Starting phenix.real_space_refine
on Tue Jan 14 20:32:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vi2_43246/01_2025/8vi2_43246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vi2_43246/01_2025/8vi2_43246.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vi2_43246/01_2025/8vi2_43246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vi2_43246/01_2025/8vi2_43246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vi2_43246/01_2025/8vi2_43246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vi2_43246/01_2025/8vi2_43246.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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      27      5.16       5
     C    5004      2.51       5
     N    1141      2.21       5
     O    1210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 7382
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2473
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 308, 2449
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 13, 'TRANS': 294}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 308, 2452
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 13, 'TRANS': 294}
          bond proxies already assigned to first conformer: 2507
      Conformer: "C"
        Number of residues, atoms: 307, 2434
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 13, 'TRANS': 293}
          Chain breaks: 1
          Unresolved chain link angles: 6
          Unresolved chain link dihedrals: 12
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 3
          bond proxies already assigned to first conformer: 2507
    Chain: "B"
      Number of atoms: 2457
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 308, 2452
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 13, 'TRANS': 294}
      Conformer: "B"
        Number of residues, atoms: 308, 2452
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 13, 'TRANS': 294}
          bond proxies already assigned to first conformer: 2527
    Chain: "C"
      Number of atoms: 2452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2452
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 13, 'TRANS': 294}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLU A  69 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU A  69 " occ=0.50
  Time building chain proxies: 9.13, per 1000 atoms: 1.24
  Number of scatterers: 7382
  At special positions: 0
  Unit cell: (92.258, 100.748, 62.26, 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      27     16.00
     O    1210      8.00
     N    1141      7.00
     C    5004      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1716

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 0 sheets defined
      90.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 13
    Processing helix  chain 'A' and resid 14 through 29
    Processing helix  chain 'A' and resid 34 through 66
      removed outlier: 3.883A  pdb=" N   ARG A  38 " --> pdb=" O   PHE A  34 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   MET A  39 " --> pdb=" O   PRO A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 76
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.973A  pdb=" N   ILE A  83 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA A  84 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 79 through 84'
    Processing helix  chain 'A' and resid 84 through 98
    Processing helix  chain 'A' and resid 101 through 124
    Processing helix  chain 'A' and resid 125 through 130
    Processing helix  chain 'A' and resid 134 through 138
      removed outlier: 3.747A  pdb=" N   THR A 138 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 141
      No H-bonds generated for 'chain 'A' and resid 139 through 141'
    Processing helix  chain 'A' and resid 142 through 147
      removed outlier: 3.827A  pdb=" N   ALA A 146 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 161
    Processing helix  chain 'A' and resid 162 through 191
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 194 through 204
      removed outlier: 4.734A  pdb=" N   ALA A 199 " --> pdb=" O   GLN A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 219
      removed outlier: 3.989A  pdb=" N   PHE A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL A 212 " --> pdb=" O   ALA A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 249
      Proline residue:  A 246  - end of helix
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 257 through 277
      removed outlier: 4.002A  pdb=" N   SER A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   PHE A 262 " --> pdb=" O   TRP A 258 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   GLY A 263 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A 273 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 309
    Processing helix  chain 'B' and resid 10 through 13
    Processing helix  chain 'B' and resid 14 through 29
    Processing helix  chain 'B' and resid 34 through 66
      removed outlier: 3.877A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  34 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   MET B  39 " --> pdb=" O   PRO B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 76
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.943A  pdb=" N   ILE B  83 " --> pdb=" O   ARG B  79 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ALA B  84 " --> pdb=" O   PHE B  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 79 through 84'
