Starting phenix.real_space_refine
on Thu Nov 14 05:23:58 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsv_61784/11_2024/9jsv_61784.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsv_61784/11_2024/9jsv_61784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsv_61784/11_2024/9jsv_61784.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsv_61784/11_2024/9jsv_61784.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsv_61784/11_2024/9jsv_61784.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsv_61784/11_2024/9jsv_61784.cif"
  }
  resolution = 1.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.061
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       8      5.16       5
     C    1424      2.51       5
     N     360      2.21       5
     O     352      1.98       5
     H    2104      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 4248
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 531
          Classifications: {'peptide': 34}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "E"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 531
          Classifications: {'peptide': 34}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "B"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 531
          Classifications: {'peptide': 34}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "F"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 531
          Classifications: {'peptide': 34}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "C"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 531
          Classifications: {'peptide': 34}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "G"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 531
          Classifications: {'peptide': 34}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "D"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 531
          Classifications: {'peptide': 34}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "H"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 531
          Classifications: {'peptide': 34}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
  Time building chain proxies: 2.70, per 1000 atoms: 0.64
  Number of scatterers: 4248
  At special positions: 0
  Unit cell: (85.2048, 83.448, 44.7984, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       8     16.00
     O     352      8.00
     N     360      7.00
     C    1424      6.00
     H    2104      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 287.1 milliseconds
  

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  448

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 60.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 163
      removed outlier: 6.571A  pdb=" N   VAL A 150 " --> pdb=" O   TYR B 151 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   TRP B 153 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   VAL A 152 " --> pdb=" O   TRP B 153 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   THR B 155 " --> pdb=" O   VAL A 152 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   LYS A 154 " --> pdb=" O   THR B 155 " (cutoff:3.500A)
      removed outlier: 10.630A  pdb=" N   GLY B 157 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      removed outlier: 9.084A  pdb=" N   TRP A 156 " --> pdb=" O   GLY B 157 " (cutoff:3.500A)
      removed outlier: 10.399A  pdb=" N   TYR B 159 " --> pdb=" O   TRP A 156 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   GLN A 158 " --> pdb=" O   TYR B 159 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   GLN B 161 " --> pdb=" O   GLN A 158 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   TRP A 160 " --> pdb=" O   GLN B 161 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   LEU B 163 " --> pdb=" O   TRP A 160 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL A 162 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   THR C 155 " --> pdb=" O   LYS B 154 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   TRP B 156 " --> pdb=" O   THR C 155 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   GLY C 157 " --> pdb=" O   TRP B 156 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   GLN B 158 " --> pdb=" O   GLY C 157 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   TYR C 159 " --> pdb=" O   GLN B 158 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   THR D 155 " --> pdb=" O   LYS C 154 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   TRP C 156 " --> pdb=" O   THR D 155 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   GLY D 157 " --> pdb=" O   TRP C 156 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   GLN C 158 " --> pdb=" O   GLY D 157 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   TYR D 159 " --> pdb=" O   GLN C 158 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 172
