Starting phenix.real_space_refine
on Mon Apr 28 09:37:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vi4_43248/04_2025/8vi4_43248.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vi4_43248/04_2025/8vi4_43248.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/8vi4_43248/04_2025/8vi4_43248.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vi4_43248/04_2025/8vi4_43248.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vi4_43248/04_2025/8vi4_43248.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vi4_43248/04_2025/8vi4_43248.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=   0.015
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    4988      2.51       5
     N    1140      2.21       5
     O    1204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 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: 7359
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2455
      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: 2529
    Chain: "B"
      Number of atoms: 2452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2452
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 13, 'TRANS': 294}
    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}
  Time building chain proxies: 6.90, per 1000 atoms: 0.94
  Number of scatterers: 7359
  At special positions: 0
  Unit cell: (100.182, 90.56, 61.694, 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    1204      8.00
     N    1140      7.00
     C    4988      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: 1.84
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      90.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  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 36 through 66
    Processing helix  chain 'A' and resid 66 through 76
    Processing helix  chain 'A' and resid 79 through 83
    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
    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: 3.867A  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 192
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 194 through 199
      removed outlier: 4.287A  pdb=" N   ALA A 199 " --> pdb=" O   PRO A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 203
    Processing helix  chain 'A' and resid 204 through 219
      removed outlier: 4.731A  pdb=" N   ALA A 208 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   PHE A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 3.679A  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 257
    Processing helix  chain 'A' and resid 258 through 277
      removed outlier: 3.991A  pdb=" N   PHE A 262 " --> pdb=" O   TRP A 258 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLY A 263 " --> pdb=" O   ALA A 259 " (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 36 through 66
    Processing helix  chain 'B' and resid 66 through 76
    Processing helix  chain 'B' and resid 78 through 83
      removed outlier: 3.769A  pdb=" N   SER B  81 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
    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: 3.521A  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: 3.816A  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: 4.271A  pdb=" N   ALA B 199 " --> pdb=" O   PRO B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 203
    Processing helix  chain 'B' and resid 204 through 219
      removed outlier: 4.741A  pdb=" N   ALA B 208 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   PHE B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 249
      removed outlier: 3.551A  pdb=" N   LYS B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
      Proline residue:  B 246  - end of helix
    Processing helix  chain 'B' and resid 254 through 257
    Processing helix  chain 'B' and resid 258 through 277
      removed outlier: 3.988A  pdb=" N   PHE B 262 " --> pdb=" O   TRP B 258 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY B 263 " --> pdb=" O   ALA B 259 " (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 36 through 66
    Processing helix  chain 'C' and resid 66 through 76
    Processing helix  chain 'C' and resid 79 through 83
    Processing helix  chain 'C' and resid 84 through 98
    Processing helix  chain 'C' and resid 101 through 124
    Processing helix  chain 'C' and resid 125 through 130
    Processing helix  chain 'C' and resid 134 through 138
      removed outlier: 3.554A  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: 3.822A  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 199
      removed outlier: 4.309A  pdb=" N   ALA C 199 " --> pdb=" O   PRO C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 203
    Processing helix  chain 'C' and resid 204 through 219
      removed outlier: 4.770A  pdb=" N   ALA C 208 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE C 209 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 3.662A  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 257
    Processing helix  chain 'C' and resid 258 through 277
      removed outlier: 4.020A  pdb=" N   PHE C 262 " --> pdb=" O   TRP C 258 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   GLY C 263 " --> pdb=" O   ALA C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 309

    572 hydrogen bonds defined for protein.
