Starting phenix.real_space_refine
on Tue Mar 11 15:23:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxp_36708/03_2025/8jxp_36708_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxp_36708/03_2025/8jxp_36708.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxp_36708/03_2025/8jxp_36708.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxp_36708/03_2025/8jxp_36708.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxp_36708/03_2025/8jxp_36708_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxp_36708/03_2025/8jxp_36708_neut.cif"
  }
  resolution = 2.7
  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=   0.009
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: 5
    Type Number    sf(0)   Gaussians
     K      18      8.98       5
     S      42      5.16       5
     C    4176      2.51       5
     N     954      2.21       5
     O    1104      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6294
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2069
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 11, 'TRANS': 250}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 26
          Unusual residues: {'  K': 6, 'RET': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    518  SG  CYS A  72      33.958  19.202  56.026  1.00 30.00           S

  Restraints were copied for chains:
    C, B
  Time building chain proxies: 6.29, per 1000 atoms: 1.00
  Number of scatterers: 6294
  At special positions: 0
  Unit cell: (74.2, 72.1, 90.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K      18     19.00
     S      42     16.00
     O    1104      8.00
     N     954      7.00
     C    4176      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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.73
  Conformation dependent library (CDL) restraints added in 863.0 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      81.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 12
    Processing helix  chain 'A' and resid 17 through 45
    Processing helix  chain 'A' and resid 59 through 62
    Processing helix  chain 'A' and resid 63 through 89
    Processing helix  chain 'A' and resid 103 through 120
      removed outlier: 4.484A  pdb=" N   ILE A 107 " --> pdb=" O   SER A 103 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 124 through 145
      removed outlier: 3.830A  pdb=" N   VAL A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 174
      removed outlier: 3.626A  pdb=" N   TYR A 151 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR A 152 " --> pdb=" O   PRO A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
      removed outlier: 3.826A  pdb=" N   TRP A 185 " --> pdb=" O   ASP A 181 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   TYR A 186 " --> pdb=" O   SER A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 205
      removed outlier: 3.587A  pdb=" N   PHE A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
      Proline residue:  A 202  - end of helix
      removed outlier: 3.533A  pdb=" N   TRP A 205 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 216 through 231
      removed outlier: 3.534A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 263
    Processing helix  chain 'B' and resid 8 through 12
    Processing helix  chain 'B' and resid 17 through 45
    Processing helix  chain 'B' and resid 59 through 62
    Processing helix  chain 'B' and resid 63 through 89
    Processing helix  chain 'B' and resid 103 through 120
      removed outlier: 4.484A  pdb=" N   ILE B 107 " --> pdb=" O   SER B 103 " (cutoff:3.500A)
      Proline residue:  B 110  - end of helix
    Processing helix  chain 'B' and resid 124 through 145
      removed outlier: 3.830A  pdb=" N   VAL B 140 " --> pdb=" O   LEU B 136 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE B 143 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 174
      removed outlier: 3.626A  pdb=" N   TYR B 151 " --> pdb=" O   ALA B 147 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR B 152 " --> pdb=" O   PRO B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 3.826A  pdb=" N   TRP B 185 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   TYR B 186 " --> pdb=" O   SER B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 205
      removed outlier: 3.587A  pdb=" N   PHE B 201 " --> pdb=" O   GLY B 197 " (cutoff:3.500A)
      Proline residue:  B 202  - end of helix
      removed outlier: 3.533A  pdb=" N   TRP B 205 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 208
      No H-bonds generated for 'chain 'B' and resid 206 through 208'
    Processing helix  chain 'B' and resid 216 through 231
      removed outlier: 3.534A  pdb=" N   ILE B 226 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 263
    Processing helix  chain 'C' and resid 8 through 12
