Starting phenix.real_space_refine
on Fri Aug 22 16:58:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxp_36708/08_2025/8jxp_36708_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxp_36708/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxp_36708/08_2025/8jxp_36708_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxp_36708/08_2025/8jxp_36708_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxp_36708/08_2025/8jxp_36708.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxp_36708/08_2025/8jxp_36708.map"
  }
  resolution = 2.7
  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=   0.009
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C
  Time building chain proxies: 1.37, per 1000 atoms: 0.22
  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: 0.44
  Conformation dependent library (CDL) restraints added in 325.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.12
  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: 0.99

  Time building geometry restraints manager: 0.62 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             23.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.530
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.930
-------------------------------------------------------------------------------
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   6468  Z= 0.645
  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 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: -2.49 (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
 ARG   0.003   0.001   ARG B 176 
 TYR   0.010   0.002   TYR A 102 
 PHE   0.037   0.003   PHE A 143 
 TRP   0.011   0.002   TRP A 219 
 HIS   0.005   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00868 ( 6465)
  covalent geometry    : angle       1.32543 ( 8826)
  hydrogen bonds       : bond        0.16354 (  456)
  hydrogen bonds       : angle       6.48951 ( 1341)
  Misc. bond           : bond        0.05116 (    3)

*********************** 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  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7067 (mt)
REVERT: A  203 LEU cc_start: 0.8053 (mt) cc_final: 0.7844 (tp)
REVERT: B  126 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7087 (mt)
REVERT: B  203 LEU cc_start: 0.8043 (mt) cc_final: 0.7811 (tp)
REVERT: C  126 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7137 (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: 0.3982
  time to fit residues: 96.3520
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  : 0.239 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0050
   chunk 45 optimal weight:    0.2980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4594

-------------------------------------------------------------------------------
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  99 GLN
C 175 GLN
C 210 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.167532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.142206 restraints weight = 6042.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3848 rms_B_bonded: 1.47
r_work: 0.3799 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3703 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6468  Z= 0.150
  Angle     :  0.616   8.308   8826  Z= 0.322
  Chirality :  0.040   0.146    954
  Planarity :  0.007   0.081   1095
  Dihedral  : 10.555  69.121    929
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  3.59 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 19.25 %
    Favored  : 74.02 %
  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:  1.05 (0.29), residues: 780
  helix:  1.25 (0.20), residues: 570
  sheet:  None (None), residues: 0
  loop : -0.69 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 243 
 TYR   0.015   0.002   TYR B  86 
 PHE   0.011   0.001   PHE B 195 
 TRP   0.013   0.001   TRP B 198 
 HIS   0.004   0.002   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6465)
  covalent geometry    : angle       0.61635 ( 8826)
  hydrogen bonds       : bond        0.04607 (  456)
  hydrogen bonds       : angle       4.11045 ( 1341)
  Misc. bond           : bond        0.00054 (    3)

*********************** 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
  94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 51
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7527 (pt0)
REVERT: A   11 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.6840 (mp10)
REVERT: A   13 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7468 (mt-10)
REVERT: A  194 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7735 (t80)
REVERT: A  203 LEU cc_start: 0.8099 (mt) cc_final: 0.7748 (tp)
REVERT: B    6 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7520 (pt0)
REVERT: B   13 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7340 (mt-10)
REVERT: B  194 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7710 (t80)
REVERT: B  203 LEU cc_start: 0.8096 (mt) cc_final: 0.7766 (tp)
REVERT: C    6 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7557 (pt0)
REVERT: C   13 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7591 (mt-10)
REVERT: C  132 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7661 (mp)
REVERT: C  194 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7738 (t80)
REVERT: C  203 LEU cc_start: 0.8147 (mt) cc_final: 0.7780 (tp)
  outliers start: 43
  outliers final: 21
  residues processed: 87
  average time/residue: 0.3775
  time to fit residues: 34.9722
Evaluate side-chains
  70 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 41
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
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  194 PHE
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  194 PHE
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  132 ILE
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  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 15 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    1.5786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.146905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.121119 restraints weight = 6141.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 1.49
r_work: 0.3586 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6468  Z= 0.222
  Angle     :  0.650  11.448   8826  Z= 0.326
  Chirality :  0.042   0.127    954
  Planarity :  0.006   0.060   1095
  Dihedral  :  9.788  88.673    901
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  3.08 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 22.54 %
    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 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:  2.28 (0.30), residues: 780
  helix:  2.11 (0.20), residues: 570
  sheet:  None (None), residues: 0
  loop : -0.12 (0.46), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 243 
 TYR   0.018   0.002   TYR B  86 
 PHE   0.013   0.002   PHE A 116 
 TRP   0.018   0.002   TRP B 219 
 HIS   0.008   0.003   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 6465)
  covalent geometry    : angle       0.64951 ( 8826)
  hydrogen bonds       : bond        0.05323 (  456)
  hydrogen bonds       : angle       4.02145 ( 1341)
  Misc. bond           : bond        0.00156 (    3)