    1631 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: 2.16

  Time building geometry restraints manager: 2.19 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2154
        1.34 -     1.46: 1613
        1.46 -     1.57: 3785
        1.57 -     1.69: 0
        1.69 -     1.81: 51
  Bond restraints: 7603
  Sorted by residual:
  bond pdb=" CA  SER C 191 "
       pdb=" CB  SER C 191 "
    ideal  model  delta    sigma   weight residual
    1.532  1.490  0.042 1.54e-02 4.22e+03 7.46e+00
  bond pdb=" N   SER C 191 "
       pdb=" CA  SER C 191 "
    ideal  model  delta    sigma   weight residual
    1.455  1.479 -0.024 1.09e-02 8.42e+03 4.65e+00
  bond pdb=" N   SER C 192 "
       pdb=" CA  SER C 192 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.20e-02 6.94e+03 4.27e+00
  bond pdb=" N   LYS B 308 "
       pdb=" CA  LYS B 308 "
    ideal  model  delta    sigma   weight residual
    1.456  1.483 -0.027 1.31e-02 5.83e+03 4.24e+00
  bond pdb=" N   LEU C 193 "
       pdb=" CA  LEU C 193 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.026 1.29e-02 6.01e+03 3.98e+00
  ... (remaining 7598 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.94: 9966
        0.94 -     1.89: 308
        1.89 -     2.83: 50
        2.83 -     3.78: 27
        3.78 -     4.72: 21
  Bond angle restraints: 10372
  Sorted by residual:
  angle pdb=" CA  ARG B  64 "
        pdb=" C   ARG B  64 "
        pdb=" O   ARG B  64 "
      ideal   model   delta    sigma   weight residual
     120.70  117.07    3.63 1.03e+00 9.43e-01 1.24e+01
  angle pdb=" C   PHE B   7 "
        pdb=" CA  PHE B   7 "
        pdb=" CB  PHE B   7 "
      ideal   model   delta    sigma   weight residual
     109.31  112.83   -3.52 1.23e+00 6.61e-01 8.19e+00
  angle pdb=" CA  SER C 191 "
        pdb=" C   SER C 191 "
        pdb=" O   SER C 191 "
      ideal   model   delta    sigma   weight residual
     120.84  117.08    3.76 1.33e+00 5.65e-01 8.01e+00
  angle pdb=" N   LYS C 308 "
        pdb=" CA  LYS C 308 "
        pdb=" CB  LYS C 308 "
      ideal   model   delta    sigma   weight residual
     110.41  105.77    4.64 1.68e+00 3.54e-01 7.62e+00
  angle pdb=" N   PHE B   7 "
        pdb=" CA  PHE B   7 "
        pdb=" CB  PHE B   7 "
      ideal   model   delta    sigma   weight residual
     109.90  113.65   -3.75 1.54e+00 4.22e-01 5.94e+00
  ... (remaining 10367 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 3910
       16.92 -    33.85: 297
       33.85 -    50.77: 55
       50.77 -    67.69: 10
       67.69 -    84.62: 2
  Dihedral angle restraints: 4274
    sinusoidal: 1603
      harmonic: 2671
  Sorted by residual:
  dihedral pdb=" CA  ILE B 190 "
           pdb=" C   ILE B 190 "
           pdb=" N   SER B 191 "
           pdb=" CA  SER B 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.11  -16.89     0      5.00e+00 4.00e-02 1.14e+01
  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  -84.62   84.62     1      3.00e+01 1.11e-03 9.67e+00
  dihedral pdb=" CG  ARG B 198 "
           pdb=" CD  ARG B 198 "
           pdb=" NE  ARG B 198 "
           pdb=" CZ  ARG B 198 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.05  -42.05     2      1.50e+01 4.44e-03 9.57e+00
  ... (remaining 4271 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1028
       0.061 -    0.122: 139
       0.122 -    0.183: 2
       0.183 -    0.244: 1
       0.244 -    0.305: 1
  Chirality restraints: 1171
  Sorted by residual:
  chirality pdb=" CA  PHE B   7 "
            pdb=" N   PHE B   7 "
            pdb=" C   PHE B   7 "
            pdb=" CB  PHE B   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" CA  LYS C 308 "
            pdb=" N   LYS C 308 "
            pdb=" C   LYS C 308 "
            pdb=" CB  LYS C 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.27e-01
  chirality pdb=" CA  LYS B 308 "
            pdb=" N   LYS B 308 "
            pdb=" C   LYS B 308 "
            pdb=" CB  LYS B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.69e-01
  ... (remaining 1168 not shown)

  Planarity restraints: 1258
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 190 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.10e+00
        pdb=" C   ILE C 190 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ILE C 190 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   SER C 191 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 231 "   -0.022 2.00e-02 2.50e+03   1.48e-02 5.46e+00
        pdb=" CG  TRP B 231 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 231 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 231 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 231 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 231 "   -0.004 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 "    0.002 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 "    0.023 2.00e-02 2.50e+03   1.47e-02 5.42e+00
        pdb=" CG  TRP C 231 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 231 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 231 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 231 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 231 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 231 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 231 "    0.004 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 1255 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 82