    Processing helix  chain 'C' and resid 17 through 45
    Processing helix  chain 'C' and resid 59 through 62
    Processing helix  chain 'C' and resid 63 through 89
    Processing helix  chain 'C' and resid 103 through 120
      removed outlier: 4.483A  pdb=" N   ILE C 107 " --> pdb=" O   SER C 103 " (cutoff:3.500A)
      Proline residue:  C 110  - end of helix
    Processing helix  chain 'C' and resid 124 through 145
      removed outlier: 3.830A  pdb=" N   VAL C 140 " --> pdb=" O   LEU C 136 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE C 143 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 174
      removed outlier: 3.626A  pdb=" N   TYR C 151 " --> pdb=" O   ALA C 147 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR C 152 " --> pdb=" O   PRO C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 180 through 196
      removed outlier: 3.826A  pdb=" N   TRP C 185 " --> pdb=" O   ASP C 181 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   TYR C 186 " --> pdb=" O   SER C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 205
      removed outlier: 3.587A  pdb=" N   PHE C 201 " --> pdb=" O   GLY C 197 " (cutoff:3.500A)
      Proline residue:  C 202  - end of helix
      removed outlier: 3.533A  pdb=" N   TRP C 205 " --> pdb=" O   PHE C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 208
      No H-bonds generated for 'chain 'C' and resid 206 through 208'
    Processing helix  chain 'C' and resid 216 through 231
      removed outlier: 3.534A  pdb=" N   ILE C 226 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 263

    456 hydrogen bonds defined for protein.
    1341 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: 1.63

  Time building geometry restraints manager: 1.92 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 981
        1.32 -     1.44: 1938
        1.44 -     1.56: 3492
        1.56 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 6465
  Sorted by residual:
  bond pdb=" CA  LEU B 192 "
       pdb=" C   LEU B 192 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.053 1.24e-02 6.50e+03 1.80e+01
  bond pdb=" CA  LEU C 192 "
       pdb=" C   LEU C 192 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.053 1.24e-02 6.50e+03 1.80e+01
  bond pdb=" CA  LEU A 192 "
       pdb=" C   LEU A 192 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.053 1.24e-02 6.50e+03 1.80e+01
  bond pdb=" C   ASP C  82 "
       pdb=" O   ASP C  82 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.043 1.17e-02 7.31e+03 1.34e+01
  bond pdb=" C   ASP A  82 "
       pdb=" O   ASP A  82 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.043 1.17e-02 7.31e+03 1.33e+01
  ... (remaining 6460 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 8319
        2.41 -     4.83: 409
        4.83 -     7.24: 47
        7.24 -     9.65: 39
        9.65 -    12.06: 12
  Bond angle restraints: 8826
  Sorted by residual:
  angle pdb=" N   ALA A 137 "
        pdb=" CA  ALA A 137 "
        pdb=" C   ALA A 137 "
      ideal   model   delta    sigma   weight residual
     113.41  101.83   11.58 1.22e+00 6.72e-01 9.01e+01
  angle pdb=" N   ALA C 137 "
        pdb=" CA  ALA C 137 "
        pdb=" C   ALA C 137 "
      ideal   model   delta    sigma   weight residual
     113.41  101.86   11.55 1.22e+00 6.72e-01 8.96e+01
  angle pdb=" N   ALA B 137 "
        pdb=" CA  ALA B 137 "
        pdb=" C   ALA B 137 "
      ideal   model   delta    sigma   weight residual
     113.41  101.87   11.54 1.22e+00 6.72e-01 8.95e+01
  angle pdb=" N   LEU B 192 "
        pdb=" CA  LEU B 192 "
        pdb=" C   LEU B 192 "
      ideal   model   delta    sigma   weight residual
     110.97  100.70   10.27 1.09e+00 8.42e-01 8.87e+01
  angle pdb=" N   LEU A 192 "
        pdb=" CA  LEU A 192 "
        pdb=" C   LEU A 192 "
      ideal   model   delta    sigma   weight residual
     110.97  100.71   10.26 1.09e+00 8.42e-01 8.87e+01
  ... (remaining 8821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 2928
       17.06 -    34.11: 390
       34.11 -    51.17: 216
       51.17 -    68.23: 96
       68.23 -    85.28: 15
  Dihedral angle restraints: 3645
    sinusoidal: 1371
      harmonic: 2274
  Sorted by residual:
  dihedral pdb=" C   ALA B 147 "
           pdb=" N   ALA B 147 "
           pdb=" CA  ALA B 147 "
           pdb=" CB  ALA B 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.54   11.94     0      2.50e+00 1.60e-01 2.28e+01
  dihedral pdb=" C   ALA A 147 "
           pdb=" N   ALA A 147 "
           pdb=" CA  ALA A 147 "
           pdb=" CB  ALA A 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.53   11.93     0      2.50e+00 1.60e-01 2.28e+01
  dihedral pdb=" C   ALA C 147 "
           pdb=" N   ALA C 147 "
           pdb=" CA  ALA C 147 "
           pdb=" CB  ALA C 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.50   11.90     0      2.50e+00 1.60e-01 2.27e+01
