Starting phenix.real_space_refine
on Wed Sep 17 08:49:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vi2_43246/09_2025/8vi2_43246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vi2_43246/09_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_43246/09_2025/8vi2_43246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vi2_43246/09_2025/8vi2_43246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vi2_43246/09_2025/8vi2_43246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vi2_43246/09_2025/8vi2_43246.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.21, per 1000 atoms: 0.43
  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: 0.71
  Conformation dependent library (CDL) restraints added in 532.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.15
  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: 1.10

  Time building geometry restraints manager: 0.92 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:             6.840
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.680
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.110
-------------------------------------------------------------------------------
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 : 6.12
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG B  79 
 TYR   0.014   0.001   TYR A 167 
 PHE   0.013   0.001   PHE C   7 
 TRP   0.037   0.001   TRP B 231 
 HIS   0.002   0.000   HIS A 163 

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

*********************** 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  : 0.272 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0844
  time to fit residues: 8.5601
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  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3501 r_free = 0.3501 target = 0.124982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.102189 restraints weight = 27864.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 3.00
r_work: 0.3000 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1170

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= 0.152
  Angle     :  0.513   5.836  10418  Z= 0.266
  Chirality :  0.041   0.149   1177
  Planarity :  0.005   0.055   1265
  Dihedral  :  3.669  19.396   1002
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.37 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.01 (0.28), residues: 926
  helix:  2.06 (0.19), residues: 711
  sheet:  None (None), residues: 0
  loop :  2.07 (0.50), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  79 
 TYR   0.018   0.001   TYR C 167 
 PHE   0.013   0.001   PHE C   7 
 TRP   0.027   0.001   TRP B 231 
 HIS   0.002   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7631)
  covalent geometry    : angle       0.51319 (10418)
  hydrogen bonds       : bond        0.04376 (  570)
  hydrogen bonds       : angle       4.55176 ( 1614)

*********************** 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  : 0.263 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9079 (mtp85) cc_final: 0.8785 (mtp-110)
REVERT: A  201 MET cc_start: 0.8812 (mmm) cc_final: 0.8603 (tpp)
REVERT: C  278 ASN cc_start: 0.8899 (t0) cc_final: 0.8692 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 76
  average time/residue: 0.0990
  time to fit residues: 10.1959
Evaluate side-chains
  74 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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 37 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0770
   chunk 55 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 86 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 = 0.3489 r_free = 0.3489 target = 0.124373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.101644 restraints weight = 28928.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 3.15
r_work: 0.2986 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    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 = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1541

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= 0.132
  Angle     :  0.487   6.787  10418  Z= 0.246
  Chirality :  0.040   0.145   1177
  Planarity :  0.004   0.054   1265
  Dihedral  :  3.654  19.254   1002
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  4.15 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.41 (0.29), residues: 926
  helix:  2.50 (0.20), residues: 703
  sheet:  None (None), residues: 0
  loop :  1.65 (0.50), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  79 
 TYR   0.014   0.001   TYR C 167 
 PHE   0.011   0.001   PHE A 288 
 TRP   0.020   0.001   TRP C 231 
 HIS   0.004   0.001   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7631)
  covalent geometry    : angle       0.48695 (10418)
  hydrogen bonds       : bond        0.03926 (  570)
  hydrogen bonds       : angle       4.21343 ( 1614)

*********************** 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  : 0.274 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9121 (mtp85) cc_final: 0.8846 (mtp-110)
REVERT: A  201 MET cc_start: 0.8810 (mmm) cc_final: 0.8603 (tpp)
REVERT: C  201 MET cc_start: 0.8886 (mmm) cc_final: 0.8652 (tpp)
REVERT: C  278 ASN cc_start: 0.8972 (t0) cc_final: 0.8720 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 77
  average time/residue: 0.1030
  time to fit residues: 10.5746
Evaluate side-chains
  78 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
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 79 optimal weight:    0.3980
   chunk 73 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.121958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.100102 restraints weight = 23810.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.84
r_work: 0.2978 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2988
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2988 r_free = 0.2988    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 = 0.2988 r_free = 0.2988    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2988
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1698

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= 0.133
  Angle     :  0.477   6.749  10418  Z= 0.240
  Chirality :  0.039   0.139   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.652  19.205   1002
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  4.54 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.47 (0.29), residues: 926
  helix:  2.52 (0.20), residues: 709
  sheet:  None (None), residues: 0
  loop :  1.70 (0.51), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  79 
 TYR   0.011   0.001   TYR C 167 
 PHE   0.011   0.001   PHE A 288 
 TRP   0.020   0.001   TRP C 231 
 HIS   0.004   0.001   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7631)
  covalent geometry    : angle       0.47693 (10418)
  hydrogen bonds       : bond        0.03806 (  570)
  hydrogen bonds       : angle       4.09742 ( 1614)

