through 210))
  selection = (chain 'K' and (resid 2 through 3 or resid 5 through 8 or resid 10 through 12 or \ 
 resid 14 through 28 or resid 31 or resid 34 through 37 or resid 39 through 46 o \ 
r resid 48 through 50 or resid 52 through 53 or resid 55 or resid 57 through 60  \ 
or resid 62 through 70 or resid 72 through 76 or resid 79 or resid 82 through 85 \ 
 or resid 87 or resid 89 or resid 91 or resid 96 or resid 98 through 100 or resi \ 
d 102 through 105 or resid 107 through 149 or resid 160 through 211))
  selection = (chain 'L' and (resid 2 through 3 or resid 5 through 8 or resid 10 through 12 or \ 
 resid 14 through 28 or resid 31 or resid 33 through 36 or resid 38 through 45 o \ 
r resid 47 through 49 or resid 51 through 52 or resid 54 or resid 56 through 59  \ 
or resid 61 through 69 or resid 71 through 75 or resid 78 or resid 81 through 84 \ 
 or resid 86 or resid 88 or resid 90 or resid 95 or resid 97 through 99 or resid \ 
 101 through 104 or resid 106 through 148 or resid 159 through 210))
}

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=0.50 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:             0.920
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.870
  Find NCS groups from input model:        0.160
  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:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
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      :  0.004   0.045  11133  Z= 0.165
  Angle     :  0.613   7.625  15148  Z= 0.333
  Chirality :  0.045   0.168   1700
  Planarity :  0.005   0.097   1933
  Dihedral  : 13.075  87.893   3970
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.08 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.92 (0.22), residues: 1400
  helix: -0.59 (0.57), residues: 83
  sheet: -1.13 (0.20), residues: 646
  loop : -1.39 (0.24), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  18 
 TYR   0.019   0.001   TYR L 186 
 PHE   0.015   0.001   PHE A  79 
 TRP   0.024   0.002   TRP A 158 
 HIS   0.003   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (11121)
  covalent geometry    : angle       0.61221 (15124)
  SS BOND              : bond        0.00359 (   12)
  SS BOND              : angle       0.95231 (   24)
  hydrogen bonds       : bond        0.12939 (  419)
  hydrogen bonds       : angle       7.58703 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: J  145 LEU cc_start: 0.8710 (mt) cc_final: 0.8461 (mt)
REVERT: J  152 TYR cc_start: 0.7908 (p90) cc_final: 0.7511 (p90)
REVERT: J  204 ASN cc_start: 0.7890 (p0) cc_final: 0.7489 (p0)
REVERT: K   80 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7866 (mt-10)
REVERT: K  140 PHE cc_start: 0.8928 (p90) cc_final: 0.8463 (p90)
REVERT: K  143 ARG cc_start: 0.8375 (ttt-90) cc_final: 0.7987 (tpt90)
REVERT: H   73 ASP cc_start: 0.8279 (t0) cc_final: 0.7849 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1202
  time to fit residues: 28.2029
Evaluate side-chains
  145 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.0470
   chunk 124 optimal weight:    0.0670
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.4020

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 ASN
** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 159 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 177 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.112186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.071505 restraints weight = 20572.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.41
r_work: 0.2873 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.0941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11133  Z= 0.156
  Angle     :  0.583   7.547  15148  Z= 0.304
  Chirality :  0.044   0.154   1700
  Planarity :  0.005   0.075   1933
  Dihedral  :  4.776  71.658   1526
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  6.21 %