  ... (remaining 3642 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 804
       0.110 -    0.221: 114
       0.221 -    0.331: 24
       0.331 -    0.441: 6
       0.441 -    0.551: 6
  Chirality restraints: 954
  Sorted by residual:
  chirality pdb=" CA  ALA A 147 "
            pdb=" N   ALA A 147 "
            pdb=" C   ALA A 147 "
            pdb=" CB  ALA A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.93    0.55 2.00e-01 2.50e+01 7.60e+00
  chirality pdb=" CA  ALA B 147 "
            pdb=" N   ALA B 147 "
            pdb=" C   ALA B 147 "
            pdb=" CB  ALA B 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.93    0.55 2.00e-01 2.50e+01 7.59e+00
  chirality pdb=" CA  ALA C 147 "
            pdb=" N   ALA C 147 "
            pdb=" C   ALA C 147 "
            pdb=" CB  ALA C 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.94    0.55 2.00e-01 2.50e+01 7.53e+00
  ... (remaining 951 not shown)

  Planarity restraints: 1095
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 109 "   -0.113 5.00e-02 4.00e+02   1.65e-01 4.34e+01
        pdb=" N   PRO A 110 "    0.284 5.00e-02 4.00e+02
        pdb=" CA  PRO A 110 "   -0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO A 110 "   -0.096 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 109 "   -0.113 5.00e-02 4.00e+02   1.65e-01 4.34e+01
        pdb=" N   PRO B 110 "    0.284 5.00e-02 4.00e+02
        pdb=" CA  PRO B 110 "   -0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO B 110 "   -0.096 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 109 "    0.113 5.00e-02 4.00e+02   1.65e-01 4.34e+01
        pdb=" N   PRO C 110 "   -0.284 5.00e-02 4.00e+02
        pdb=" CA  PRO C 110 "    0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO C 110 "    0.096 5.00e-02 4.00e+02
  ... (remaining 1092 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.34: 12
        2.34 -     3.04: 4128
        3.04 -     3.74: 12479
        3.74 -     4.44: 20818
        4.44 -     5.14: 31787
  Nonbonded interactions: 69224
  Sorted by model distance:
  nonbonded pdb=" CG  MET A 239 "
            pdb=" K     K A 401 "
     model   vdw
     1.644 3.250
  nonbonded pdb=" CG  MET C 239 "
            pdb=" K     K C 401 "
     model   vdw
     1.644 3.250
  nonbonded pdb=" CG  MET B 239 "
            pdb=" K     K B 401 "
     model   vdw
     1.645 3.250
  nonbonded pdb=" CB  MET A 239 "
            pdb=" K     K A 401 "
     model   vdw
     1.890 3.250
  nonbonded pdb=" CB  MET B 239 "
            pdb=" K     K B 401 "
     model   vdw
     1.890 3.250
  ... (remaining 69219 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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=1.00 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:             10.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.880
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
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      :  0.009   0.053   6465  Z= 0.558
  Angle     :  1.325  12.064   8826  Z= 0.904
  Chirality :  0.095   0.551    954
  Planarity :  0.016   0.165   1095
  Dihedral  : 22.329  85.284   2193
  Min Nonbonded Distance : 1.644

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  1.92 %
    Allowed  :  6.92 %
    Favored  : 91.15 %
  Rotamer:
    Outliers : 24.41 %
    Allowed  : 13.15 %
    Favored  : 62.44 %
  Cbeta Deviations :  0.83 %
  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 (0.26), residues: 780
  helix: -1.57 (0.17), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.35 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 219 
 HIS   0.005   0.002   HIS C 210 
 PHE   0.037   0.003   PHE A 143 
 TYR   0.010   0.002   TYR A 102 
 ARG   0.003   0.001   ARG B 176 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 156
    poor density    : 99
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7068 (mt)
REVERT: A  203 LEU cc_start: 0.8053 (mt) cc_final: 0.7842 (tp)
REVERT: B  126 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7089 (mt)
REVERT: B  203 LEU cc_start: 0.8043 (mt) cc_final: 0.7810 (tp)
REVERT: C  126 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7139 (mt)
REVERT: C  203 LEU cc_start: 0.8047 (mt) cc_final: 0.7818 (tp)
  outliers start: 156
  outliers final: 25
  residues processed: 228
  average time/residue: 0.8980
  time to fit residues: 217.9219
Evaluate side-chains
  91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 63
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  149 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  202 PRO
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain B residue    4 CYS
Chi-restraints excluded: chain B residue    5 CYS
Chi-restraints excluded: chain B residue  115 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  149 TYR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  202 PRO