      removed outlier: 7.981A  pdb=" N   SER A 168 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   SER B 171 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
      removed outlier: 8.831A  pdb=" N   LEU A 170 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   SER B 168 " --> pdb=" O   GLY C 169 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   SER C 171 " --> pdb=" O   SER B 168 " (cutoff:3.500A)
      removed outlier: 8.807A  pdb=" N   LEU B 170 " --> pdb=" O   SER C 171 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   SER C 168 " --> pdb=" O   GLY D 169 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   SER D 171 " --> pdb=" O   SER C 168 " (cutoff:3.500A)
      removed outlier: 8.863A  pdb=" N   LEU C 170 " --> pdb=" O   SER D 171 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 179
      removed outlier: 6.502A  pdb=" N   ARG A 176 " --> pdb=" O   ALA B 177 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   LEU B 179 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   MET A 178 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   ARG B 176 " --> pdb=" O   ALA C 177 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   LEU C 179 " --> pdb=" O   ARG B 176 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   MET B 178 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ARG C 176 " --> pdb=" O   ALA D 177 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   LEU D 179 " --> pdb=" O   ARG C 176 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   MET C 178 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 150 through 153
      removed outlier: 6.614A  pdb=" N   VAL E 150 " --> pdb=" O   TYR F 151 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   TRP F 153 " --> pdb=" O   VAL E 150 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL E 152 " --> pdb=" O   TRP F 153 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   VAL F 150 " --> pdb=" O   TYR G 151 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   TRP G 153 " --> pdb=" O   VAL F 150 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   VAL F 152 " --> pdb=" O   TRP G 153 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 156 through 163
      removed outlier: 6.937A  pdb=" N   GLY F 157 " --> pdb=" O   TRP E 156 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLN E 158 " --> pdb=" O   GLY F 157 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   TYR F 159 " --> pdb=" O   GLN E 158 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   GLY G 157 " --> pdb=" O   TRP F 156 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   GLN F 158 " --> pdb=" O   GLY G 157 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   TYR G 159 " --> pdb=" O   GLN F 158 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   GLY H 157 " --> pdb=" O   TRP G 156 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN G 158 " --> pdb=" O   GLY H 157 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   TYR H 159 " --> pdb=" O   GLN G 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 167 through 172
      removed outlier: 7.971A  pdb=" N   SER E 168 " --> pdb=" O   GLY F 169 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   SER F 171 " --> pdb=" O   SER E 168 " (cutoff:3.500A)
      removed outlier: 8.910A  pdb=" N   LEU E 170 " --> pdb=" O   SER F 171 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   SER F 168 " --> pdb=" O   GLY G 169 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   SER G 171 " --> pdb=" O   SER F 168 " (cutoff:3.500A)
      removed outlier: 8.851A  pdb=" N   LEU F 170 " --> pdb=" O   SER G 171 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   SER G 168 " --> pdb=" O   GLY H 169 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   SER H 171 " --> pdb=" O   SER G 168 " (cutoff:3.500A)
      removed outlier: 8.876A  pdb=" N   LEU G 170 " --> pdb=" O   SER H 171 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 175 through 179
      removed outlier: 6.506A  pdb=" N   ARG E 176 " --> pdb=" O   ALA F 177 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   LEU F 179 " --> pdb=" O   ARG E 176 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   MET E 178 " --> pdb=" O   LEU F 179 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ARG F 176 " --> pdb=" O   ALA G 177 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   LEU G 179 " --> pdb=" O   ARG F 176 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   MET F 178 " --> pdb=" O   LEU G 179 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ARG G 176 " --> pdb=" O   ALA H 177 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   LEU H 179 " --> pdb=" O   ARG G 176 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   MET G 178 " --> pdb=" O   LEU H 179 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    31 hydrogen bonds defined for protein.