*********************** 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
  88 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9090 (mtp85) cc_final: 0.8780 (mtp-110)
REVERT: A  201 MET cc_start: 0.8786 (mmm) cc_final: 0.8559 (tpp)
REVERT: C  201 MET cc_start: 0.8856 (mmm) cc_final: 0.8596 (tpp)
REVERT: C  278 ASN cc_start: 0.8955 (t0) cc_final: 0.8711 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 83
  average time/residue: 0.1057
  time to fit residues: 11.7093
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  : 0.282 
-------------------------------------------------------------------------------
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 48 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0170
   chunk 28 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 = 0.122655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.099670 restraints weight = 32526.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 3.36
r_work: 0.2954 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    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 = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1832

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= 0.123
  Angle     :  0.469   5.608  10418  Z= 0.236
  Chirality :  0.039   0.137   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.641  18.971   1002
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  5.58 %
    Favored  : 94.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.35 (0.29), residues: 926
  helix:  2.44 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.56 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.010   0.001   TYR C 167 
 PHE   0.011   0.001   PHE A 288 
 TRP   0.019   0.001   TRP C 231 
 HIS   0.004   0.001   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7631)
  covalent geometry    : angle       0.46925 (10418)
  hydrogen bonds       : bond        0.03688 (  570)
  hydrogen bonds       : angle       4.04329 ( 1614)

*********************** 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: 3
    poor density    : 79
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9109 (mtp85) cc_final: 0.8806 (mtp-110)
REVERT: A  201 MET cc_start: 0.8813 (mmm) cc_final: 0.8578 (tpp)
REVERT: C  201 MET cc_start: 0.8873 (mmm) cc_final: 0.8615 (tpp)
REVERT: C  278 ASN cc_start: 0.8950 (t0) cc_final: 0.8722 (t0)
  outliers start: 3
  outliers final: 3
  residues processed: 80
  average time/residue: 0.1022
  time to fit residues: 10.9182
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  : 0.172 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0970
   chunk 62 optimal weight:    0.0870
   chunk 34 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 51 optimal weight:    0.1980
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.3556

-------------------------------------------------------------------------------
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 = 0.125143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.102395 restraints weight = 29876.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 3.24
r_work: 0.2990 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    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 = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7631  Z= 0.104
  Angle     :  0.449   7.202  10418  Z= 0.225
  Chirality :  0.038   0.130   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.558  18.564   1002
  Min Nonbonded Distance : 2.659

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.53 (0.29), residues: 926
  helix:  2.58 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.58 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  79 
 TYR   0.009   0.001   TYR C 167 
 PHE   0.012   0.001   PHE A 288 
 TRP   0.018   0.001   TRP C 231 
 HIS   0.004   0.001   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7631)
  covalent geometry    : angle       0.44863 (10418)
  hydrogen bonds       : bond        0.03444 (  570)
  hydrogen bonds       : angle       3.93085 ( 1614)

*********************** 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
  84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9116 (mtp85) cc_final: 0.8803 (mtp-110)
REVERT: A  201 MET cc_start: 0.8775 (mmm) cc_final: 0.8540 (tpp)
REVERT: B  198 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7676 (mtt180)
REVERT: C  201 MET cc_start: 0.8848 (mmm) cc_final: 0.8609 (tpp)
  outliers start: 5
  outliers final: 5
  residues processed: 83
  average time/residue: 0.0949
  time to fit residues: 10.6367
Evaluate side-chains
  80 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain B residue  267 MET
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 83 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0470
   chunk 30 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 86 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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 = 0.123252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.101038 restraints weight = 25612.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 3.00
r_work: 0.2981 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    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 = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2026

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= 0.123
  Angle     :  0.470   7.251  10418  Z= 0.233
  Chirality :  0.039   0.134   1177
  Planarity :  0.004   0.052   1265
  Dihedral  :  3.581  18.721   1002
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.44 (0.29), residues: 926
  helix:  2.51 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.59 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.009   0.001   TYR C 167 
 PHE   0.010   0.001   PHE A 288 
 TRP   0.019   0.001   TRP C 231 
 HIS   0.003   0.001   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7631)
  covalent geometry    : angle       0.46981 (10418)
  hydrogen bonds       : bond        0.03575 (  570)
  hydrogen bonds       : angle       3.96202 ( 1614)

*********************** 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
  82 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9097 (mtp85) cc_final: 0.8774 (mtp-110)
REVERT: A  201 MET cc_start: 0.8788 (mmm) cc_final: 0.8540 (tpp)
REVERT: C  201 MET cc_start: 0.8843 (mmm) cc_final: 0.8591 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 81
  average time/residue: 0.0943
  time to fit residues: 10.3708
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  : 0.212 
-------------------------------------------------------------------------------
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 40 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0010
   chunk 73 optimal weight:    0.0770
   chunk 43 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.4944

-------------------------------------------------------------------------------
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 = 0.124224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.101357 restraints weight = 29375.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 3.24
r_work: 0.2972 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    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 = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7631  Z= 0.112
  Angle     :  0.458   6.499  10418  Z= 0.228
  Chirality :  0.038   0.131   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.566  18.547   1002
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.50 (0.29), residues: 926
  helix:  2.56 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.58 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.009   0.001   TYR C 167 
 PHE   0.011   0.001   PHE A 288 
 TRP   0.018   0.001   TRP C 231 
 HIS   0.003   0.000   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7631)
  covalent geometry    : angle       0.45847 (10418)
  hydrogen bonds       : bond        0.03486 (  570)
  hydrogen bonds       : angle       3.93263 ( 1614)