    Favored  : 92.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.71 (0.22), residues: 1400
  helix: -0.27 (0.58), residues: 86
  sheet: -0.94 (0.19), residues: 646
  loop : -1.34 (0.24), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  45 
 TYR   0.015   0.001   TYR H 151 
 PHE   0.017   0.001   PHE H 128 
 TRP   0.013   0.001   TRP A  35 
 HIS   0.003   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (11121)
  covalent geometry    : angle       0.58190 (15124)
  SS BOND              : bond        0.00315 (   12)
  SS BOND              : angle       0.91126 (   24)
  hydrogen bonds       : bond        0.03419 (  419)
  hydrogen bonds       : angle       5.94790 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 168
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: B  105 ASP cc_start: 0.7272 (t0) cc_final: 0.7058 (t0)
REVERT: B  123 GLU cc_start: 0.8721 (mp0) cc_final: 0.8517 (mp0)
REVERT: C   76 ASP cc_start: 0.8516 (t0) cc_final: 0.8273 (t0)
REVERT: J   43 GLN cc_start: 0.8530 (mm110) cc_final: 0.8305 (mm110)
REVERT: J  145 LEU cc_start: 0.8739 (mt) cc_final: 0.8519 (mt)
REVERT: J  152 TYR cc_start: 0.8329 (p90) cc_final: 0.7955 (p90)
REVERT: K  117 PHE cc_start: 0.8411 (m-80) cc_final: 0.7867 (m-80)
REVERT: K  143 ARG cc_start: 0.8584 (ttt-90) cc_final: 0.8183 (tpt90)
REVERT: L   24 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7597 (mmm160)
REVERT: L  211 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7055 (ttp-110)
REVERT: H   73 ASP cc_start: 0.8706 (t0) cc_final: 0.8125 (t70)
  outliers start: 10
  outliers final: 8
  residues processed: 173
  average time/residue: 0.1191
  time to fit residues: 27.9999
Evaluate side-chains
  156 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 GLN
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 134 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 178 GLN
K 161 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 210 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.110273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.069324 restraints weight = 20705.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.41
r_work: 0.2830 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  11133  Z= 0.214
  Angle     :  0.595   7.257  15148  Z= 0.311
  Chirality :  0.045   0.153   1700
  Planarity :  0.005   0.084   1933
  Dihedral  :  4.845  70.952   1526
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  8.99 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 are not related in a simple way.
  whole: -1.67 (0.22), residues: 1400
  helix: -0.12 (0.59), residues: 85
  sheet: -0.89 (0.19), residues: 652
  loop : -1.37 (0.24), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  45 
 TYR   0.017   0.002   TYR L  91 
 PHE   0.016   0.002   PHE A  79 
 TRP   0.011   0.002   TRP A  35 
 HIS   0.004   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (11121)
  covalent geometry    : angle       0.59385 (15124)
  SS BOND              : bond        0.00335 (   12)
  SS BOND              : angle       1.05605 (   24)
  hydrogen bonds       : bond        0.03350 (  419)
  hydrogen bonds       : angle       5.69738 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.324 
Fit side-chains
REVERT: C   76 ASP cc_start: 0.8561 (t0) cc_final: 0.8167 (t0)
REVERT: J  145 LEU cc_start: 0.8723 (mt) cc_final: 0.8489 (mt)
REVERT: J  152 TYR cc_start: 0.8356 (p90) cc_final: 0.7972 (p90)
REVERT: K  140 PHE cc_start: 0.8780 (p90) cc_final: 0.8298 (p90)
REVERT: K  143 ARG cc_start: 0.8592 (ttt-90) cc_final: 0.8171 (tpt90)
REVERT: K  168 ASP cc_start: 0.8738 (t0) cc_final: 0.8309 (t0)
REVERT: K  171 ASP cc_start: 0.8385 (p0) cc_final: 0.8095 (p0)
REVERT: L   24 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7639 (mmm160)
REVERT: L  134 CYS cc_start: 0.7534 (t) cc_final: 0.7169 (t)
REVERT: L  142 ARG cc_start: 0.8444 (tpt90) cc_final: 0.8112 (tpt90)
