Starting phenix.real_space_refine
on Mon Apr 28 09:39:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vi2_43246/04_2025/8vi2_43246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vi2_43246/04_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_43246/04_2025/8vi2_43246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vi2_43246/04_2025/8vi2_43246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vi2_43246/04_2025/8vi2_43246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vi2_43246/04_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 9.58, per 1000 atoms: 1.30
  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: 1.96
  Conformation dependent library (CDL) restraints added in 1.8 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: 0.75
  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: 2.34

  Time building geometry restraints manager: 2.36 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:             14.680
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     28.350
  Find NCS groups from input model:        0.310
  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:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.800
-------------------------------------------------------------------------------
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= 0.149
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13893 (  570)
  hydrogen bonds       : angle       7.85809 ( 1614)
  covalent geometry    : bond        0.00262 ( 7631)
  covalent geometry    : angle       0.48425 (10418)

*********************** 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  : 0.715 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1850
  time to fit residues: 18.8080
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  : 0.710 
-------------------------------------------------------------------------------
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:    0.9980
   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:    0.6996

-------------------------------------------------------------------------------
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 = 0.3502 r_free = 0.3502 target = 0.125066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.101498 restraints weight = 34987.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 3.37
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) = 0.087         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1230

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= 0.151
  Angle     :  0.517   5.866  10418  Z= 0.267
  Chirality :  0.041   0.152   1177
  Planarity :  0.005   0.054   1265
  Dihedral  :  3.701  19.579   1002
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.50 %
    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:  3.00 (0.28), residues: 926
  helix:  2.14 (0.19), residues: 699
  sheet:  None (None), residues: 0
  loop :  1.77 (0.49), residues: 227

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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04259 (  570)
  hydrogen bonds       : angle       4.51242 ( 1614)
  covalent geometry    : bond        0.00363 ( 7631)
  covalent geometry    : angle       0.51749 (10418)

*********************** 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
  78 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9081 (mtp85) cc_final: 0.8797 (mtp-110)
REVERT: C  201 MET cc_start: 0.8891 (mmm) cc_final: 0.8647 (tpp)
REVERT: C  278 ASN cc_start: 0.8919 (t0) cc_final: 0.8714 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 76
  average time/residue: 0.2122
  time to fit residues: 21.6798
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  : 0.694 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3495 r_free = 0.3495 target = 0.124592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.102576 restraints weight = 26214.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.87
r_work: 0.3009 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    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 = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1603

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= 0.133
  Angle     :  0.487   7.028  10418  Z= 0.246
  Chirality :  0.040   0.138   1177
  Planarity :  0.004   0.055   1265
  Dihedral  :  3.661  18.983   1002
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  4.54 %
    Favored  : 94.94 %
  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:  3.42 (0.29), residues: 926
  helix:  2.48 (0.19), residues: 709
  sheet:  None (None), residues: 0
  loop :  1.73 (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   0.013   0.001   TYR C 167 
 ARG   0.006   0.001   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03917 (  570)
  hydrogen bonds       : angle       4.18687 ( 1614)
  covalent geometry    : bond        0.00318 ( 7631)
  covalent geometry    : angle       0.48695 (10418)

*********************** 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  : 0.813 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9108 (mtp85) cc_final: 0.8825 (mtp-110)
REVERT: C  201 MET cc_start: 0.8869 (mmm) cc_final: 0.8620 (tpp)
REVERT: C  278 ASN cc_start: 0.8980 (t0) cc_final: 0.8733 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 77
  average time/residue: 0.2257
  time to fit residues: 23.3292
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  : 0.716 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3454 r_free = 0.3454 target = 0.121812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.099376 restraints weight = 28821.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 3.13
r_work: 0.2954 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    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 = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1741

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= 0.133
  Angle     :  0.476   6.209  10418  Z= 0.240
  Chirality :  0.039   0.140   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.652  19.072   1002
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.10
  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:  3.50 (0.29), residues: 926
  helix:  2.56 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop :  1.67 (0.50), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   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   0.005   0.001   ARG C  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03796 (  570)
  hydrogen bonds       : angle       4.09166 ( 1614)
  covalent geometry    : bond        0.00324 ( 7631)
  covalent geometry    : angle       0.47643 (10418)

