Starting phenix.real_space_refine
on Wed Sep 17 08:47:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vi4_43248/09_2025/8vi4_43248.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vi4_43248/09_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_43248/09_2025/8vi4_43248.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vi4_43248/09_2025/8vi4_43248.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vi4_43248/09_2025/8vi4_43248.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vi4_43248/09_2025/8vi4_43248.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=   0.015
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): 0.01s

  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: 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: 2.23, per 1000 atoms: 0.30
  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: 0.61
  Conformation dependent library (CDL) restraints added in 453.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.26
  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: 1.35

  Time building geometry restraints manager: 0.83 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:             8.720
  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:          0.180
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     9.290
  Find NCS groups from input model:        0.150
  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:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.520
-------------------------------------------------------------------------------
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 : 4.86
  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 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:  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
 ARG   0.003   0.000   ARG B  79 
 TYR   0.004   0.001   TYR C 143 
 PHE   0.014   0.001   PHE C 288 
 TRP   0.040   0.001   TRP B 231 
 HIS   0.003   0.001   HIS A 163 

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

*********************** 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  : 0.285 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0876
  time to fit residues: 8.8256
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  : 0.225 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0070
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5198

-------------------------------------------------------------------------------
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 = 0.3307 r_free = 0.3307 target = 0.115699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.098678 restraints weight = 16232.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.33
r_work: 0.2910 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7603  Z= 0.126
  Angle     :  0.478   5.899  10372  Z= 0.244
  Chirality :  0.039   0.120   1171
  Planarity :  0.004   0.025   1258
  Dihedral  :  3.710  15.901    992
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  2.35 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.46 (0.29), residues: 919
  helix:  1.97 (0.19), residues: 733
  sheet:  None (None), residues: 0
  loop :  0.40 (0.52), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  79 
 TYR   0.010   0.001   TYR A 304 
 PHE   0.015   0.001   PHE A 274 
 TRP   0.039   0.001   TRP A 231 
 HIS   0.002   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7603)
  covalent geometry    : angle       0.47767 (10372)
  hydrogen bonds       : bond        0.03876 (  572)
  hydrogen bonds       : angle       4.36752 ( 1631)

*********************** 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
  88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7680 (mtp) cc_final: 0.7448 (mtt)
REVERT: A  114 ILE cc_start: 0.7946 (mt) cc_final: 0.7726 (mm)
REVERT: A  304 TYR cc_start: 0.7770 (t80) cc_final: 0.7404 (t80)
REVERT: C   58 MET cc_start: 0.7664 (mtp) cc_final: 0.7429 (mtt)
  outliers start: 4
  outliers final: 3
  residues processed: 88
  average time/residue: 0.0817
  time to fit residues: 10.1707
Evaluate side-chains
  80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  231 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.118858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.103986 restraints weight = 10903.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.63
r_work: 0.3012 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2895
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7603  Z= 0.152
  Angle     :  0.479   5.961  10372  Z= 0.244
  Chirality :  0.039   0.120   1171
  Planarity :  0.004   0.026   1258
  Dihedral  :  3.782  16.651    992
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  3.13 %
    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 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:  2.26 (0.28), residues: 919
  helix:  1.80 (0.19), residues: 739
  sheet:  None (None), residues: 0
  loop :  0.45 (0.53), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  79 
 TYR   0.011   0.001   TYR A 304 
 PHE   0.011   0.001   PHE A 274 
 TRP   0.043   0.001   TRP A 231 
 HIS   0.003   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 7603)
  covalent geometry    : angle       0.47867 (10372)
  hydrogen bonds       : bond        0.03935 (  572)
  hydrogen bonds       : angle       4.34743 ( 1631)

*********************** 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
  85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7932 (mtp) cc_final: 0.7687 (mtm)
REVERT: A  114 ILE cc_start: 0.8094 (mt) cc_final: 0.7863 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0785
  time to fit residues: 9.2313
Evaluate side-chains
  81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 SER
Chi-restraints excluded: chain B residue  191 SER
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.122051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.107224 restraints weight = 10983.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.61
r_work: 0.3055 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1348

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= 0.122
  Angle     :  0.451   5.794  10372  Z= 0.229
  Chirality :  0.038   0.117   1171
  Planarity :  0.004   0.029   1258
  Dihedral  :  3.705  16.449    992
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  3.92 %
    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 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:  2.35 (0.28), residues: 919
  helix:  1.82 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.57 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  79 
 TYR   0.006   0.001   TYR A 143 
 PHE   0.010   0.001   PHE A 274 
 TRP   0.031   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7603)
  covalent geometry    : angle       0.45139 (10372)
  hydrogen bonds       : bond        0.03625 (  572)
  hydrogen bonds       : angle       4.21363 ( 1631)