REVERT: L  158 ASN cc_start: 0.8920 (p0) cc_final: 0.8696 (p0)
REVERT: L  189 HIS cc_start: 0.8213 (m170) cc_final: 0.7838 (m170)
REVERT: L  210 ASN cc_start: 0.8393 (m-40) cc_final: 0.8035 (m-40)
REVERT: L  211 ARG cc_start: 0.7848 (mtm180) cc_final: 0.7254 (mtm180)
REVERT: H    6 GLU cc_start: 0.8799 (mp0) cc_final: 0.8490 (mp0)
REVERT: H   73 ASP cc_start: 0.8673 (t0) cc_final: 0.8290 (t70)
  outliers start: 20
  outliers final: 17
  residues processed: 164
  average time/residue: 0.1162
  time to fit residues: 25.8470
Evaluate side-chains
  165 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 GLN
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 136 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 135 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0170
   chunk 126 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   overall best weight:    2.2026

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

Flipped N/Q/H residues before XYZ refinement:
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 204 ASN
K 161 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 161 ASN
H 177 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.110337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.069468 restraints weight = 20568.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.40
r_work: 0.2834 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  11133  Z= 0.202
  Angle     :  0.581   7.379  15148  Z= 0.303
  Chirality :  0.044   0.152   1700
  Planarity :  0.005   0.087   1933
  Dihedral  :  4.803  70.850   1526
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.95 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.56 (0.22), residues: 1400
  helix: -0.05 (0.59), residues: 85
  sheet: -0.79 (0.19), residues: 655
  loop : -1.33 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  45 
 TYR   0.017   0.002   TYR H 151 
 PHE   0.015   0.001   PHE A  79 
 TRP   0.012   0.002   TRP J 161 
 HIS   0.004   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (11121)
  covalent geometry    : angle       0.58029 (15124)
  SS BOND              : bond        0.00268 (   12)
  SS BOND              : angle       0.88758 (   24)
  hydrogen bonds       : bond        0.03176 (  419)
  hydrogen bonds       : angle       5.54719 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   76 ASP cc_start: 0.8573 (t0) cc_final: 0.8116 (t0)
REVERT: J  145 LEU cc_start: 0.8721 (mt) cc_final: 0.8484 (mt)
REVERT: J  152 TYR cc_start: 0.8354 (p90) cc_final: 0.7942 (p90)
REVERT: K  143 ARG cc_start: 0.8601 (ttt-90) cc_final: 0.8201 (tpt90)
REVERT: K  168 ASP cc_start: 0.8741 (t0) cc_final: 0.8228 (t0)
REVERT: K  171 ASP cc_start: 0.8359 (p0) cc_final: 0.8115 (p0)
REVERT: L   24 ARG cc_start: 0.8009 (mtp-110) cc_final: 0.7685 (mmm160)
REVERT: L  134 CYS cc_start: 0.7728 (t) cc_final: 0.7363 (t)
REVERT: L  142 ARG cc_start: 0.8441 (tpt90) cc_final: 0.8107 (tpt90)
REVERT: L  158 ASN cc_start: 0.8909 (p0) cc_final: 0.8602 (p0)
REVERT: L  189 HIS cc_start: 0.8134 (m170) cc_final: 0.7885 (m170)
REVERT: L  210 ASN cc_start: 0.8409 (m-40) cc_final: 0.8078 (m-40)
REVERT: L  211 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7410 (mtm180)
REVERT: H    6 GLU cc_start: 0.8835 (mp0) cc_final: 0.8613 (mp0)
REVERT: H   73 ASP cc_start: 0.8610 (t0) cc_final: 0.8237 (t70)
  outliers start: 25
  outliers final: 18
  residues processed: 175
  average time/residue: 0.1181
  time to fit residues: 28.5644
Evaluate side-chains
  167 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 132 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 73 optimal weight:   20.0000
   chunk 130 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 204 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.109691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.069051 restraints weight = 20478.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 2.36