Chi-restraints excluded: chain B residue  260 LYS
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain C residue    4 CYS
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  202 PRO
Chi-restraints excluded: chain C residue  260 LYS
Chi-restraints excluded: chain C residue  261 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
A 210 HIS
B  99 GLN
B 210 HIS
C  98 ASN
C  99 GLN
C 175 GLN
C 210 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.161903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.136295 restraints weight = 5954.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.47
r_work: 0.3810 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6465  Z= 0.232
  Angle     :  0.628   8.624   8826  Z= 0.324
  Chirality :  0.040   0.130    954
  Planarity :  0.007   0.081   1095
  Dihedral  : 10.503  68.811    929
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  3.46 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  7.51 %
    Allowed  : 18.31 %
    Favored  : 74.18 %
  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:  1.14 (0.29), residues: 780
  helix:  1.28 (0.20), residues: 573
  sheet:  None (None), residues: 0
  loop : -0.58 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 198 
 HIS   0.004   0.002   HIS A 224 
 PHE   0.011   0.001   PHE A 195 
 TYR   0.017   0.002   TYR B  86 
 ARG   0.002   0.000   ARG C 243 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 61
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7455 (pt0)
REVERT: A   11 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.6850 (mp10)
REVERT: A   13 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7467 (mt-10)
REVERT: A  203 LEU cc_start: 0.8155 (mt) cc_final: 0.7855 (tp)
REVERT: B    6 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7559 (pt0)
REVERT: B   13 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7375 (mt-10)
REVERT: B  203 LEU cc_start: 0.8117 (mt) cc_final: 0.7849 (tp)
REVERT: C    6 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7551 (pt0)
REVERT: C   13 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7662 (mt-10)
REVERT: C  203 LEU cc_start: 0.8186 (mt) cc_final: 0.7881 (tp)
  outliers start: 48
  outliers final: 20
  residues processed: 101
  average time/residue: 0.7950
  time to fit residues: 86.6805
Evaluate side-chains
  67 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 43
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLN
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain B residue   13 GLU
Chi-restraints excluded: chain B residue   56 GLU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  260 LYS
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  200 PHE
Chi-restraints excluded: chain C residue  260 LYS
Chi-restraints excluded: chain C residue  261 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0980
   chunk 18 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.151874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.126456 restraints weight = 6115.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.48
r_work: 0.3635 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3537 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.4445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6465  Z= 0.233
  Angle     :  0.583   9.422   8826  Z= 0.295
  Chirality :  0.040   0.119    954
  Planarity :  0.006   0.060   1095
  Dihedral  :  9.338  83.065    900
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  3.46 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 22.54 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.30), residues: 780
  helix:  2.24 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.16 (0.47), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 219 
 HIS   0.006   0.002   HIS B 210 
 PHE   0.011   0.001   PHE B 195 
 TYR   0.013   0.002   TYR C  86 
 ARG   0.005   0.001   ARG B 243 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 57
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7538 (pt0)
REVERT: A   64 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7579 (tt)
REVERT: A  200 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7412 (t80)
REVERT: A  203 LEU cc_start: 0.8336 (mt) cc_final: 0.8053 (tp)
REVERT: B    6 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7576 (pt0)
REVERT: B   64 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8052 (tp)
REVERT: B  200 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7429 (t80)
REVERT: B  203 LEU cc_start: 0.8360 (mt) cc_final: 0.8036 (tp)
REVERT: C    6 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7610 (pt0)
REVERT: C  200 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7472 (t80)
REVERT: C  203 LEU cc_start: 0.8373 (mt) cc_final: 0.8046 (tp)