    Processing helix  chain 'B' and resid 84 through 98
    Processing helix  chain 'B' and resid 101 through 124
    Processing helix  chain 'B' and resid 125 through 130
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.746A  pdb=" N   THR B 138 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 141
      No H-bonds generated for 'chain 'B' and resid 139 through 141'
    Processing helix  chain 'B' and resid 142 through 147
      removed outlier: 3.830A  pdb=" N   ALA B 146 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 161
    Processing helix  chain 'B' and resid 162 through 192
      Proline residue:  B 182  - end of helix
    Processing helix  chain 'B' and resid 194 through 199
      removed outlier: 4.381A  pdb=" N   ALA B 199 " --> pdb=" O   PRO B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 204
    Processing helix  chain 'B' and resid 205 through 219
      removed outlier: 3.996A  pdb=" N   PHE B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 249
      Proline residue:  B 246  - end of helix
    Processing helix  chain 'B' and resid 254 through 256
      No H-bonds generated for 'chain 'B' and resid 254 through 256'
    Processing helix  chain 'B' and resid 257 through 277
      removed outlier: 3.994A  pdb=" N   SER B 261 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   PHE B 262 " --> pdb=" O   TRP B 258 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   GLY B 263 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA B 273 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 309
    Processing helix  chain 'C' and resid 10 through 13
    Processing helix  chain 'C' and resid 14 through 29
    Processing helix  chain 'C' and resid 34 through 66
      removed outlier: 3.844A  pdb=" N   ARG C  38 " --> pdb=" O   PHE C  34 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET C  39 " --> pdb=" O   PRO C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 76
    Processing helix  chain 'C' and resid 79 through 84
      removed outlier: 3.958A  pdb=" N   ILE C  83 " --> pdb=" O   ARG C  79 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ALA C  84 " --> pdb=" O   PHE C  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 79 through 84'
    Processing helix  chain 'C' and resid 84 through 98
    Processing helix  chain 'C' and resid 101 through 123
    Processing helix  chain 'C' and resid 125 through 130
    Processing helix  chain 'C' and resid 134 through 138
      removed outlier: 3.853A  pdb=" N   THR C 138 " --> pdb=" O   GLN C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 141
      No H-bonds generated for 'chain 'C' and resid 139 through 141'
    Processing helix  chain 'C' and resid 142 through 147
      removed outlier: 3.818A  pdb=" N   ALA C 146 " --> pdb=" O   PHE C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 161
    Processing helix  chain 'C' and resid 162 through 191
      Proline residue:  C 182  - end of helix
    Processing helix  chain 'C' and resid 194 through 204
      removed outlier: 4.711A  pdb=" N   ALA C 199 " --> pdb=" O   GLN C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 219
      removed outlier: 3.942A  pdb=" N   PHE C 209 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL C 212 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 249
      Proline residue:  C 246  - end of helix
    Processing helix  chain 'C' and resid 254 through 256
      No H-bonds generated for 'chain 'C' and resid 254 through 256'
    Processing helix  chain 'C' and resid 257 through 277
      removed outlier: 4.021A  pdb=" N   SER C 261 " --> pdb=" O   LEU C 257 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   PHE C 262 " --> pdb=" O   TRP C 258 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   GLY C 263 " --> pdb=" O   ALA C 259 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA C 273 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 309

    570 hydrogen bonds defined for protein.
    1614 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: 2.31

  Time building geometry restraints manager: 2.40 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1279
        1.33 -     1.45: 2150
        1.45 -     1.57: 4151
        1.57 -     1.69: 0
        1.69 -     1.81: 51
  Bond restraints: 7631
  Sorted by residual:
  bond pdb=" N   LEU B   9 "
       pdb=" CA  LEU B   9 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.13e-02 7.83e+03 1.04e+01
  bond pdb=" N   PHE B   7 "
       pdb=" CA  PHE B   7 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.14e-02 7.69e+03 7.32e+00
  bond pdb=" N   PHE C   7 "
       pdb=" CA  PHE C   7 "
    ideal  model  delta    sigma   weight residual
    1.453  1.484 -0.030 1.16e-02 7.43e+03 6.83e+00
  bond pdb=" N   LEU C   9 "
       pdb=" CA  LEU C   9 "
    ideal  model  delta    sigma   weight residual
    1.462  1.491 -0.030 1.19e-02 7.06e+03 6.23e+00
  bond pdb=" N   LEU A   9 "
       pdb=" CA  LEU A   9 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.028 1.19e-02 7.06e+03 5.43e+00
  ... (remaining 7626 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 10103
        1.17 -     2.34: 253
        2.34 -     3.50: 26
        3.50 -     4.67: 32
        4.67 -     5.84: 4
  Bond angle restraints: 10418
  Sorted by residual:
  angle pdb=" C   PRO C   8 "
        pdb=" N   LEU C   9 "