r_work: 0.2830 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  11133  Z= 0.215
  Angle     :  0.588   7.701  15148  Z= 0.308
  Chirality :  0.044   0.156   1700
  Planarity :  0.005   0.089   1933
  Dihedral  :  4.815  70.732   1526
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.75 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.46 (0.22), residues: 1400
  helix: -0.05 (0.60), residues: 85
  sheet: -0.72 (0.20), residues: 651
  loop : -1.25 (0.24), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K  18 
 TYR   0.016   0.002   TYR L 140 
 PHE   0.016   0.002   PHE K 117 
 TRP   0.016   0.002   TRP J 161 
 HIS   0.004   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (11121)
  covalent geometry    : angle       0.58730 (15124)
  SS BOND              : bond        0.00274 (   12)
  SS BOND              : angle       0.84577 (   24)
  hydrogen bonds       : bond        0.03166 (  419)
  hydrogen bonds       : angle       5.47621 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 ARG cc_start: 0.6684 (tmt170) cc_final: 0.6069 (tmt170)
REVERT: C   76 ASP cc_start: 0.8527 (t0) cc_final: 0.8008 (t0)
REVERT: J  145 LEU cc_start: 0.8735 (mt) cc_final: 0.8513 (mt)
REVERT: J  152 TYR cc_start: 0.8359 (p90) cc_final: 0.7963 (p90)
REVERT: K  140 PHE cc_start: 0.8703 (p90) cc_final: 0.8340 (p90)
REVERT: K  143 ARG cc_start: 0.8593 (ttt-90) cc_final: 0.8167 (tpt90)
REVERT: K  168 ASP cc_start: 0.8820 (t0) cc_final: 0.8293 (t0)
REVERT: K  171 ASP cc_start: 0.8394 (p0) cc_final: 0.8113 (p0)
REVERT: L   24 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7705 (mmm160)
REVERT: L  134 CYS cc_start: 0.7655 (t) cc_final: 0.7314 (t)
REVERT: L  142 ARG cc_start: 0.8447 (tpt90) cc_final: 0.8104 (tpt90)
REVERT: L  158 ASN cc_start: 0.8901 (p0) cc_final: 0.8621 (p0)
REVERT: L  187 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7556 (mm-30)
REVERT: L  189 HIS cc_start: 0.8064 (m170) cc_final: 0.7735 (m170)
REVERT: L  199 GLN cc_start: 0.8468 (tt0) cc_final: 0.8265 (pt0)
REVERT: L  210 ASN cc_start: 0.8448 (m-40) cc_final: 0.8130 (m-40)
REVERT: L  211 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7591 (mtm180)
REVERT: H   73 ASP cc_start: 0.8625 (t0) cc_final: 0.8216 (t70)
REVERT: H   89 GLU cc_start: 0.9011 (pm20) cc_final: 0.8690 (pp20)
  outliers start: 28
  outliers final: 19
  residues processed: 173
  average time/residue: 0.1179
  time to fit residues: 28.0021
Evaluate side-chains
  165 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain L residue  211 ARG
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0870
   chunk 132 optimal weight:    7.9990
   chunk 118 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 126 optimal weight:    8.9990
   chunk 91 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    3.0164

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 204 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.108871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.067852 restraints weight = 20655.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 2.37
r_work: 0.2806 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  11133  Z= 0.260
  Angle     :  0.614   8.289  15148  Z= 0.322
  Chirality :  0.045   0.182   1700
  Planarity :  0.005   0.093   1933
  Dihedral  :  4.915  70.533   1526
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.32 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.50 (0.22), residues: 1400
  helix: -0.04 (0.60), residues: 85
  sheet: -0.74 (0.20), residues: 651
  loop : -1.29 (0.24), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K  18 
 TYR   0.019   0.002   TYR H 151 
 PHE   0.016   0.002   PHE H 128 
 TRP   0.037   0.002   TRP K  97 
 HIS   0.005   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (11121)
  covalent geometry    : angle       0.61345 (15124)