*********************** 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
  82 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9106 (mtp85) cc_final: 0.8786 (mtp-110)
REVERT: A  201 MET cc_start: 0.8790 (mmm) cc_final: 0.8556 (tpp)
REVERT: B  198 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7622 (mtt180)
REVERT: C   79 ARG cc_start: 0.9109 (mtp85) cc_final: 0.8853 (mtp-110)
REVERT: C  201 MET cc_start: 0.8836 (mmm) cc_final: 0.8589 (tpp)
  outliers start: 5
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1068
  time to fit residues: 11.5208
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  : 0.262 
-------------------------------------------------------------------------------
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 43 optimal weight:    0.0000
   chunk 56 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0570
   chunk 50 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.3902

-------------------------------------------------------------------------------
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 = 0.125246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.102206 restraints weight = 31665.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 3.37
r_work: 0.2982 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3023
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    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 = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3023
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2163

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= 0.104
  Angle     :  0.452   6.454  10418  Z= 0.224
  Chirality :  0.038   0.128   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.533  18.310   1002
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.61 (0.29), residues: 926
  helix:  2.64 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.59 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.009   0.001   TYR C 167 
 PHE   0.012   0.001   PHE A 288 
 TRP   0.017   0.001   TRP C 231 
 HIS   0.003   0.000   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7631)
  covalent geometry    : angle       0.45156 (10418)
  hydrogen bonds       : bond        0.03396 (  570)
  hydrogen bonds       : angle       3.88799 ( 1614)

*********************** 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
  85 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9126 (mtp85) cc_final: 0.8818 (mtp-110)
REVERT: A  201 MET cc_start: 0.8784 (mmm) cc_final: 0.8551 (tpp)
REVERT: B   79 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8835 (mtm110)
REVERT: B  198 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7639 (mtt180)
REVERT: C   79 ARG cc_start: 0.9117 (mtp85) cc_final: 0.8865 (mtp-110)
REVERT: C  201 MET cc_start: 0.8826 (mmm) cc_final: 0.8591 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 85
  average time/residue: 0.1010
  time to fit residues: 11.5548
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  : 0.274 
-------------------------------------------------------------------------------
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 13 optimal weight:    0.0370
   chunk 54 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0030
   chunk 11 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.4268

-------------------------------------------------------------------------------
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 = 0.3435 r_free = 0.3435 target = 0.122090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.099175 restraints weight = 25496.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 3.13
r_work: 0.2944 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    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 = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7631  Z= 0.107
  Angle     :  0.456   6.959  10418  Z= 0.227
  Chirality :  0.038   0.129   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.525  18.265   1002
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.62 (0.29), residues: 926
  helix:  2.66 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.59 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.009   0.001   TYR C 167 
 PHE   0.010   0.001   PHE A 288 
 TRP   0.018   0.001   TRP C 231 
 HIS   0.003   0.000   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7631)
  covalent geometry    : angle       0.45577 (10418)
  hydrogen bonds       : bond        0.03404 (  570)
  hydrogen bonds       : angle       3.87858 ( 1614)

********************** 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: 4
    poor density    : 80
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.9075 (mtp85) cc_final: 0.8749 (mtp-110)
REVERT: A  201 MET cc_start: 0.8729 (mmm) cc_final: 0.8473 (tpp)
REVERT: C   79 ARG cc_start: 0.9079 (mtp85) cc_final: 0.8821 (mtp-110)
REVERT: C  201 MET cc_start: 0.8779 (mmm) cc_final: 0.8521 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 84
  average time/residue: 0.1003
  time to fit residues: 11.2958
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  : 0.292 
-------------------------------------------------------------------------------
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 15 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0070
   chunk 4 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.5398

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.121333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.097434 restraints weight = 33721.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 3.60
r_work: 0.2893 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    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 = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2180

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= 0.115
  Angle     :  0.460   6.570  10418  Z= 0.229
  Chirality :  0.038   0.131   1177
  Planarity :  0.004   0.053   1265
  Dihedral  :  3.537  18.291   1002
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  5.97 %
    Favored  : 93.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.60 (0.29), residues: 926
  helix:  2.64 (0.20), residues: 721
  sheet:  None (None), residues: 0
  loop :  1.58 (0.52), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.009   0.001   TYR C 167 
 PHE   0.011   0.001   PHE B 197 
 TRP   0.018   0.001   TRP C 231 
 HIS   0.003   0.000   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7631)
  covalent geometry    : angle       0.46021 (10418)
  hydrogen bonds       : bond        0.03454 (  570)
  hydrogen bonds       : angle       3.89554 ( 1614)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1939.19 seconds
wall clock time: 33 minutes 59.60 seconds (2039.60 seconds total)