*********************** 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
  99 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7562 (pt0)
REVERT: A   64 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7581 (tt)
REVERT: A  200 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7391 (t80)
REVERT: A  203 LEU cc_start: 0.8367 (mt) cc_final: 0.8115 (tp)
REVERT: B    6 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7551 (pt0)
REVERT: B  200 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7418 (t80)
REVERT: B  203 LEU cc_start: 0.8363 (mt) cc_final: 0.8121 (tp)
REVERT: C    6 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7609 (pt0)
REVERT: C  203 LEU cc_start: 0.8410 (mt) cc_final: 0.8101 (tp)
  outliers start: 28
  outliers final: 10
  residues processed: 96
  average time/residue: 0.2625
  time to fit residues: 27.5247
Evaluate side-chains
  66 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  200 PHE
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 32 optimal weight:    0.2980
   chunk 69 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0770
   chunk 73 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 17 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5940

-------------------------------------------------------------------------------
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 = 0.142121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.116206 restraints weight = 5825.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.31
r_work: 0.3260 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6468  Z= 0.124
  Angle     :  0.538  10.349   8826  Z= 0.267
  Chirality :  0.038   0.118    954
  Planarity :  0.005   0.052   1095
  Dihedral  :  8.305  87.882    883
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.82 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 23.63 %
    Favored  : 72.61 %
  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:  2.90 (0.30), residues: 780
  helix:  2.49 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.30 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 123 
 TYR   0.012   0.001   TYR A  86 
 PHE   0.008   0.001   PHE C 194 
 TRP   0.009   0.001   TRP A 184 
 HIS   0.005   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6465)
  covalent geometry    : angle       0.53849 ( 8826)
  hydrogen bonds       : bond        0.04207 (  456)
  hydrogen bonds       : angle       3.83544 ( 1341)
  Misc. bond           : bond        0.00001 (    3)

*********************** 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
  74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 50
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7477 (pt0)
REVERT: A  200 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7394 (t80)
REVERT: A  203 LEU cc_start: 0.8311 (mt) cc_final: 0.7961 (tp)
REVERT: B    6 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7353 (pt0)
REVERT: B  200 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7384 (t80)
REVERT: B  203 LEU cc_start: 0.8311 (mt) cc_final: 0.7931 (tp)
REVERT: C    6 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7449 (pt0)
REVERT: C  200 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7445 (t80)
  outliers start: 24
  outliers final: 13
  residues processed: 68
  average time/residue: 0.2711
  time to fit residues: 20.1984
Evaluate side-chains
  58 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
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  261 LEU
Chi-restraints excluded: chain B residue  121 ASN
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  136 LEU
Chi-restraints excluded: chain C residue  168 LEU
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 64 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.140503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.114485 restraints weight = 5936.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.28
r_work: 0.3244 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.5046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6468  Z= 0.138
  Angle     :  0.544  11.034   8826  Z= 0.267
  Chirality :  0.038   0.120    954
  Planarity :  0.005   0.049   1095
  Dihedral  :  8.198  87.014    882
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.95 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 23.79 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.30), residues: 780
  helix:  2.58 (0.20), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.40 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  51 
 TYR   0.016   0.001   TYR C  86 
 PHE   0.008   0.001   PHE A 195 
 TRP   0.010   0.001   TRP A 184 
 HIS   0.005   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6465)
  covalent geometry    : angle       0.54425 ( 8826)
  hydrogen bonds       : bond        0.04287 (  456)
  hydrogen bonds       : angle       3.78749 ( 1341)
  Misc. bond           : bond        0.00015 (    3)