*********************** 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
  87 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9100 (mtp85) cc_final: 0.8795 (mtp-110)
REVERT: C  201 MET cc_start: 0.8877 (mmm) cc_final: 0.8622 (tpp)
REVERT: C  278 ASN cc_start: 0.8956 (t0) cc_final: 0.8717 (t0)
  outliers start: 4
  outliers final: 3
  residues processed: 83
  average time/residue: 0.2824
  time to fit residues: 32.0907
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  : 1.505 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 62 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.122505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.099723 restraints weight = 31053.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 3.28
r_work: 0.2950 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    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 = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1863

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= 0.125
  Angle     :  0.471   5.628  10418  Z= 0.237
  Chirality :  0.039   0.137   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.648  19.032   1002
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  5.19 %
    Favored  : 94.29 %
  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:  3.34 (0.29), residues: 926
  helix:  2.43 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.58 (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 A 288 
 TYR   0.010   0.001   TYR C 167 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (  570)
  hydrogen bonds       : angle       4.04402 ( 1614)
  covalent geometry    : bond        0.00301 ( 7631)
  covalent geometry    : angle       0.47063 (10418)

*********************** 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
  84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 1.227 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9094 (mtp85) cc_final: 0.8786 (mtp-110)
REVERT: C  201 MET cc_start: 0.8862 (mmm) cc_final: 0.8601 (tpp)
REVERT: C  278 ASN cc_start: 0.8950 (t0) cc_final: 0.8723 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 81
  average time/residue: 0.2762
  time to fit residues: 30.4489
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  : 1.057 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0970
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.122102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.099273 restraints weight = 30996.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 3.28
r_work: 0.2940 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    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 = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1946

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= 0.129
  Angle     :  0.470   6.966  10418  Z= 0.236
  Chirality :  0.039   0.139   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.648  18.924   1002
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  5.71 %
    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:  3.34 (0.29), residues: 926
  helix:  2.43 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.59 (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 A 288 
 TYR   0.009   0.001   TYR C 167 
 ARG   0.005   0.001   ARG C  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03683 (  570)
  hydrogen bonds       : angle       4.00864 ( 1614)
  covalent geometry    : bond        0.00313 ( 7631)
  covalent geometry    : angle       0.46965 (10418)

*********************** 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
  81 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9106 (mtp85) cc_final: 0.8791 (mtp-110)
REVERT: C  201 MET cc_start: 0.8867 (mmm) cc_final: 0.8607 (tpp)
  outliers start: 3
  outliers final: 3
  residues processed: 81
  average time/residue: 0.2548
  time to fit residues: 28.8113
Evaluate side-chains
  77 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.121314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.098888 restraints weight = 28116.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 3.11
r_work: 0.2945 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2945
-------------------------------------------------------------------------------
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: 0.8313
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7631  Z= 0.137
  Angle     :  0.486   7.617  10418  Z= 0.242
  Chirality :  0.039   0.139   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.674  19.074   1002
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  5.84 %
    Favored  : 93.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.28 (0.29), residues: 926
  helix:  2.41 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.48 (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   0.010   0.001   PHE A 288 
 TYR   0.008   0.001   TYR C 167 
 ARG   0.005   0.000   ARG C  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  570)
  hydrogen bonds       : angle       4.02595 ( 1614)
  covalent geometry    : bond        0.00338 ( 7631)
  covalent geometry    : angle       0.48596 (10418)

*********************** 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
  78 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 1.426 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9087 (mtp85) cc_final: 0.8764 (mtp-110)
REVERT: C  201 MET cc_start: 0.8850 (mmm) cc_final: 0.8584 (tpp)
  outliers start: 3
  outliers final: 3
  residues processed: 78
  average time/residue: 0.3203
  time to fit residues: 33.8316
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  : 1.482 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0170
   chunk 68 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.4818

-------------------------------------------------------------------------------
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 = 0.3468 r_free = 0.3468 target = 0.123080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.101870 restraints weight = 20188.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.61
r_work: 0.3004 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    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 = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7631  Z= 0.112
  Angle     :  0.460   6.338  10418  Z= 0.230
  Chirality :  0.038   0.132   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.617  18.625   1002
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  5.97 %
    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:  3.43 (0.29), residues: 926
  helix:  2.52 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.50 (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 A 288 
 TYR   0.008   0.001   TYR A  59 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03501 (  570)
  hydrogen bonds       : angle       3.95010 ( 1614)
  covalent geometry    : bond        0.00262 ( 7631)
  covalent geometry    : angle       0.45985 (10418)