        pdb=" CA  LEU C   9 "
      ideal   model   delta    sigma   weight residual
     123.46  117.62    5.84 1.35e+00 5.49e-01 1.87e+01
  angle pdb=" N   PRO B  10 "
        pdb=" CA  PRO B  10 "
        pdb=" C   PRO B  10 "
      ideal   model   delta    sigma   weight residual
     110.80  105.24    5.56 1.51e+00 4.39e-01 1.36e+01
  angle pdb=" C   LEU C   9 "
        pdb=" N   PRO C  10 "
        pdb=" CA  PRO C  10 "
      ideal   model   delta    sigma   weight residual
     119.90  123.63   -3.73 1.02e+00 9.61e-01 1.34e+01
  angle pdb=" C   LEU A   9 "
        pdb=" N   PRO A  10 "
        pdb=" CA  PRO A  10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.98   -3.08 1.02e+00 9.61e-01 9.12e+00
  angle pdb=" CA  PRO B  10 "
        pdb=" C   PRO B  10 "
        pdb=" O   PRO B  10 "
      ideal   model   delta    sigma   weight residual
     121.03  117.61    3.42 1.14e+00 7.69e-01 8.98e+00
  ... (remaining 10413 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 3951
       17.28 -    34.57: 293
       34.57 -    51.85: 44
       51.85 -    69.14: 11
       69.14 -    86.42: 3
  Dihedral angle restraints: 4302
    sinusoidal: 1611
      harmonic: 2691
  Sorted by residual:
  dihedral pdb=" CB  GLU A 134 "
           pdb=" CG  GLU A 134 "
           pdb=" CD  GLU A 134 "
           pdb=" OE1 GLU A 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.42   86.42     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" CB  LYS C 251 "
           pdb=" CG  LYS C 251 "
           pdb=" CD  LYS C 251 "
           pdb=" CE  LYS C 251 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.07   58.93     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CB  LYS A 251 "
           pdb=" CG  LYS A 251 "
           pdb=" CD  LYS A 251 "
           pdb=" CE  LYS A 251 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.09   58.91     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 4299 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 849
       0.031 -    0.062: 187
       0.062 -    0.092: 110
       0.092 -    0.123: 27
       0.123 -    0.154: 4
  Chirality restraints: 1177
  Sorted by residual:
  chirality pdb=" CA  PRO B  10 "
            pdb=" N   PRO B  10 "
            pdb=" C   PRO B  10 "
            pdb=" CB  PRO B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.87   -0.15 2.00e-01 2.50e+01 5.92e-01
  chirality pdb=" CB  ILE A 218 "
            pdb=" CA  ILE A 218 "
            pdb=" CG1 ILE A 218 "
            pdb=" CG2 ILE A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  PRO B 207 "
            pdb=" N   PRO B 207 "
            pdb=" C   PRO B 207 "
            pdb=" CB  PRO B 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.86e-01
  ... (remaining 1174 not shown)

  Planarity restraints: 1265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 206 "   -0.037 5.00e-02 4.00e+02   5.64e-02 5.08e+00
        pdb=" N   PRO B 207 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B 207 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 207 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 231 "   -0.021 2.00e-02 2.50e+03   1.37e-02 4.71e+00
        pdb=" CG  TRP B 231 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 231 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 231 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 231 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 231 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 231 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 231 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 231 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 231 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 231 "   -0.020 2.00e-02 2.50e+03   1.32e-02 4.34e+00
        pdb=" CG  TRP C 231 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 231 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 231 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 231 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 231 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 231 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 231 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 231 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 231 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1262 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 43
        2.60 -     3.18: 7397
        3.18 -     3.75: 12073
        3.75 -     4.33: 17340
        4.33 -     4.90: 29133
  Nonbonded interactions: 65986
  Sorted by model distance:
  nonbonded pdb=" O   THR B 121 "
            pdb=" OG  SER B 125 "
     model   vdw
     2.029 3.040
  nonbonded pdb=" O   THR C 121 "
            pdb=" OG  SER C 125 "
     model   vdw
     2.053 3.040
  nonbonded pdb=" O   THR A 121 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" OH  TYR B 215 "
            pdb=" OD2 ASP B 224 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OH  TYR C  13 "
            pdb=" O   PHE C 311 "
     model   vdw
     2.113 3.040
  ... (remaining 65981 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' and (resid 6 through 68 or resid 70 through 102 or resid 104 through  \ 
119 or resid 121 through 154 or resid 156 through 283 or resid 285 through 290 o \ 
r resid 292 through 313))
  selection = (chain 'B' and (resid 6 through 68 or resid 70 through 102 or resid 104 through  \ 