*********************** 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
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7957 (mtp) cc_final: 0.7711 (mtm)
REVERT: A  114 ILE cc_start: 0.8074 (mt) cc_final: 0.7864 (mm)
REVERT: A  304 TYR cc_start: 0.7911 (t80) cc_final: 0.7594 (t80)
REVERT: B  253 LEU cc_start: 0.8654 (mm) cc_final: 0.8422 (mt)
REVERT: C  196 GLN cc_start: 0.9058 (pm20) cc_final: 0.8827 (pm20)
  outliers start: 7
  outliers final: 7
  residues processed: 86
  average time/residue: 0.0832
  time to fit residues: 10.0639
Evaluate side-chains
  85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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  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 45 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 34 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.122255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.105409 restraints weight = 16369.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.16
r_work: 0.3002 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1437

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= 0.122
  Angle     :  0.446   5.807  10372  Z= 0.226
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.030   1258
  Dihedral  :  3.677  16.596    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  3.79 %
    Favored  : 95.04 %
  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:  2.41 (0.28), residues: 919
  helix:  1.86 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.60 (0.55), residues: 165

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7603)
  covalent geometry    : angle       0.44634 (10372)
  hydrogen bonds       : bond        0.03582 (  572)
  hydrogen bonds       : angle       4.15513 ( 1631)

*********************** 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
  88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   58 MET cc_start: 0.8032 (mtp) cc_final: 0.7794 (mtm)
REVERT: A  304 TYR cc_start: 0.7911 (t80) cc_final: 0.7624 (t80)
REVERT: B   31 GLU cc_start: 0.7210 (tt0) cc_final: 0.6876 (mt-10)
REVERT: B  253 LEU cc_start: 0.8695 (mm) cc_final: 0.8428 (mt)
REVERT: C  196 GLN cc_start: 0.9054 (pm20) cc_final: 0.8825 (pm20)
  outliers start: 9
  outliers final: 8
  residues processed: 85
  average time/residue: 0.0806
  time to fit residues: 9.7453
Evaluate side-chains
  85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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  191 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.3386 r_free = 0.3386 target = 0.120583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.105758 restraints weight = 10632.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.62
r_work: 0.3055 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7603  Z= 0.139
  Angle     :  0.463   6.062  10372  Z= 0.233
  Chirality :  0.039   0.118   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.715  16.735    992
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  4.18 %
    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 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:  2.34 (0.28), residues: 919
  helix:  1.80 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.60 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  79 
 TYR   0.006   0.001   TYR B 233 
 PHE   0.008   0.001   PHE A 274 
 TRP   0.032   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7603)
  covalent geometry    : angle       0.46282 (10372)
  hydrogen bonds       : bond        0.03677 (  572)
  hydrogen bonds       : angle       4.17883 ( 1631)

*********************** 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
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7968 (mtp) cc_final: 0.7717 (mtm)
REVERT: A  304 TYR cc_start: 0.7921 (t80) cc_final: 0.7661 (t80)
REVERT: B   31 GLU cc_start: 0.7258 (tt0) cc_final: 0.6913 (mt-10)
REVERT: B  253 LEU cc_start: 0.8700 (mm) cc_final: 0.8452 (mt)
REVERT: C  196 GLN cc_start: 0.9067 (pm20) cc_final: 0.8830 (pm20)
  outliers start: 10
  outliers final: 8
  residues processed: 83
  average time/residue: 0.0749
  time to fit residues: 8.7012
Evaluate side-chains
  85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3389 r_free = 0.3389 target = 0.120871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.105401 restraints weight = 12456.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.79
r_work: 0.3023 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.1503

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= 0.131
  Angle     :  0.456   6.604  10372  Z= 0.229
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.697  16.701    992
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  4.44 %
    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 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:  2.38 (0.28), residues: 919
  helix:  1.83 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.63 (0.55), residues: 165

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7603)
  covalent geometry    : angle       0.45588 (10372)
  hydrogen bonds       : bond        0.03614 (  572)
  hydrogen bonds       : angle       4.13948 ( 1631)

*********************** 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
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8799 (mtp85) cc_final: 0.8573 (mtp180)
REVERT: A  304 TYR cc_start: 0.7934 (t80) cc_final: 0.7727 (t80)
REVERT: B   31 GLU cc_start: 0.7310 (tt0) cc_final: 0.6943 (mt-10)
REVERT: B  253 LEU cc_start: 0.8723 (mm) cc_final: 0.8473 (mt)
  outliers start: 9
  outliers final: 8
  residues processed: 83
  average time/residue: 0.0780
  time to fit residues: 9.1488
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 79 optimal weight:    0.3980
   chunk 59 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0770
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.122535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.105312 restraints weight = 19355.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.30
r_work: 0.3005 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    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 = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.1608