  SS BOND              : bond        0.00290 (   12)
  SS BOND              : angle       0.86259 (   24)
  hydrogen bonds       : bond        0.03281 (  419)
  hydrogen bonds       : angle       5.50561 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 ARG cc_start: 0.6674 (tmt170) cc_final: 0.6114 (tmt170)
REVERT: B  105 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7483 (m-30)
REVERT: C   76 ASP cc_start: 0.8555 (t0) cc_final: 0.7988 (t0)
REVERT: J    1 GLN cc_start: 0.8676 (pm20) cc_final: 0.8460 (pm20)
REVERT: J   43 GLN cc_start: 0.8645 (mm110) cc_final: 0.8421 (mm110)
REVERT: J  145 LEU cc_start: 0.8744 (mt) cc_final: 0.8536 (mt)
REVERT: J  152 TYR cc_start: 0.8367 (p90) cc_final: 0.7969 (p90)
REVERT: K  117 PHE cc_start: 0.8310 (m-80) cc_final: 0.7856 (m-80)
REVERT: K  143 ARG cc_start: 0.8607 (ttt-90) cc_final: 0.8260 (tpt90)
REVERT: K  168 ASP cc_start: 0.8910 (t0) cc_final: 0.8407 (t0)
REVERT: K  171 ASP cc_start: 0.8397 (p0) cc_final: 0.8095 (p0)
REVERT: L   24 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7708 (mmm160)
REVERT: L  142 ARG cc_start: 0.8466 (tpt90) cc_final: 0.8112 (tpt90)
REVERT: L  158 ASN cc_start: 0.8870 (p0) cc_final: 0.8523 (p0)
REVERT: L  187 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7590 (mm-30)
REVERT: L  199 GLN cc_start: 0.8544 (tt0) cc_final: 0.8341 (pt0)
REVERT: L  210 ASN cc_start: 0.8478 (m-40) cc_final: 0.8147 (m-40)
REVERT: L  211 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7610 (mtm180)
REVERT: H   34 MET cc_start: 0.9375 (mmm) cc_final: 0.9172 (mmp)
REVERT: H   73 ASP cc_start: 0.8649 (t0) cc_final: 0.8242 (t70)
REVERT: H   89 GLU cc_start: 0.8986 (pm20) cc_final: 0.8694 (pp20)
  outliers start: 30
  outliers final: 21
  residues processed: 166
  average time/residue: 0.1132
  time to fit residues: 26.0843
Evaluate side-chains
  164 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  105 ASP
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain L residue  211 ARG
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 59 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 123 optimal weight:    0.0980
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 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 = 0.3669 r_free = 0.3669 target = 0.111118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.070698 restraints weight = 20435.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 2.40
r_work: 0.2860 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2738
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2738 r_free = 0.2738    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2738 r_free = 0.2738    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2738
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11133  Z= 0.139
  Angle     :  0.567   6.859  15148  Z= 0.294
  Chirality :  0.044   0.165   1700
  Planarity :  0.005   0.094   1933
  Dihedral  :  4.757  70.815   1526
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.71 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.38 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.27 (0.22), residues: 1400
  helix:  0.16 (0.60), residues: 85
  sheet: -0.58 (0.20), residues: 645
  loop : -1.15 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K  18 
 TYR   0.015   0.001   TYR L 140 
 PHE   0.017   0.001   PHE H 128 
 TRP   0.019   0.002   TRP J 161 
 HIS   0.003   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (11121)
  covalent geometry    : angle       0.56627 (15124)
  SS BOND              : bond        0.00257 (   12)
  SS BOND              : angle       0.72095 (   24)
  hydrogen bonds       : bond        0.02882 (  419)
  hydrogen bonds       : angle       5.28089 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 ASP cc_start: 0.7565 (t0) cc_final: 0.7225 (m-30)
REVERT: C   76 ASP cc_start: 0.8511 (t0) cc_final: 0.7989 (t0)