119 or resid 121 through 154 or resid 156 through 283 or resid 285 through 290 o \ 
r resid 292 through 313))
  selection = (chain 'C' and (resid 6 through 68 or resid 70 through 102 or resid 104 through  \ 
119 or resid 121 through 154 or resid 156 through 283 or resid 285 through 290 o \ 
r resid 292 through 313))
}

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=0.47 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:             4.360
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.900
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
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      :  0.003   0.036   7631  Z= 0.172
  Angle     :  0.484   5.840  10418  Z= 0.284
  Chirality :  0.036   0.154   1177
  Planarity :  0.005   0.056   1265
  Dihedral  : 12.423  86.422   2586
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  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:  0.67 (0.29), residues: 926
  helix:  0.49 (0.21), residues: 699
  sheet:  None (None), residues: 0
  loop :  0.77 (0.44), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP B 231 
 HIS   0.002   0.000   HIS A 163 
 PHE   0.013   0.001   PHE C   7 
 TYR   0.014   0.001   TYR A 167 
 ARG   0.002   0.000   ARG B  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.777 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1926
  time to fit residues: 19.6880
Evaluate side-chains
  66 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0060
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A  29 HIS
A 163 HIS
A 276 HIS
B 163 HIS
B 276 HIS
C 163 HIS
C 276 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.125429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.101686 restraints weight = 34999.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 3.40
r_work: 0.2973 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7631  Z= 0.234
  Angle     :  0.514   5.879  10418  Z= 0.266
  Chirality :  0.041   0.151   1177
  Planarity :  0.005   0.054   1265
  Dihedral  :  3.684  19.425   1002
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.63 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.01 (0.28), residues: 926
  helix:  2.06 (0.19), residues: 711
  sheet:  None (None), residues: 0
  loop :  2.08 (0.50), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 231 
 HIS   0.002   0.001   HIS A 187 
 PHE   0.013   0.001   PHE C   7 
 TYR   0.018   0.001   TYR C 167 
 ARG   0.003   0.001   ARG B  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.878 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9083 (mtp85) cc_final: 0.8794 (mtp-110)
REVERT: A  201 MET cc_start: 0.8831 (mmm) cc_final: 0.8627 (tpp)
REVERT: C  278 ASN cc_start: 0.8916 (t0) cc_final: 0.8706 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 75
  average time/residue: 0.2246
  time to fit residues: 22.9067
Evaluate side-chains
  73 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  231 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0870
   chunk 9 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3496 r_free = 0.3496 target = 0.124911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.102550 restraints weight = 26240.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 3.01
r_work: 0.3005 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7631  Z= 0.194
  Angle     :  0.482   6.744  10418  Z= 0.244
  Chirality :  0.040   0.139   1177
  Planarity :  0.004   0.054   1265
  Dihedral  :  3.638  18.949   1002
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  4.41 %
    Favored  : 95.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.45 (0.29), residues: 926
  helix:  2.50 (0.19), residues: 709
  sheet:  None (None), residues: 0
  loop :  1.75 (0.51), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 231 
 HIS   0.004   0.001   HIS A  29 
 PHE   0.012   0.001   PHE A 288 
 TYR   0.014   0.001   TYR C 167 
 ARG   0.005   0.001   ARG C  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9112 (mtp85) cc_final: 0.8837 (mtp-110)
REVERT: A  201 MET cc_start: 0.8791 (mmm) cc_final: 0.8583 (tpp)
REVERT: C  201 MET cc_start: 0.8872 (mmm) cc_final: 0.8638 (tpp)
REVERT: C  278 ASN cc_start: 0.8968 (t0) cc_final: 0.8716 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 78
  average time/residue: 0.2231
  time to fit residues: 23.1503
Evaluate side-chains
  77 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  231 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0270
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.5438

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.123218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.100665 restraints weight = 28732.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 3.15
r_work: 0.2969 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7631  Z= 0.185
  Angle     :  0.466   6.921  10418  Z= 0.234
  Chirality :  0.039   0.136   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.612  19.173   1002
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  4.67 %
    Favored  : 94.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.55 (0.29), residues: 926
  helix:  2.59 (0.20), residues: 709
  sheet:  None (None), residues: 0
  loop :  1.70 (0.51), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 231 
 HIS   0.004   0.001   HIS B  29 
 PHE   0.011   0.001   PHE A 288 
 TYR   0.011   0.001   TYR C 167 