        2.69 -     3.24: 7806
        3.24 -     3.79: 12327
        3.79 -     4.35: 17372
        4.35 -     4.90: 28588
  Nonbonded interactions: 66175
  Sorted by model distance:
  nonbonded pdb=" O   THR A 121 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" O   THR C 121 "
            pdb=" OG  SER C 125 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   THR B 121 "
            pdb=" OG  SER B 125 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" NE1 TRP A 177 "
            pdb=" OE1 GLU A 181 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" NE1 TRP B 177 "
            pdb=" OE1 GLU B 181 "
     model   vdw
     2.186 3.120
  ... (remaining 66170 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 283 or resid 285 through 313))
  selection = (chain 'B' and (resid 6 through 283 or resid 285 through 313))
  selection = (chain 'C' and (resid 6 through 283 or resid 285 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.870
  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:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.550
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.030
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
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   0.042   7603  Z= 0.134
  Angle     :  0.463   4.725  10372  Z= 0.260
  Chirality :  0.038   0.305   1171
  Planarity :  0.003   0.030   1258
  Dihedral  : 12.375  84.619   2568
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.26 %
    Favored  : 99.61 %
  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:  2.48 (0.29), residues: 919
  helix:  2.08 (0.20), residues: 724
  sheet:  None (None), residues: 0
  loop :  0.06 (0.48), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP B 231 
 HIS   0.003   0.001   HIS A 163 
 PHE   0.014   0.001   PHE C 288 
 TYR   0.004   0.001   TYR C 143 
 ARG   0.003   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10874 (  572)
  hydrogen bonds       : angle       4.98465 ( 1631)
  covalent geometry    : bond        0.00253 ( 7603)
  covalent geometry    : angle       0.46306 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.753 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1857
  time to fit residues: 18.7511
Evaluate side-chains
  67 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 81 optimal weight:    0.4980
   overall best weight:    0.8184

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.113112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.098244 restraints weight = 10556.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.76
r_work: 0.2925 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.0976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7603  Z= 0.150
  Angle     :  0.492   5.972  10372  Z= 0.251
  Chirality :  0.040   0.121   1171
  Planarity :  0.004   0.024   1258
  Dihedral  :  3.778  16.215    992
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  2.09 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.28), residues: 919
  helix:  1.87 (0.19), residues: 733
  sheet:  None (None), residues: 0
  loop :  0.40 (0.52), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP A 231 
 HIS   0.002   0.001   HIS B 187 
 PHE   0.015   0.001   PHE A 274 
 TYR   0.012   0.001   TYR A 304 
 ARG   0.005   0.001   ARG A  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04056 (  572)
  hydrogen bonds       : angle       4.42786 ( 1631)
  covalent geometry    : bond        0.00369 ( 7603)
  covalent geometry    : angle       0.49210 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7763 (mtp) cc_final: 0.7536 (mtt)
REVERT: A  304 TYR cc_start: 0.7813 (t80) cc_final: 0.7460 (t80)
REVERT: B  231 TRP cc_start: 0.8564 (OUTLIER) cc_final: 0.8175 (m-10)
REVERT: C   58 MET cc_start: 0.7761 (mtp) cc_final: 0.7534 (mtt)
  outliers start: 5
  outliers final: 4
  residues processed: 84
  average time/residue: 0.2235
  time to fit residues: 26.7942
Evaluate side-chains
  76 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  155 SER
Chi-restraints excluded: chain C residue  193 LEU
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 58 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0170
   chunk 34 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
C 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.120692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.105671 restraints weight = 10974.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.66
r_work: 0.3041 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2899
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2899
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7603  Z= 0.120
  Angle     :  0.454   5.819  10372  Z= 0.231
  Chirality :  0.038   0.117   1171
  Planarity :  0.004   0.027   1258
  Dihedral  :  3.696  16.357    992
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  3.52 %
    Favored  : 95.82 %
  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:  2.37 (0.29), residues: 919
  helix:  1.82 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.61 (0.56), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP A 231 
 HIS   0.002   0.000   HIS B 187 
 PHE   0.011   0.001   PHE A 274 
 TYR   0.010   0.001   TYR A 304 
 ARG   0.004   0.000   ARG A  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (  572)