REVERT: J  152 TYR cc_start: 0.8353 (p90) cc_final: 0.7956 (p90)
REVERT: J  189 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8173 (m)
REVERT: K  117 PHE cc_start: 0.8299 (m-80) cc_final: 0.7877 (m-80)
REVERT: K  143 ARG cc_start: 0.8571 (ttt-90) cc_final: 0.8262 (tpt90)
REVERT: K  168 ASP cc_start: 0.8932 (t0) cc_final: 0.8392 (t0)
REVERT: K  171 ASP cc_start: 0.8426 (p0) cc_final: 0.8084 (p0)
REVERT: L   24 ARG cc_start: 0.7969 (mtp-110) cc_final: 0.7675 (mmm160)
REVERT: L  123 GLU cc_start: 0.8269 (pm20) cc_final: 0.7992 (pm20)
REVERT: L  142 ARG cc_start: 0.8449 (tpt90) cc_final: 0.8116 (tpt90)
REVERT: L  158 ASN cc_start: 0.8811 (p0) cc_final: 0.8539 (p0)
REVERT: L  189 HIS cc_start: 0.8073 (m170) cc_final: 0.7858 (m170)
REVERT: L  210 ASN cc_start: 0.8413 (m-40) cc_final: 0.8108 (m-40)
REVERT: H   34 MET cc_start: 0.9345 (mmm) cc_final: 0.9112 (mmp)
REVERT: H   73 ASP cc_start: 0.8638 (t0) cc_final: 0.8235 (t70)
REVERT: H   89 GLU cc_start: 0.8969 (pm20) cc_final: 0.8689 (pp20)
REVERT: H  123 LYS cc_start: 0.8188 (tttm) cc_final: 0.7845 (tmtt)
  outliers start: 25
  outliers final: 19
  residues processed: 175
  average time/residue: 0.1182
  time to fit residues: 28.6473
Evaluate side-chains
  161 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain J residue  189 VAL
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  204 VAL
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 121 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 135 optimal weight:    1.9990
   chunk 68 optimal weight:    9.9990
   chunk 118 optimal weight:    8.9990
   chunk 93 optimal weight:    1.9990
   chunk 132 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 122 optimal weight:    0.7980
   chunk 105 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.110192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.069281 restraints weight = 20442.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.40
r_work: 0.2833 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  11133  Z= 0.197
  Angle     :  0.588   7.186  15148  Z= 0.305
  Chirality :  0.044   0.159   1700
  Planarity :  0.005   0.096   1933
  Dihedral  :  4.775  70.623   1526
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.64 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.03 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.28 (0.22), residues: 1400
  helix:  0.15 (0.60), residues: 85
  sheet: -0.58 (0.20), residues: 649
  loop : -1.16 (0.25), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K  18 
 TYR   0.020   0.001   TYR H 151 
 PHE   0.016   0.001   PHE H 128 
 TRP   0.017   0.002   TRP J 161 
 HIS   0.004   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (11121)
  covalent geometry    : angle       0.58816 (15124)
  SS BOND              : bond        0.00305 (   12)
  SS BOND              : angle       0.77086 (   24)
  hydrogen bonds       : bond        0.03020 (  419)
  hydrogen bonds       : angle       5.29108 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   76 ASP cc_start: 0.8530 (t0) cc_final: 0.7985 (t0)
REVERT: J  152 TYR cc_start: 0.8346 (p90) cc_final: 0.7950 (p90)
REVERT: K  117 PHE cc_start: 0.8306 (m-80) cc_final: 0.7869 (m-80)
REVERT: K  143 ARG cc_start: 0.8575 (ttt-90) cc_final: 0.8246 (tpt90)
REVERT: K  168 ASP cc_start: 0.8956 (t0) cc_final: 0.8473 (t0)
REVERT: K  171 ASP cc_start: 0.8445 (p0) cc_final: 0.8154 (p0)
REVERT: L   24 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7714 (mmm160)
REVERT: L  123 GLU cc_start: 0.8255 (pm20) cc_final: 0.7980 (pm20)
REVERT: L  142 ARG cc_start: 0.8411 (tpt90) cc_final: 0.8078 (tpt90)
REVERT: L  158 ASN cc_start: 0.8806 (p0) cc_final: 0.8515 (p0)
REVERT: L  199 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8318 (pt0)
REVERT: L  210 ASN cc_start: 0.8310 (m-40) cc_final: 0.8050 (m-40)