 ARG   0.004   0.000   ARG B  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9104 (mtp85) cc_final: 0.8802 (mtp-110)
REVERT: A  201 MET cc_start: 0.8786 (mmm) cc_final: 0.8554 (tpp)
REVERT: C  201 MET cc_start: 0.8870 (mmm) cc_final: 0.8619 (tpp)
REVERT: C  278 ASN cc_start: 0.8945 (t0) cc_final: 0.8712 (t0)
  outliers start: 4
  outliers final: 3
  residues processed: 85
  average time/residue: 0.2195
  time to fit residues: 25.1153
Evaluate side-chains
  78 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  231 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0870
   chunk 81 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.122566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.099694 restraints weight = 31084.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 3.29
r_work: 0.2950 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7631  Z= 0.204
  Angle     :  0.475   6.151  10418  Z= 0.238
  Chirality :  0.039   0.137   1177
  Planarity :  0.004   0.054   1265
  Dihedral  :  3.638  18.935   1002
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  5.32 %
    Favored  : 94.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.33 (0.29), residues: 926
  helix:  2.43 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.56 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 231 
 HIS   0.003   0.001   HIS B  29 
 PHE   0.011   0.001   PHE B 197 
 TYR   0.010   0.001   TYR C 167 
 ARG   0.005   0.000   ARG B  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9096 (mtp85) cc_final: 0.8785 (mtp-110)
REVERT: A  201 MET cc_start: 0.8800 (mmm) cc_final: 0.8560 (tpp)
REVERT: C  201 MET cc_start: 0.8862 (mmm) cc_final: 0.8605 (tpp)
REVERT: C  278 ASN cc_start: 0.8944 (t0) cc_final: 0.8717 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 79
  average time/residue: 0.2245
  time to fit residues: 24.0264
Evaluate side-chains
  79 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  231 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3416 r_free = 0.3416 target = 0.118796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.096235 restraints weight = 31324.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 3.26
r_work: 0.2903 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7631  Z= 0.278
  Angle     :  0.505   5.756  10418  Z= 0.254
  Chirality :  0.041   0.147   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.774  19.440   1002
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.45 %
    Favored  : 93.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.07 (0.29), residues: 926
  helix:  2.28 (0.20), residues: 718
  sheet:  None (None), residues: 0
  loop :  1.37 (0.52), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 231 
 HIS   0.003   0.001   HIS A 187 
 PHE   0.011   0.001   PHE B 262 
 TYR   0.009   0.001   TYR C 167 
 ARG   0.006   0.001   ARG C  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9089 (mtp85) cc_final: 0.8756 (mtp-110)
REVERT: A  201 MET cc_start: 0.8855 (mmm) cc_final: 0.8597 (tpp)
REVERT: C  201 MET cc_start: 0.8888 (mmm) cc_final: 0.8606 (tpp)
REVERT: C  278 ASN cc_start: 0.8934 (t0) cc_final: 0.8724 (t0)
  outliers start: 5
  outliers final: 5
  residues processed: 78
  average time/residue: 0.2275
  time to fit residues: 23.8009
Evaluate side-chains
  75 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  231 TRP
Chi-restraints excluded: chain C residue  302 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 42 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 83 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3449 r_free = 0.3449 target = 0.121642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.099103 restraints weight = 28066.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 3.13
r_work: 0.2947 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7631  Z= 0.203
  Angle     :  0.471   5.636  10418  Z= 0.238
  Chirality :  0.039   0.139   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.696  18.915   1002
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  5.58 %
    Favored  : 93.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.21 (0.29), residues: 926
  helix:  2.37 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.40 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 231 
 HIS   0.003   0.000   HIS B  29 
 PHE   0.010   0.001   PHE A 288 
 TYR   0.013   0.001   TYR A  65 
 ARG   0.005   0.000   ARG B  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9078 (mtp85) cc_final: 0.8750 (mtp-110)
REVERT: A  201 MET cc_start: 0.8800 (mmm) cc_final: 0.8547 (tpp)
REVERT: C  201 MET cc_start: 0.8851 (mmm) cc_final: 0.8562 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 80
  average time/residue: 0.2239
  time to fit residues: 24.1639
Evaluate side-chains
  77 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  231 TRP
Chi-restraints excluded: chain C residue  302 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0470
   chunk 50 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.3450 r_free = 0.3450 target = 0.121709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.100614 restraints weight = 20257.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.61
r_work: 0.2990 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7631  Z= 0.190
  Angle     :  0.475   7.780  10418  Z= 0.236
  Chirality :  0.039   0.136   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.655  18.689   1002