  outliers start: 27
  outliers final: 9
  residues processed: 78
  average time/residue: 0.6071
  time to fit residues: 52.2813
Evaluate side-chains
  60 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  194 PHE
Chi-restraints excluded: chain C residue  200 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 77 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 25 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.143022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.117147 restraints weight = 5878.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.27
r_work: 0.3277 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.4786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6465  Z= 0.201
  Angle     :  0.548  10.504   8826  Z= 0.270
  Chirality :  0.038   0.122    954
  Planarity :  0.005   0.051   1095
  Dihedral  :  7.740  85.482    878
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.69 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 23.63 %
    Favored  : 72.46 %
  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:  2.87 (0.30), residues: 780
  helix:  2.48 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.27 (0.47), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 219 
 HIS   0.006   0.003   HIS B 210 
 PHE   0.007   0.001   PHE C 242 
 TYR   0.013   0.001   TYR C  86 
 ARG   0.002   0.000   ARG B 243 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 52
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7449 (pt0)
REVERT: A  200 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7450 (t80)
REVERT: B    6 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7466 (pt0)
REVERT: B  200 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7482 (t80)
REVERT: C    6 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7553 (pt0)
REVERT: C  200 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7494 (t80)
REVERT: C  203 LEU cc_start: 0.8371 (mt) cc_final: 0.8005 (tp)
  outliers start: 25
  outliers final: 14
  residues processed: 71
  average time/residue: 0.6614
  time to fit residues: 51.3735
Evaluate side-chains
  66 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain B residue   56 GLU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  194 PHE
Chi-restraints excluded: chain C residue  200 PHE
Chi-restraints excluded: chain C residue  261 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.142457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.117091 restraints weight = 5784.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.24
r_work: 0.3257 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.4970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6465  Z= 0.214
  Angle     :  0.551  11.109   8826  Z= 0.269
  Chirality :  0.038   0.120    954
  Planarity :  0.005   0.047   1095
  Dihedral  :  7.871  86.657    878
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.33 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 22.69 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (0.30), residues: 780
  helix:  2.52 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.40 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 184 
 HIS   0.005   0.002   HIS B 210 
 PHE   0.007   0.001   PHE A 242 
 TYR   0.012   0.001   TYR C  76 
 ARG   0.002   0.000   ARG C 243 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 50
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7511 (pt0)
REVERT: A  200 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7529 (t80)
REVERT: A  203 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8097 (tm)
REVERT: B    6 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7509 (pt0)
REVERT: B  200 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7522 (t80)
REVERT: B  203 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8057 (tm)
REVERT: C  200 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7586 (t80)
REVERT: C  203 LEU cc_start: 0.8431 (mt) cc_final: 0.8052 (tm)
  outliers start: 26
  outliers final: 15
  residues processed: 62
  average time/residue: 0.7679
  time to fit residues: 51.7379
Evaluate side-chains
  67 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 47
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain B residue   56 GLU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  200 PHE
Chi-restraints excluded: chain C residue  261 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 66 optimal weight:    0.1980
   chunk 60 optimal weight:    0.5980
   chunk 25 optimal weight:   10.0000
   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 = 0.3705 r_free = 0.3705 target = 0.144013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.118562 restraints weight = 5782.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.32
r_work: 0.3291 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6465  Z= 0.158