REVERT: H   34 MET cc_start: 0.9386 (mmm) cc_final: 0.9170 (mmp)
REVERT: H   73 ASP cc_start: 0.8622 (t0) cc_final: 0.8226 (t70)
REVERT: H   89 GLU cc_start: 0.8962 (pm20) cc_final: 0.8691 (pp20)
  outliers start: 25
  outliers final: 20
  residues processed: 163
  average time/residue: 0.1137
  time to fit residues: 25.7883
Evaluate side-chains
  161 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain L residue  199 GLN
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  204 VAL
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 73 optimal weight:   20.0000
   chunk 109 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 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 = 0.3680 r_free = 0.3680 target = 0.111862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.071281 restraints weight = 20311.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 2.42
r_work: 0.2882 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11133  Z= 0.134
  Angle     :  0.565   7.087  15148  Z= 0.292
  Chirality :  0.043   0.152   1700
  Planarity :  0.005   0.095   1933
  Dihedral  :  4.696  71.093   1526
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.79 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.62 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.15 (0.23), residues: 1400
  helix:  0.26 (0.60), residues: 85
  sheet: -0.44 (0.20), residues: 638
  loop : -1.14 (0.24), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG K  18 
 TYR   0.016   0.001   TYR L 140 
 PHE   0.018   0.001   PHE H 128 
 TRP   0.018   0.001   TRP A 158 
 HIS   0.004   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (11121)
  covalent geometry    : angle       0.56491 (15124)
  SS BOND              : bond        0.00286 (   12)
  SS BOND              : angle       0.71458 (   24)
  hydrogen bonds       : bond        0.02824 (  419)
  hydrogen bonds       : angle       5.16610 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   76 ASP cc_start: 0.8525 (t0) cc_final: 0.8008 (t0)
REVERT: J  152 TYR cc_start: 0.8341 (p90) cc_final: 0.7956 (p90)
REVERT: K  117 PHE cc_start: 0.8281 (m-80) cc_final: 0.7879 (m-80)
REVERT: K  143 ARG cc_start: 0.8547 (ttt-90) cc_final: 0.8237 (tpt90)
REVERT: K  168 ASP cc_start: 0.8959 (t0) cc_final: 0.8479 (t0)
REVERT: K  171 ASP cc_start: 0.8502 (p0) cc_final: 0.8184 (p0)
REVERT: L   24 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7664 (mmm160)
REVERT: L  123 GLU cc_start: 0.8205 (pm20) cc_final: 0.7960 (pm20)
REVERT: L  142 ARG cc_start: 0.8405 (tpt90) cc_final: 0.8119 (tpt90)
REVERT: L  158 ASN cc_start: 0.8800 (p0) cc_final: 0.8540 (p0)
REVERT: L  199 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8396 (pt0)
REVERT: L  210 ASN cc_start: 0.8193 (m-40) cc_final: 0.7960 (m-40)
REVERT: H   34 MET cc_start: 0.9342 (mmm) cc_final: 0.9113 (mmp)
REVERT: H   73 ASP cc_start: 0.8644 (t0) cc_final: 0.8279 (t70)
REVERT: H   89 GLU cc_start: 0.8963 (pm20) cc_final: 0.8705 (pp20)
REVERT: H  123 LYS cc_start: 0.8230 (tttm) cc_final: 0.7929 (tmtt)
  outliers start: 24
  outliers final: 19
  residues processed: 167
  average time/residue: 0.1073
  time to fit residues: 25.1961
Evaluate side-chains
  161 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain L residue  199 GLN
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  204 VAL
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 111 optimal weight:   10.0000
   chunk 81 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 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 = 0.3635 r_free = 0.3635 target = 0.108829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.067843 restraints weight = 20396.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 2.37
r_work: 0.2806 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079  11133  Z= 0.271
  Angle     :  0.640   7.866  15148  Z= 0.335
  Chirality :  0.045   0.161   1700