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  5.84 %
    Favored  : 93.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.29 (0.29), residues: 926
  helix:  2.43 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.41 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 231 
 HIS   0.003   0.000   HIS B  29 
 PHE   0.010   0.001   PHE A 288 
 TYR   0.018   0.001   TYR A  65 
 ARG   0.005   0.000   ARG B  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9076 (mtp85) cc_final: 0.8745 (mtp-110)
REVERT: A  201 MET cc_start: 0.8757 (mmm) cc_final: 0.8500 (tpp)
REVERT: C  201 MET cc_start: 0.8823 (mmm) cc_final: 0.8528 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 80
  average time/residue: 0.2219
  time to fit residues: 23.8311
Evaluate side-chains
  79 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  231 TRP
Chi-restraints excluded: chain C residue  302 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    0.0670
   chunk 35 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0670
   chunk 77 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.4056

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.124058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.101375 restraints weight = 29359.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.23
r_work: 0.2975 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7631  Z= 0.158
  Angle     :  0.458   7.055  10418  Z= 0.228
  Chirality :  0.038   0.130   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.585  18.201   1002
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  5.84 %
    Favored  : 93.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.45 (0.29), residues: 926
  helix:  2.50 (0.19), residues: 731
  sheet:  None (None), residues: 0
  loop :  1.59 (0.54), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 231 
 HIS   0.003   0.000   HIS B  29 
 PHE   0.011   0.001   PHE A 288 
 TYR   0.016   0.001   TYR A  65 
 ARG   0.006   0.000   ARG C  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9100 (mtp85) cc_final: 0.8781 (mtp-110)
REVERT: A  201 MET cc_start: 0.8784 (mmm) cc_final: 0.8540 (tpp)
REVERT: B   79 ARG cc_start: 0.9134 (mtp85) cc_final: 0.8820 (mtm110)
REVERT: C   79 ARG cc_start: 0.9100 (mtp85) cc_final: 0.8837 (mtp-110)
REVERT: C  153 SER cc_start: 0.8587 (m) cc_final: 0.8284 (m)
REVERT: C  201 MET cc_start: 0.8839 (mmm) cc_final: 0.8561 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 84
  average time/residue: 0.2206
  time to fit residues: 24.9542
Evaluate side-chains
  83 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  231 TRP
Chi-restraints excluded: chain C residue  302 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0570
   chunk 77 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.119594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.096740 restraints weight = 26024.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.13
r_work: 0.2900 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7631  Z= 0.197
  Angle     :  0.471   6.884  10418  Z= 0.235
  Chirality :  0.039   0.135   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.595  18.417   1002
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  6.10 %
    Favored  : 93.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.37 (0.29), residues: 926
  helix:  2.50 (0.19), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.40 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 231 
 HIS   0.002   0.000   HIS A 187 
 PHE   0.011   0.001   PHE A 288 
 TYR   0.016   0.001   TYR A  65 
 ARG   0.005   0.000   ARG B  79 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9084 (mtp85) cc_final: 0.8744 (mtp-110)
REVERT: A  201 MET cc_start: 0.8747 (mmm) cc_final: 0.8483 (tpp)
REVERT: C   79 ARG cc_start: 0.9072 (mtp85) cc_final: 0.8795 (mtp-110)
REVERT: C  153 SER cc_start: 0.8575 (m) cc_final: 0.8267 (m)
REVERT: C  201 MET cc_start: 0.8805 (mmm) cc_final: 0.8498 (tpp)
  outliers start: 5
  outliers final: 5
  residues processed: 84
  average time/residue: 0.2221
  time to fit residues: 25.0448
Evaluate side-chains
  82 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  231 TRP
Chi-restraints excluded: chain C residue  302 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 54 optimal weight:    0.4980
   chunk 82 optimal weight:    0.3980
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.119956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.096152 restraints weight = 33720.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 3.57
r_work: 0.2879 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7631  Z= 0.188
  Angle     :  0.468   6.639  10418  Z= 0.233
  Chirality :  0.039   0.134   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.592  18.412   1002
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.97 %
    Favored  : 93.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.41 (0.29), residues: 926
  helix:  2.53 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.37 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 231 
 HIS   0.003   0.000   HIS B  29 
 PHE   0.011   0.001   PHE B 197 
 TYR   0.015   0.001   TYR A  65 
 ARG   0.005   0.000   ARG B  79 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3636.56 seconds
wall clock time: 65 minutes 37.39 seconds (3937.39 seconds total)