  hydrogen bonds       : angle       4.25251 ( 1631)
  covalent geometry    : bond        0.00287 ( 7603)
  covalent geometry    : angle       0.45405 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7939 (mtp) cc_final: 0.7697 (mtm)
REVERT: B  231 TRP cc_start: 0.8542 (OUTLIER) cc_final: 0.8010 (m-10)
REVERT: C  196 GLN cc_start: 0.9050 (pm20) cc_final: 0.8823 (pm20)
  outliers start: 5
  outliers final: 2
  residues processed: 84
  average time/residue: 0.1766
  time to fit residues: 21.0381
Evaluate side-chains
  81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  193 LEU
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 51 optimal weight:    0.2980
   chunk 19 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 42 optimal weight:    0.3980
   chunk 81 optimal weight:    0.0570
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 86 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.3498

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

Flipped N/Q/H residues before XYZ refinement:
C 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.123218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.108135 restraints weight = 10834.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.66
r_work: 0.3079 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7603  Z= 0.104
  Angle     :  0.438   5.720  10372  Z= 0.222
  Chirality :  0.037   0.116   1171
  Planarity :  0.004   0.029   1258
  Dihedral  :  3.615  16.310    992
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  4.18 %
    Favored  : 95.17 %
  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:  2.54 (0.28), residues: 919
  helix:  1.95 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.60 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 
 PHE   0.010   0.001   PHE A 274 
 TYR   0.006   0.001   TYR A 143 
 ARG   0.004   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  572)
  hydrogen bonds       : angle       4.14064 ( 1631)
  covalent geometry    : bond        0.00237 ( 7603)
  covalent geometry    : angle       0.43807 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7971 (mtp) cc_final: 0.7728 (mtm)
REVERT: A  304 TYR cc_start: 0.7901 (t80) cc_final: 0.7641 (t80)
REVERT: B  231 TRP cc_start: 0.8450 (OUTLIER) cc_final: 0.7904 (m-10)
REVERT: B  253 LEU cc_start: 0.8622 (mm) cc_final: 0.8383 (mt)
REVERT: C  196 GLN cc_start: 0.9056 (pm20) cc_final: 0.8824 (pm20)
  outliers start: 5
  outliers final: 4
  residues processed: 88
  average time/residue: 0.1878
  time to fit residues: 23.4466
Evaluate side-chains
  83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
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  159 LEU
Chi-restraints excluded: chain C residue  193 LEU
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 32 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   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 = 0.3411 r_free = 0.3411 target = 0.122214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.108113 restraints weight = 8840.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.44
r_work: 0.3069 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7603  Z= 0.123
  Angle     :  0.447   5.826  10372  Z= 0.226
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.030   1258
  Dihedral  :  3.645  16.491    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  4.44 %
    Favored  : 94.52 %
  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:  2.49 (0.28), residues: 919
  helix:  1.91 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.62 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP C 231 
 HIS   0.003   0.000   HIS B 187 
 PHE   0.009   0.001   PHE A 274 
 TYR   0.006   0.001   TYR B 233 
 ARG   0.004   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  572)
  hydrogen bonds       : angle       4.13689 ( 1631)
  covalent geometry    : bond        0.00299 ( 7603)
  covalent geometry    : angle       0.44689 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 1.887 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7934 (mtp) cc_final: 0.7682 (mtm)
REVERT: A  304 TYR cc_start: 0.7873 (t80) cc_final: 0.7657 (t80)
REVERT: B   31 GLU cc_start: 0.7106 (tt0) cc_final: 0.6797 (mt-10)
REVERT: B   43 VAL cc_start: 0.8785 (t) cc_final: 0.8584 (t)
REVERT: B  231 TRP cc_start: 0.8564 (OUTLIER) cc_final: 0.7933 (m-10)
REVERT: B  253 LEU cc_start: 0.8638 (mm) cc_final: 0.8394 (mt)
REVERT: C  196 GLN cc_start: 0.9057 (pm20) cc_final: 0.8824 (pm20)
  outliers start: 8
  outliers final: 5
  residues processed: 84
  average time/residue: 0.2407
  time to fit residues: 28.7869
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 1.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  155 SER
Chi-restraints excluded: chain C residue  159 LEU
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 22 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.121043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.106082 restraints weight = 10967.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.66
r_work: 0.3040 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7603  Z= 0.133
  Angle     :  0.456   5.991  10372  Z= 0.230
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.684  16.722    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  4.31 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.28), residues: 919