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= 0.109
  Angle     :  0.442   6.256  10372  Z= 0.221
  Chirality :  0.037   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.609  16.412    992
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  4.70 %
    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 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:  2.54 (0.28), residues: 919
  helix:  1.94 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.64 (0.54), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.006   0.001   TYR B 233 
 PHE   0.008   0.001   PHE A 274 
 TRP   0.029   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7603)
  covalent geometry    : angle       0.44176 (10372)
  hydrogen bonds       : bond        0.03430 (  572)
  hydrogen bonds       : angle       4.06403 ( 1631)

*********************** 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
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  304 TYR cc_start: 0.7956 (t80) cc_final: 0.7732 (t80)
REVERT: B   31 GLU cc_start: 0.7323 (tt0) cc_final: 0.6934 (mt-10)
REVERT: B  253 LEU cc_start: 0.8718 (mm) cc_final: 0.8446 (mt)
  outliers start: 8
  outliers final: 8
  residues processed: 84
  average time/residue: 0.0725
  time to fit residues: 8.6576
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
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  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 47 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0970
   chunk 30 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.121993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.105361 restraints weight = 16339.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.12
r_work: 0.3011 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.1609

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     :  0.447   6.892  10372  Z= 0.224
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.627  16.453    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  4.96 %
    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 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:  2.52 (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
 ARG   0.005   0.000   ARG B  79 
 TYR   0.006   0.001   TYR B 233 
 PHE   0.008   0.001   PHE A 274 
 TRP   0.030   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7603)
  covalent geometry    : angle       0.44696 (10372)
  hydrogen bonds       : bond        0.03509 (  572)
  hydrogen bonds       : angle       4.07630 ( 1631)

*********************** 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
  86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   58 MET cc_start: 0.8037 (mtp) cc_final: 0.7795 (mtm)
REVERT: B   31 GLU cc_start: 0.7339 (tt0) cc_final: 0.6932 (mt-10)
REVERT: B   43 VAL cc_start: 0.8765 (t) cc_final: 0.8528 (t)
REVERT: B  253 LEU cc_start: 0.8716 (mm) cc_final: 0.8425 (mt)
  outliers start: 8
  outliers final: 8
  residues processed: 83
  average time/residue: 0.0779
  time to fit residues: 9.1172
Evaluate side-chains
  85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0970
   chunk 55 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.122339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.107532 restraints weight = 10549.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.61
r_work: 0.3061 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1622

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= 0.116
  Angle     :  0.450   6.794  10372  Z= 0.223
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.616  16.417    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  4.83 %
    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 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:  2.57 (0.28), residues: 919
  helix:  1.96 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.68 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.008   0.001   TYR A 304 
 PHE   0.008   0.001   PHE A 274 
 TRP   0.031   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7603)
  covalent geometry    : angle       0.44980 (10372)
  hydrogen bonds       : bond        0.03475 (  572)
  hydrogen bonds       : angle       4.05377 ( 1631)

********************** 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
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.286 
Fit side-chains
REVERT: B   31 GLU cc_start: 0.7282 (tt0) cc_final: 0.6883 (mt-10)
REVERT: B   43 VAL cc_start: 0.8751 (t) cc_final: 0.8507 (t)
REVERT: B  253 LEU cc_start: 0.8692 (mm) cc_final: 0.8434 (mt)
  outliers start: 8
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0793
  time to fit residues: 9.0696
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.106430 restraints weight = 15021.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.01
r_work: 0.3029 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7603  Z= 0.111
  Angle     :  0.445   6.782  10372  Z= 0.222
  Chirality :  0.038   0.116   1171
  Planarity :  0.004   0.031   1258
  Dihedral  :  3.596  16.374    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  5.09 %
    Favored  : 93.86 %
  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:  2.62 (0.28), residues: 919
  helix:  1.99 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.71 (0.55), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.009   0.001   TYR A 304 
 PHE   0.007   0.001   PHE A 274 
 TRP   0.030   0.001   TRP C 231 
 HIS   0.002   0.000   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7603)
  covalent geometry    : angle       0.44500 (10372)
  hydrogen bonds       : bond        0.03440 (  572)
  hydrogen bonds       : angle       4.04524 ( 1631)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1981.52 seconds
wall clock time: 34 minutes 43.30 seconds (2083.30 seconds total)