    93 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: 1.49

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 2104
        1.12 -     1.29: 288
        1.29 -     1.47: 947
        1.47 -     1.64: 973
        1.64 -     1.82: 16
  Bond restraints: 4328
  Sorted by residual:
  bond pdb=" CD2 TYR G 159 "
       pdb=" HD2 TYR G 159 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   LEU F 179 "
       pdb=" H   LEU F 179 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   ILE C 172 "
       pdb=" H   ILE C 172 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   MET A 178 "
       pdb=" H   MET A 178 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   TYR F 159 "
       pdb=" H   TYR F 159 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 4323 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 5435
        1.65 -     3.29: 1626
        3.29 -     4.94: 415
        4.94 -     6.59: 243
        6.59 -     8.23: 25
  Bond angle restraints: 7744
  Sorted by residual:
  angle pdb=" C   GLY E 165 "
        pdb=" N   PRO E 166 "
        pdb=" CA  PRO E 166 "
      ideal   model   delta    sigma   weight residual
     119.90  124.25   -4.35 1.02e+00 9.61e-01 1.82e+01
  angle pdb=" CB  HIS G 182 "
        pdb=" CG  HIS G 182 "
        pdb=" CD2 HIS G 182 "
      ideal   model   delta    sigma   weight residual
     131.20  125.72    5.48 1.30e+00 5.92e-01 1.78e+01
  angle pdb=" OE1 GLN F 161 "
        pdb=" CD  GLN F 161 "
        pdb=" NE2 GLN F 161 "
      ideal   model   delta    sigma   weight residual
     122.60  118.40    4.20 1.00e+00 1.00e+00 1.77e+01
  angle pdb=" C   GLY H 165 "
        pdb=" N   PRO H 166 "
        pdb=" CA  PRO H 166 "
      ideal   model   delta    sigma   weight residual
     119.78  124.06   -4.28 1.03e+00 9.43e-01 1.73e+01
  angle pdb=" CB  HIS H 182 "
        pdb=" CG  HIS H 182 "
        pdb=" CD2 HIS H 182 "
      ideal   model   delta    sigma   weight residual
     131.20  125.84    5.36 1.30e+00 5.92e-01 1.70e+01
  ... (remaining 7739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.10: 1729
       13.10 -    26.21: 110
       26.21 -    39.31: 28
       39.31 -    52.42: 55
       52.42 -    65.52: 94
  Dihedral angle restraints: 2016
    sinusoidal: 1016
      harmonic: 1000
  Sorted by residual:
  dihedral pdb=" CA  TRP B 160 "
           pdb=" C   TRP B 160 "
           pdb=" N   GLN B 161 "
           pdb=" CA  GLN B 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.79   15.21     0      5.00e+00 4.00e-02 9.26e+00
  dihedral pdb=" C   TYR C 159 "
           pdb=" N   TYR C 159 "
           pdb=" CA  TYR C 159 "
           pdb=" CB  TYR C 159 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.83    7.23     0      2.50e+00 1.60e-01 8.35e+00
  dihedral pdb=" CA  TRP D 160 "
           pdb=" C   TRP D 160 "
           pdb=" N   GLN D 161 "
           pdb=" CA  GLN D 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.56   14.44     0      5.00e+00 4.00e-02 8.34e+00
  ... (remaining 2013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 114
       0.044 -    0.087: 99
       0.087 -    0.130: 63
       0.130 -    0.174: 27
       0.174 -    0.217: 9
  Chirality restraints: 312
  Sorted by residual:
  chirality pdb=" CA  TYR E 159 "
            pdb=" N   TYR E 159 "
            pdb=" C   TYR E 159 "
            pdb=" CB  TYR E 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CB  THR D 155 "
            pdb=" CA  THR D 155 "
            pdb=" OG1 THR D 155 "
            pdb=" CG2 THR D 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  TYR A 159 "
            pdb=" N   TYR A 159 "
            pdb=" C   TYR A 159 "
            pdb=" CB  TYR A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 309 not shown)

  Planarity restraints: 608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 160 "    0.040 2.00e-02 2.50e+03   3.56e-02 5.08e+01
        pdb=" CG  TRP C 160 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 160 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 160 "   -0.042 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 160 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 160 "   -0.055 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 160 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 160 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 160 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 160 "    0.018 2.00e-02 2.50e+03