  helix:  1.87 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.62 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP C 231 
 HIS   0.002   0.001   HIS B 187 
 PHE   0.009   0.001   PHE A 274 
 TYR   0.006   0.001   TYR B 233 
 ARG   0.004   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  572)
  hydrogen bonds       : angle       4.16143 ( 1631)
  covalent geometry    : bond        0.00327 ( 7603)
  covalent geometry    : angle       0.45616 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 1.864 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7973 (mtp) cc_final: 0.7730 (mtm)
REVERT: B   31 GLU cc_start: 0.7248 (tt0) cc_final: 0.6919 (mt-10)
REVERT: B   43 VAL cc_start: 0.8777 (t) cc_final: 0.8571 (t)
REVERT: B  231 TRP cc_start: 0.8614 (OUTLIER) cc_final: 0.7956 (m-10)
REVERT: B  253 LEU cc_start: 0.8694 (mm) cc_final: 0.8439 (mt)
  outliers start: 11
  outliers final: 10
  residues processed: 83
  average time/residue: 0.2162
  time to fit residues: 26.5159
Evaluate side-chains
  88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  155 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  101 ASN
Chi-restraints excluded: chain C residue  155 SER
Chi-restraints excluded: chain C residue  159 LEU
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 42 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 77 optimal weight:    0.2980
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0980
   chunk 89 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.123166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.108353 restraints weight = 10506.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 1.61
r_work: 0.3073 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7603  Z= 0.110
  Angle     :  0.441   6.473  10372  Z= 0.221
  Chirality :  0.037   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.603  16.439    992
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  4.31 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.28), residues: 919
  helix:  1.94 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.65 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 
 PHE   0.009   0.001   PHE A 274 
 TYR   0.008   0.001   TYR A 304 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03429 (  572)
  hydrogen bonds       : angle       4.07287 ( 1631)
  covalent geometry    : bond        0.00258 ( 7603)
  covalent geometry    : angle       0.44120 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7972 (mtp) cc_final: 0.7719 (mtm)
REVERT: B   31 GLU cc_start: 0.7251 (tt0) cc_final: 0.6891 (mt-10)
REVERT: B   43 VAL cc_start: 0.8754 (t) cc_final: 0.8536 (t)
REVERT: B  231 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.7874 (m-10)
REVERT: B  253 LEU cc_start: 0.8665 (mm) cc_final: 0.8395 (mt)
  outliers start: 11
  outliers final: 10
  residues processed: 85
  average time/residue: 0.2704
  time to fit residues: 31.6788
Evaluate side-chains
  88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  101 ASN
Chi-restraints excluded: chain B residue  155 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  101 ASN
Chi-restraints excluded: chain C residue  155 SER
Chi-restraints excluded: chain C residue  159 LEU
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 78 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 62 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5982

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.122367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.108258 restraints weight = 8913.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.45
r_work: 0.3077 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7603  Z= 0.119
  Angle     :  0.449   6.670  10372  Z= 0.224
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.622  16.467    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  4.44 %
    Favored  : 94.13 %
  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:  2.53 (0.28), residues: 919
  helix:  1.93 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.68 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 
 PHE   0.008   0.001   PHE A 274 
 TYR   0.007   0.001   TYR A 304 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  572)
  hydrogen bonds       : angle       4.07951 ( 1631)
  covalent geometry    : bond        0.00287 ( 7603)
  covalent geometry    : angle       0.44888 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 1.104 
Fit side-chains
REVERT: B   29 HIS cc_start: 0.7944 (m170) cc_final: 0.7603 (m170)
REVERT: B   31 GLU cc_start: 0.7291 (tt0) cc_final: 0.6905 (mt-10)
REVERT: B   43 VAL cc_start: 0.8729 (t) cc_final: 0.8508 (t)
REVERT: B  231 TRP cc_start: 0.8548 (OUTLIER) cc_final: 0.7910 (m-10)
REVERT: B  253 LEU cc_start: 0.8661 (mm) cc_final: 0.8395 (mt)
  outliers start: 11
  outliers final: 10
  residues processed: 84
  average time/residue: 0.2679
  time to fit residues: 32.8925
Evaluate side-chains
  88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 1.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  101 ASN
Chi-restraints excluded: chain B residue  155 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  101 ASN
Chi-restraints excluded: chain C residue  155 SER
Chi-restraints excluded: chain C residue  159 LEU
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 71 optimal weight:    0.3980