*********************** 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
  86 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 1.459 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9089 (mtp85) cc_final: 0.8759 (mtp-110)
REVERT: C   79 ARG cc_start: 0.9074 (mtp85) cc_final: 0.8793 (mtp-110)
REVERT: C  153 SER cc_start: 0.8553 (m) cc_final: 0.8251 (m)
REVERT: C  201 MET cc_start: 0.8802 (mmm) cc_final: 0.8527 (tpp)
  outliers start: 3
  outliers final: 3
  residues processed: 86
  average time/residue: 0.2818
  time to fit residues: 33.9684
Evaluate side-chains
  83 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 61 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0980
   chunk 77 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.120061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.096372 restraints weight = 28942.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 3.42
r_work: 0.2873 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7631  Z= 0.114
  Angle     :  0.463   6.706  10418  Z= 0.230
  Chirality :  0.038   0.132   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.588  18.454   1002
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  6.23 %
    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:  3.45 (0.29), residues: 926
  helix:  2.54 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.51 (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 A 288 
 TYR   0.007   0.001   TYR C 167 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03488 (  570)
  hydrogen bonds       : angle       3.93206 ( 1614)
  covalent geometry    : bond        0.00270 ( 7631)
  covalent geometry    : angle       0.46287 (10418)

*********************** 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
  81 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9038 (mtp85) cc_final: 0.8689 (mtp-110)
REVERT: B   79 ARG cc_start: 0.9086 (mtp85) cc_final: 0.8744 (mtm110)
REVERT: C   79 ARG cc_start: 0.9038 (mtp85) cc_final: 0.8753 (mtp-110)
REVERT: C  153 SER cc_start: 0.8571 (m) cc_final: 0.8249 (m)
REVERT: C  201 MET cc_start: 0.8823 (mmm) cc_final: 0.8543 (tpp)
  outliers start: 3
  outliers final: 3
  residues processed: 81
  average time/residue: 0.2151
  time to fit residues: 23.5168
Evaluate side-chains
  80 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
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=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:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3392 r_free = 0.3392 target = 0.118485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.095805 restraints weight = 26154.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 3.11
r_work: 0.2893 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2109

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= 0.131
  Angle     :  0.475   6.281  10418  Z= 0.236
  Chirality :  0.039   0.136   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.623  18.638   1002
  Min Nonbonded Distance : 2.663

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  6.10 %
    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:  3.37 (0.29), residues: 926
  helix:  2.48 (0.19), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.48 (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 B 197 
 TYR   0.008   0.001   TYR C 167 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03610 (  570)
  hydrogen bonds       : angle       3.97029 ( 1614)
  covalent geometry    : bond        0.00319 ( 7631)
  covalent geometry    : angle       0.47527 (10418)

********************** 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
  86 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9059 (mtp85) cc_final: 0.8710 (mtp-110)
REVERT: C  201 MET cc_start: 0.8792 (mmm) cc_final: 0.8495 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 86
  average time/residue: 0.2436
  time to fit residues: 28.4857
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  : 0.757 
-------------------------------------------------------------------------------
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 48 optimal weight:    0.2980
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   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 = 0.3398 r_free = 0.3398 target = 0.118827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.095285 restraints weight = 33862.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 3.52
r_work: 0.2874 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2130

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= 0.126
  Angle     :  0.472   6.235  10418  Z= 0.235
  Chirality :  0.039   0.135   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.627  18.632   1002
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  6.36 %
    Favored  : 93.13 %
  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:  2.51 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.47 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 231 
 HIS   0.003   0.001   HIS B  29 
 PHE   0.012   0.001   PHE B 197 
 TYR   0.008   0.001   TYR C 167 
 ARG   0.005   0.000   ARG C  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03559 (  570)
  hydrogen bonds       : angle       3.96290 ( 1614)
  covalent geometry    : bond        0.00305 ( 7631)
  covalent geometry    : angle       0.47223 (10418)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4459.77 seconds
wall clock time: 81 minutes 56.31 seconds (4916.31 seconds total)