        pdb=" HD1 TRP C 160 "    0.054 2.00e-02 2.50e+03
        pdb=" HE1 TRP C 160 "    0.034 2.00e-02 2.50e+03
        pdb=" HE3 TRP C 160 "   -0.026 2.00e-02 2.50e+03
        pdb=" HZ2 TRP C 160 "   -0.020 2.00e-02 2.50e+03
        pdb=" HZ3 TRP C 160 "    0.034 2.00e-02 2.50e+03
        pdb=" HH2 TRP C 160 "    0.064 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 160 "    0.013 2.00e-02 2.50e+03   3.28e-02 4.29e+01
        pdb=" CG  TRP D 160 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 160 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 160 "   -0.047 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 160 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 160 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 160 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 160 "   -0.039 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 160 "    0.015 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 160 "    0.004 2.00e-02 2.50e+03
        pdb=" HD1 TRP D 160 "    0.051 2.00e-02 2.50e+03
        pdb=" HE1 TRP D 160 "    0.053 2.00e-02 2.50e+03
        pdb=" HE3 TRP D 160 "   -0.005 2.00e-02 2.50e+03
        pdb=" HZ2 TRP D 160 "   -0.025 2.00e-02 2.50e+03
        pdb=" HZ3 TRP D 160 "    0.046 2.00e-02 2.50e+03
        pdb=" HH2 TRP D 160 "    0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 160 "    0.036 2.00e-02 2.50e+03   3.20e-02 4.11e+01
        pdb=" CG  TRP B 160 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 160 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 160 "   -0.051 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 160 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 160 "   -0.051 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 160 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 160 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 160 "    0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 160 "    0.008 2.00e-02 2.50e+03
        pdb=" HD1 TRP B 160 "    0.045 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 160 "    0.039 2.00e-02 2.50e+03
        pdb=" HE3 TRP B 160 "   -0.017 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B 160 "   -0.010 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B 160 "    0.042 2.00e-02 2.50e+03
        pdb=" HH2 TRP B 160 "    0.041 2.00e-02 2.50e+03
  ... (remaining 605 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 686
        2.32 -     2.89: 8600
        2.89 -     3.46: 10713
        3.46 -     4.03: 15652
        4.03 -     4.60: 20637
  Nonbonded interactions: 56288
  Sorted by model distance:
  nonbonded pdb=" O   SER F 168 "
            pdb=" H   GLY G 169 "
     model   vdw
     1.752 2.450
  nonbonded pdb=" O   SER G 168 "
            pdb=" H   GLY H 169 "
     model   vdw
     1.769 2.450
  nonbonded pdb=" O   SER B 168 "
            pdb=" H   GLY C 169 "
     model   vdw
     1.775 2.450
  nonbonded pdb="HE21 GLN B 161 "
            pdb=" OE1 GLN C 161 "
     model   vdw
     1.775 2.450
  nonbonded pdb=" O   SER C 168 "
            pdb=" H   GLY D 169 "
     model   vdw
     1.788 2.450
  ... (remaining 56283 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.040
  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:             0.070
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.680
  Find NCS groups from input model:        0.140
  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:15.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6808
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      :  0.013   0.038   2224  Z= 0.816
  Angle     :  1.775   6.533   3032  Z= 1.192
  Chirality :  0.085   0.217    312
  Planarity :  0.008   0.030    352
  Dihedral  : 11.539  53.934    704
  Min Nonbonded Distance : 2.696

Molprobity Statistics.
  All-atom Clashscore : 1.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  0.93 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.45), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.65 (0.34), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.013   TRP B 160 