   chunk 85 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.121504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.104833 restraints weight = 16454.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.14
r_work: 0.2999 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7603  Z= 0.127
  Angle     :  0.456   6.975  10372  Z= 0.228
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.654  16.601    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  4.18 %
    Favored  : 94.39 %
  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:  2.49 (0.28), residues: 919
  helix:  1.91 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.67 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP C 231 
 HIS   0.002   0.001   HIS B 187 
 PHE   0.008   0.001   PHE A 274 
 TYR   0.007   0.001   TYR B 233 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03560 (  572)
  hydrogen bonds       : angle       4.10261 ( 1631)
  covalent geometry    : bond        0.00311 ( 7603)
  covalent geometry    : angle       0.45644 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A   58 MET cc_start: 0.8068 (mtp) cc_final: 0.7823 (mtm)
REVERT: B   31 GLU cc_start: 0.7353 (tt0) cc_final: 0.6935 (mt-10)
REVERT: B   43 VAL cc_start: 0.8778 (t) cc_final: 0.8563 (t)
REVERT: B  231 TRP cc_start: 0.8622 (OUTLIER) cc_final: 0.7967 (m-10)
REVERT: B  253 LEU cc_start: 0.8707 (mm) cc_final: 0.8427 (mt)
REVERT: C   31 GLU cc_start: 0.7085 (tt0) cc_final: 0.6105 (pt0)
  outliers start: 11
  outliers final: 9
  residues processed: 82
  average time/residue: 0.1805
  time to fit residues: 20.9537
Evaluate side-chains
  86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  101 ASN
Chi-restraints excluded: chain B residue  155 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  101 ASN
Chi-restraints excluded: chain C residue  155 SER
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 20 optimal weight:    0.4980
   chunk 52 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 10 optimal weight:    0.3980
   chunk 19 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.122091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.105837 restraints weight = 16199.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.02
r_work: 0.3032 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7603  Z= 0.118
  Angle     :  0.449   6.872  10372  Z= 0.224
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.633  16.616    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  4.44 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.28), residues: 919
  helix:  1.94 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.67 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 
 PHE   0.008   0.001   PHE A 274 
 TYR   0.006   0.001   TYR B 233 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03491 (  572)
  hydrogen bonds       : angle       4.07827 ( 1631)
  covalent geometry    : bond        0.00283 ( 7603)
  covalent geometry    : angle       0.44854 (10372)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.806 
Fit side-chains
REVERT: A   58 MET cc_start: 0.8050 (mtp) cc_final: 0.7809 (mtm)
REVERT: B   31 GLU cc_start: 0.7358 (tt0) cc_final: 0.6951 (mt-10)
REVERT: B   43 VAL cc_start: 0.8779 (t) cc_final: 0.8567 (t)
REVERT: B  231 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.7952 (m-10)
REVERT: B  253 LEU cc_start: 0.8691 (mm) cc_final: 0.8418 (mt)
REVERT: C   31 GLU cc_start: 0.7073 (tt0) cc_final: 0.6122 (pt0)
  outliers start: 10
  outliers final: 9
  residues processed: 81
  average time/residue: 0.1803
  time to fit residues: 20.6653
Evaluate side-chains
  86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue  101 ASN
Chi-restraints excluded: chain B residue  155 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  231 TRP
Chi-restraints excluded: chain C residue  101 ASN
Chi-restraints excluded: chain C residue  155 SER
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 72 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.122932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.106234 restraints weight = 16320.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.12
r_work: 0.3023 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2898
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2898 r_free = 0.2898    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2898 r_free = 0.2898    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2898
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7603  Z= 0.110
  Angle     :  0.443   6.796  10372  Z= 0.221
  Chirality :  0.037   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.590  16.583    992
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  4.70 %
    Favored  : 93.99 %
  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:  2.62 (0.28), residues: 919
  helix:  2.00 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.69 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 
 PHE   0.008   0.001   PHE A 274 
 TYR   0.006   0.001   TYR B 233 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  572)
  hydrogen bonds       : angle       4.03206 ( 1631)
  covalent geometry    : bond        0.00258 ( 7603)
  covalent geometry    : angle       0.44342 (10372)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4671.98 seconds
wall clock time: 84 minutes 56.43 seconds (5096.43 seconds total)