  Angle     :  0.508  10.144   8826  Z= 0.248
  Chirality :  0.037   0.118    954
  Planarity :  0.005   0.045   1095
  Dihedral  :  7.533  83.793    878
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.82 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.32 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.17 (0.30), residues: 780
  helix:  2.72 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.32 (0.46), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 184 
 HIS   0.004   0.002   HIS B 210 
 PHE   0.007   0.001   PHE C 242 
 TYR   0.010   0.001   TYR C  76 
 ARG   0.002   0.000   ARG B 243 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.668 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7426 (pt0)
REVERT: A  200 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7451 (t80)
REVERT: A  203 LEU cc_start: 0.8375 (mt) cc_final: 0.7981 (tm)
REVERT: B  200 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7429 (t80)
REVERT: B  203 LEU cc_start: 0.8341 (mt) cc_final: 0.7948 (tm)
REVERT: C  200 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7489 (t80)
REVERT: C  203 LEU cc_start: 0.8359 (mt) cc_final: 0.7949 (tm)
  outliers start: 19
  outliers final: 9
  residues processed: 66
  average time/residue: 0.8537
  time to fit residues: 61.1768
Evaluate side-chains
  62 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  194 PHE
Chi-restraints excluded: chain C residue  200 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.138006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.112721 restraints weight = 5761.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.22
r_work: 0.3163 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.5139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6465  Z= 0.270
  Angle     :  0.588  12.957   8826  Z= 0.284
  Chirality :  0.040   0.130    954
  Planarity :  0.005   0.043   1095
  Dihedral  :  7.521  86.541    874
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  2.95 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 23.16 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.08 (0.30), residues: 780
  helix:  2.57 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.52 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 184 
 HIS   0.007   0.003   HIS B 210 
 PHE   0.008   0.001   PHE A 195 
 TYR   0.012   0.002   TYR C  76 
 ARG   0.001   0.000   ARG C 243 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A  200 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7563 (t80)
REVERT: A  203 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8179 (tm)
REVERT: B  200 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7584 (t80)
REVERT: B  203 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8159 (tm)
REVERT: C  200 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7662 (t80)
REVERT: C  203 LEU cc_start: 0.8460 (mt) cc_final: 0.8121 (tm)
  outliers start: 24
  outliers final: 11
  residues processed: 66
  average time/residue: 0.6729
  time to fit residues: 48.9899
Evaluate side-chains
  66 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  200 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0570
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
A  49 ASN
B  49 ASN
C  49 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.141089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.115219 restraints weight = 5786.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.31
r_work: 0.3177 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.5270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6465  Z= 0.190
  Angle     :  0.541  11.680   8826  Z= 0.263
  Chirality :  0.038   0.125    954
  Planarity :  0.005   0.043   1095
  Dihedral  :  7.301  85.865    874
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.82 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 24.73 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.20 (0.30), residues: 780
  helix:  2.70 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.47 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 184 
 HIS   0.005   0.002   HIS B 210 
 PHE   0.008   0.001   PHE A 251 
 TYR   0.010   0.001   TYR B  86 
 ARG   0.001   0.000   ARG A 243 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A  200 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7457 (t80)
REVERT: A  203 LEU cc_start: 0.8397 (mt) cc_final: 0.8021 (tm)
REVERT: B  200 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7460 (t80)
REVERT: B  203 LEU cc_start: 0.8380 (mt) cc_final: 0.8036 (tm)
REVERT: C  200 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7517 (t80)
REVERT: C  203 LEU cc_start: 0.8379 (mt) cc_final: 0.7998 (tm)
  outliers start: 14
  outliers final: 8
  residues processed: 52
  average time/residue: 0.8143
  time to fit residues: 46.1244