 HIS   0.004   0.002   HIS E 182 
 PHE   0.016   0.007   PHE H 149 
 TYR   0.058   0.011   TYR A 159 
 ARG   0.003   0.001   ARG B 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: E  178 MET cc_start: 0.7913 (mtm) cc_final: 0.7584 (mtp)
REVERT: F  178 MET cc_start: 0.7876 (mtm) cc_final: 0.7523 (mtp)
REVERT: G  178 MET cc_start: 0.7627 (mtm) cc_final: 0.7410 (mtp)
REVERT: D  178 MET cc_start: 0.7232 (mtm) cc_final: 0.6963 (mtp)
REVERT: H  170 LEU cc_start: 0.6935 (tt) cc_final: 0.6716 (tp)
REVERT: H  178 MET cc_start: 0.7496 (mtm) cc_final: 0.7102 (mtp)
  outliers start: 3
  outliers final: 0
  residues processed: 34
  average time/residue: 2.1888
  time to fit residues: 76.3207
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    6.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2224  Z= 0.197
  Angle     :  0.545   4.194   3032  Z= 0.303
  Chirality :  0.054   0.135    312
  Planarity :  0.003   0.018    352
  Dihedral  :  4.014  12.051    288
  Min Nonbonded Distance : 2.659

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.45), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.51 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 153 
 HIS   0.002   0.000   HIS E 182 
 PHE   0.003   0.001   PHE G 149 
 TYR   0.010   0.002   TYR C 151 
 ARG   0.001   0.000   ARG A 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.375 
Fit side-chains
REVERT: E  178 MET cc_start: 0.8028 (mtm) cc_final: 0.7712 (mtp)
REVERT: B  154 LYS cc_start: 0.6648 (mttm) cc_final: 0.6281 (mttt)
REVERT: B  181 THR cc_start: 0.6991 (m) cc_final: 0.6635 (p)
REVERT: F  178 MET cc_start: 0.7898 (mtm) cc_final: 0.7518 (mtp)
REVERT: G  178 MET cc_start: 0.7829 (mtm) cc_final: 0.7585 (mtp)
REVERT: D  178 MET cc_start: 0.7380 (mtm) cc_final: 0.7115 (mtp)
REVERT: H  178 MET cc_start: 0.7623 (mtm) cc_final: 0.7245 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 3.2389
  time to fit residues: 69.3594
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:   20.0000
   chunk 23 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    6.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2224  Z= 0.196
  Angle     :  0.532   4.268   3032  Z= 0.298
  Chirality :  0.054   0.138    312
  Planarity :  0.003   0.020    352
  Dihedral  :  3.916  11.213    288
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.44), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.68 (0.34), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 153 
 HIS   0.002   0.001   HIS A 182 
 PHE   0.004   0.001   PHE G 149 
 TYR   0.010   0.002   TYR C 151 
 ARG   0.001   0.000   ARG E 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.301 
Fit side-chains
REVERT: E  178 MET cc_start: 0.8031 (mtm) cc_final: 0.7734 (mtp)
REVERT: B  154 LYS cc_start: 0.6671 (mttm) cc_final: 0.6342 (mttt)
REVERT: F  178 MET cc_start: 0.7935 (mtm) cc_final: 0.7530 (mtp)
REVERT: G  178 MET cc_start: 0.7800 (mtm) cc_final: 0.7530 (mtp)
REVERT: D  178 MET cc_start: 0.7448 (mtm) cc_final: 0.7204 (mtp)
REVERT: H  178 MET cc_start: 0.7652 (mtm) cc_final: 0.7257 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 3.7435
  time to fit residues: 68.6566
Evaluate side-chains
  18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:    0.9980
   chunk 17 optimal weight:   20.0000
   chunk 9 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    3.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2224  Z= 0.127
  Angle     :  0.439   4.190   3032  Z= 0.249
  Chirality :  0.052   0.137    312
  Planarity :  0.003   0.020    352
  Dihedral  :  3.459  10.086    288
  Min Nonbonded Distance : 2.670

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.45), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.60 (0.34), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 153 
 HIS   0.001   0.000   HIS E 182 
 PHE   0.002   0.000   PHE G 149 
 TYR   0.008   0.001   TYR F 159 
 ARG   0.001   0.000   ARG C 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.410 
Fit side-chains
REVERT: E  178 MET cc_start: 0.8048 (mtm) cc_final: 0.7719 (mtp)
REVERT: B  154 LYS cc_start: 0.6627 (mttm) cc_final: 0.6324 (mttt)
REVERT: B  181 THR cc_start: 0.7058 (m) cc_final: 0.6766 (p)
REVERT: F  178 MET cc_start: 0.7867 (mtm) cc_final: 0.7486 (mtp)