  Planarity :  0.005   0.098   1933
  Dihedral  :  4.868  70.700   1526
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.93 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 15.20 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.33 (0.22), residues: 1400
  helix:  0.08 (0.60), residues: 85
  sheet: -0.60 (0.20), residues: 648
  loop : -1.21 (0.24), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG K  18 
 TYR   0.023   0.002   TYR L 140 
 PHE   0.022   0.002   PHE H 128 
 TRP   0.022   0.002   TRP A 158 
 HIS   0.006   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00634 (11121)
  covalent geometry    : angle       0.63920 (15124)
  SS BOND              : bond        0.00308 (   12)
  SS BOND              : angle       0.84807 (   24)
  hydrogen bonds       : bond        0.03315 (  419)
  hydrogen bonds       : angle       5.37379 ( 1281)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7169 (m-30)
REVERT: C   76 ASP cc_start: 0.8560 (t0) cc_final: 0.7998 (t0)
REVERT: J  152 TYR cc_start: 0.8370 (p90) cc_final: 0.7978 (p90)
REVERT: K  117 PHE cc_start: 0.8341 (m-80) cc_final: 0.7873 (m-80)
REVERT: K  143 ARG cc_start: 0.8573 (ttt-90) cc_final: 0.8174 (tpt90)
REVERT: K  168 ASP cc_start: 0.8995 (t0) cc_final: 0.8532 (t0)
REVERT: K  171 ASP cc_start: 0.8482 (p0) cc_final: 0.8171 (p0)
REVERT: L   24 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7745 (mmm160)
REVERT: L  123 GLU cc_start: 0.8269 (pm20) cc_final: 0.7983 (pm20)
REVERT: L  142 ARG cc_start: 0.8384 (tpt90) cc_final: 0.8056 (tpt90)
REVERT: L  158 ASN cc_start: 0.8806 (p0) cc_final: 0.8507 (p0)
REVERT: L  199 GLN cc_start: 0.8724 (pt0) cc_final: 0.8452 (pt0)
REVERT: L  210 ASN cc_start: 0.8307 (m-40) cc_final: 0.7927 (m-40)
REVERT: H   34 MET cc_start: 0.9375 (mmm) cc_final: 0.9165 (mmp)
REVERT: H   73 ASP cc_start: 0.8630 (t0) cc_final: 0.8224 (t70)
REVERT: H   89 GLU cc_start: 0.8972 (pm20) cc_final: 0.8703 (pp20)
REVERT: H  123 LYS cc_start: 0.8219 (tttm) cc_final: 0.7935 (tmtt)
  outliers start: 21
  outliers final: 20
  residues processed: 157
  average time/residue: 0.1164
  time to fit residues: 25.2464
Evaluate side-chains
  158 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  105 ASP
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  204 VAL
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 81 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0980
   chunk 129 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  43 GLN
** K  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.112677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.072281 restraints weight = 20362.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 2.42
r_work: 0.2900 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11133  Z= 0.117
  Angle     :  0.581   7.508  15148  Z= 0.300
  Chirality :  0.043   0.150   1700
  Planarity :  0.005   0.095   1933
  Dihedral  :  4.702  71.093   1526
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.71 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.52 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.12 (0.22), residues: 1400
  helix:  0.32 (0.60), residues: 85
  sheet: -0.38 (0.20), residues: 622
  loop : -1.16 (0.24), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG K  18 
 TYR   0.018   0.001   TYR L 140 
 PHE   0.015   0.001   PHE H 128 
 TRP   0.018   0.002   TRP A  48 
 HIS   0.004   0.001   HIS L  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (11121)
  covalent geometry    : angle       0.58051 (15124)
  SS BOND              : bond        0.00264 (   12)
  SS BOND              : angle       0.70868 (   24)
  hydrogen bonds       : bond        0.02823 (  419)
  hydrogen bonds       : angle       5.16501 ( 1281)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3536.01 seconds
wall clock time: 61 minutes 4.41 seconds (3664.41 seconds total)