Evaluate side-chains
  57 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  200 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 77 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 57 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 66 optimal weight:    0.4980
   chunk 62 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   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 = 0.3682 r_free = 0.3682 target = 0.141973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.116644 restraints weight = 5839.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.25
r_work: 0.3222 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.5345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6465  Z= 0.176
  Angle     :  0.527  11.217   8826  Z= 0.257
  Chirality :  0.038   0.122    954
  Planarity :  0.005   0.044   1095
  Dihedral  :  7.132  83.741    874
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.08 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 24.10 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.32 (0.30), residues: 780
  helix:  2.78 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.54 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 184 
 HIS   0.004   0.002   HIS B 210 
 PHE   0.007   0.001   PHE A 242 
 TYR   0.010   0.001   TYR C  86 
 ARG   0.001   0.000   ARG A 243 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A  200 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7566 (t80)
REVERT: A  203 LEU cc_start: 0.8471 (mt) cc_final: 0.8126 (tm)
REVERT: B  200 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7556 (t80)
REVERT: B  203 LEU cc_start: 0.8442 (mt) cc_final: 0.8123 (tm)
REVERT: C  200 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7612 (t80)
REVERT: C  203 LEU cc_start: 0.8449 (mt) cc_final: 0.8091 (tm)
  outliers start: 14
  outliers final: 9
  residues processed: 54
  average time/residue: 0.7914
  time to fit residues: 46.5636
Evaluate side-chains
  59 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  200 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3665 r_free = 0.3665 target = 0.140753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.115010 restraints weight = 5827.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.31
r_work: 0.3194 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.5346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6465  Z= 0.199
  Angle     :  0.544  11.931   8826  Z= 0.264
  Chirality :  0.039   0.125    954
  Planarity :  0.005   0.044   1095
  Dihedral  :  7.254  85.424    874
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.82 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 24.41 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.29 (0.30), residues: 780
  helix:  2.75 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.57 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 184 
 HIS   0.004   0.002   HIS B 210 
 PHE   0.007   0.001   PHE C 242 
 TYR   0.011   0.001   TYR B  76 
 ARG   0.001   0.000   ARG A 243 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A  200 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7469 (t80)
REVERT: A  203 LEU cc_start: 0.8409 (mt) cc_final: 0.8045 (tm)
REVERT: B  200 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7470 (t80)
REVERT: B  203 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8037 (tm)
REVERT: C  200 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7531 (t80)
REVERT: C  203 LEU cc_start: 0.8387 (mt) cc_final: 0.7997 (tm)
  outliers start: 12
  outliers final: 8
  residues processed: 51
  average time/residue: 0.8408
  time to fit residues: 46.4803
Evaluate side-chains
  59 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  200 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.138875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.113142 restraints weight = 5914.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.33
r_work: 0.3169 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.5342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6465  Z= 0.233
  Angle     :  0.567  12.562   8826  Z= 0.274
  Chirality :  0.039   0.130    954
  Planarity :  0.005   0.043   1095
  Dihedral  :  7.368  86.322    874
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.46 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.63 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.19 (0.30), residues: 780
  helix:  2.66 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.59 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 184 
 HIS   0.006   0.002   HIS C 210 
 PHE   0.007   0.001   PHE B 242 
 TYR   0.011   0.001   TYR B  76 
 ARG   0.002   0.000   ARG A 243 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4646.87 seconds
wall clock time: 80 minutes 9.42 seconds (4809.42 seconds total)