REVERT: G  178 MET cc_start: 0.7804 (mtm) cc_final: 0.7541 (mtp)
REVERT: H  178 MET cc_start: 0.7662 (mtm) cc_final: 0.7274 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 3.3367
  time to fit residues: 68.1154
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 1 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    2.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2224  Z= 0.104
  Angle     :  0.405   4.304   3032  Z= 0.229
  Chirality :  0.051   0.136    312
  Planarity :  0.002   0.021    352
  Dihedral  :  3.178   8.765    288
  Min Nonbonded Distance : 2.672

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.46), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.51 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 153 
 HIS   0.001   0.000   HIS A 182 
 PHE   0.001   0.000   PHE G 149 
 TYR   0.007   0.001   TYR F 159 
 ARG   0.001   0.000   ARG F 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.363 
Fit side-chains
REVERT: E  178 MET cc_start: 0.8053 (mtm) cc_final: 0.7708 (mtp)
REVERT: B  154 LYS cc_start: 0.6591 (mttm) cc_final: 0.6338 (mttt)
REVERT: B  181 THR cc_start: 0.7089 (m) cc_final: 0.6809 (p)
REVERT: F  178 MET cc_start: 0.7869 (mtm) cc_final: 0.7488 (mtp)
REVERT: G  178 MET cc_start: 0.7772 (mtm) cc_final: 0.7499 (mtp)
REVERT: H  178 MET cc_start: 0.7600 (mtm) cc_final: 0.7215 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 2.9701
  time to fit residues: 60.5621
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 14 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   overall best weight:    3.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2224  Z= 0.140
  Angle     :  0.445   4.070   3032  Z= 0.251
  Chirality :  0.052   0.139    312
  Planarity :  0.002   0.019    352
  Dihedral  :  3.400   9.979    288
  Min Nonbonded Distance : 2.671

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.46), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.55 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 153 
 HIS   0.001   0.000   HIS B 182 
 PHE   0.002   0.000   PHE E 149 
 TYR   0.007   0.001   TYR C 151 
 ARG   0.001   0.000   ARG E 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.398 
Fit side-chains
REVERT: E  178 MET cc_start: 0.8039 (mtm) cc_final: 0.7720 (mtp)
REVERT: B  154 LYS cc_start: 0.6609 (mttm) cc_final: 0.6337 (mttt)
REVERT: F  178 MET cc_start: 0.7881 (mtm) cc_final: 0.7514 (mtp)
REVERT: G  178 MET cc_start: 0.7784 (mtm) cc_final: 0.7473 (mtp)
REVERT: H  178 MET cc_start: 0.7648 (mtm) cc_final: 0.7257 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 3.5103
  time to fit residues: 67.9776
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    3.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2224  Z= 0.119
  Angle     :  0.420   4.227   3032  Z= 0.237
  Chirality :  0.051   0.137    312
  Planarity :  0.002   0.020    352
  Dihedral  :  3.238   9.305    288
  Min Nonbonded Distance : 2.673

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.46), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.52 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 153 
 HIS   0.001   0.000   HIS A 182 
 PHE   0.002   0.000   PHE G 149 
 TYR   0.008   0.001   TYR F 159 
 ARG   0.000   0.000   ARG G 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.365 
Fit side-chains
REVERT: E  178 MET cc_start: 0.8055 (mtm) cc_final: 0.7723 (mtp)
REVERT: B  154 LYS cc_start: 0.6584 (mttm) cc_final: 0.6319 (mttt)
REVERT: B  181 THR cc_start: 0.7106 (m) cc_final: 0.6841 (p)
REVERT: F  178 MET cc_start: 0.7861 (mtm) cc_final: 0.7478 (mtp)
REVERT: G  178 MET cc_start: 0.7758 (mtm) cc_final: 0.7503 (mtp)
REVERT: H  178 MET cc_start: 0.7622 (mtm) cc_final: 0.7222 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 3.3049
  time to fit residues: 67.4116
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    3.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2224  Z= 0.132
  Angle     :  0.435   4.116   3032  Z= 0.245
  Chirality :  0.052   0.139    312
  Planarity :  0.002   0.019    352
  Dihedral  :  3.323   9.860    288
  Min Nonbonded Distance : 2.674

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.46), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.55 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 153 
 HIS   0.001   0.000   HIS E 182 
 PHE   0.002   0.000   PHE E 149 
 TYR   0.007   0.001   TYR C 151 
 ARG   0.001   0.000   ARG E 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.394 
Fit side-chains
REVERT: E  178 MET cc_start: 0.8039 (mtm) cc_final: 0.7727 (mtp)
REVERT: B  154 LYS cc_start: 0.6612 (mttm) cc_final: 0.6338 (mttt)
REVERT: F  178 MET cc_start: 0.7879 (mtm) cc_final: 0.7512 (mtp)
REVERT: G  178 MET cc_start: 0.7772 (mtm) cc_final: 0.7506 (mtp)
REVERT: H  178 MET cc_start: 0.7652 (mtm) cc_final: 0.7256 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 3.4840
  time to fit residues: 67.4957
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 11 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    5.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2224  Z= 0.169
  Angle     :  0.470   3.985   3032  Z= 0.265
  Chirality :  0.053   0.140    312
  Planarity :  0.002   0.019    352
  Dihedral  :  3.493  10.430    288
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.46), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.61 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F 153 
 HIS   0.001   0.000   HIS E 182 
 PHE   0.003   0.001   PHE G 149 
 TYR   0.008   0.002   TYR C 151 
 ARG   0.001   0.000   ARG C 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.333 
Fit side-chains
REVERT: E  178 MET cc_start: 0.8032 (mtm) cc_final: 0.7733 (mtp)
REVERT: B  154 LYS cc_start: 0.6634 (mttm) cc_final: 0.6368 (mttt)
REVERT: F  178 MET cc_start: 0.7938 (mtm) cc_final: 0.7479 (mtp)
REVERT: G  178 MET cc_start: 0.7771 (mtm) cc_final: 0.7473 (mtp)
REVERT: H  178 MET cc_start: 0.7662 (mtm) cc_final: 0.7263 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 3.5735
  time to fit residues: 69.2010
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 2 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 14 optimal weight:   20.0000
   overall best weight:    5.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2224  Z= 0.174
  Angle     :  0.471   3.977   3032  Z= 0.265
  Chirality :  0.052   0.139    312
  Planarity :  0.003   0.018    352
  Dihedral  :  3.508  10.485    288
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.46), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.61 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F 153 
 HIS   0.001   0.000   HIS E 182 
 PHE   0.002   0.000   PHE G 149 
 TYR   0.009   0.002   TYR C 151 
 ARG   0.000   0.000   ARG H 176 

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.342 
Fit side-chains
REVERT: E  178 MET cc_start: 0.8031 (mtm) cc_final: 0.7737 (mtp)
REVERT: B  154 LYS cc_start: 0.6614 (mttm) cc_final: 0.6343 (mttt)
REVERT: F  178 MET cc_start: 0.7936 (mtm) cc_final: 0.7487 (mtp)
REVERT: G  178 MET cc_start: 0.7770 (mtm) cc_final: 0.7476 (mtp)
REVERT: H  178 MET cc_start: 0.7682 (mtm) cc_final: 0.7281 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 3.4414
  time to fit residues: 66.6486
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 8 optimal weight:   20.0000
   chunk 23 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    5.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.142360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.119513 restraints weight = 4684.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.22
r_work: 0.3448 rms_B_bonded: 1.28 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 2.04 restraints_weight: 0.2500
r_work: 0.3243 rms_B_bonded: 4.69 restraints_weight: 0.1250
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9355
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2224  Z= 0.174
  Angle     :  0.474   3.979   3032  Z= 0.267
  Chirality :  0.053   0.140    312
  Planarity :  0.003   0.019    352
  Dihedral  :  3.520  10.504    288
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.45), residues: 256
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.63 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F 153 
 HIS   0.001   0.000   HIS E 182 
 PHE   0.003   0.000   PHE G 149 
 TYR   0.008   0.002   TYR C 151 
 ARG   0.000   0.000   ARG C 176 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2661.97 seconds
wall clock time: 48 minutes 40.61 seconds (2920.61 seconds total)