*********************** 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
  69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 43
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7555 (pt0)
REVERT: A  200 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7511 (t80)
REVERT: B    6 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7471 (pt0)
REVERT: B  200 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7509 (t80)
REVERT: C    6 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7576 (pt0)
REVERT: C  200 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7553 (t80)
REVERT: C  203 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8076 (tm)
  outliers start: 26
  outliers final: 14
  residues processed: 59
  average time/residue: 0.3500
  time to fit residues: 22.2772
Evaluate side-chains
  60 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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  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  200 PHE
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  203 LEU
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 75 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.139881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.114107 restraints weight = 5838.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.29
r_work: 0.3211 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.5156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6468  Z= 0.142
  Angle     :  0.550  11.710   8826  Z= 0.268
  Chirality :  0.039   0.125    954
  Planarity :  0.005   0.047   1095
  Dihedral  :  8.174  86.689    882
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.08 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 23.47 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.12 (0.30), residues: 780
  helix:  2.67 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.35 (0.46), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 176 
 TYR   0.015   0.001   TYR C  86 
 PHE   0.008   0.001   PHE A 251 
 TRP   0.009   0.001   TRP A 184 
 HIS   0.006   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6465)
  covalent geometry    : angle       0.54958 ( 8826)
  hydrogen bonds       : bond        0.04283 (  456)
  hydrogen bonds       : angle       3.78336 ( 1341)
  Misc. bond           : bond        0.00015 (    3)

*********************** 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
  73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 45
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7541 (pt0)
REVERT: A  200 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7489 (t80)
REVERT: A  203 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8059 (tm)
REVERT: B    6 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7497 (pt0)
REVERT: B  200 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7490 (t80)
REVERT: B  203 LEU cc_start: 0.8427 (mt) cc_final: 0.8048 (tm)
REVERT: C  200 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7540 (t80)
REVERT: C  203 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8049 (tm)
  outliers start: 28
  outliers final: 17
  residues processed: 63
  average time/residue: 0.3082
  time to fit residues: 21.0332
Evaluate side-chains
  65 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 43
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
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  182 SER
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  121 ASN
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 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  203 LEU
Chi-restraints excluded: chain C residue  261 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 66 optimal weight:    0.2980
   chunk 56 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.140544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.114953 restraints weight = 5806.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.28
r_work: 0.3210 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.5252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6468  Z= 0.132
  Angle     :  0.536  11.564   8826  Z= 0.260
  Chirality :  0.038   0.125    954
  Planarity :  0.005   0.046   1095
  Dihedral  :  8.026  85.777    882
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.95 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.16 %
    Favored  : 72.61 %
  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:  3.20 (0.30), residues: 780
  helix:  2.72 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.41 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  51 
 TYR   0.013   0.001   TYR C  86 
 PHE   0.008   0.001   PHE B 195 
 TRP   0.009   0.001   TRP A 184 
 HIS   0.005   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6465)
  covalent geometry    : angle       0.53554 ( 8826)
  hydrogen bonds       : bond        0.04146 (  456)
  hydrogen bonds       : angle       3.76390 ( 1341)
  Misc. bond           : bond        0.00008 (    3)

*********************** 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
  73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 46
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7562 (pt0)
REVERT: A  200 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7514 (t80)
REVERT: A  203 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8068 (tm)
REVERT: B  200 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7501 (t80)
REVERT: B  203 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8076 (tm)
REVERT: C  200 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7552 (t80)
REVERT: C  203 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8097 (tm)
  outliers start: 27
  outliers final: 15
  residues processed: 61
  average time/residue: 0.3316
  time to fit residues: 21.9696
Evaluate side-chains
  63 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 42
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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  182 SER
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  121 ASN
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  203 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  194 PHE
Chi-restraints excluded: chain C residue  200 PHE
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  261 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.139780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.114453 restraints weight = 5847.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.24
r_work: 0.3190 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.5283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6468  Z= 0.138
  Angle     :  0.546  12.119   8826  Z= 0.264
  Chirality :  0.039   0.127    954
  Planarity :  0.005   0.045   1095
  Dihedral  :  8.049  86.019    882
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.21 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 24.10 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.23 (0.30), residues: 780
  helix:  2.73 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.45 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  51 
 TYR   0.013   0.001   TYR C  86 
 PHE   0.008   0.001   PHE B 195 
 TRP   0.009   0.001   TRP B 184 
 HIS   0.005   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6465)
  covalent geometry    : angle       0.54584 ( 8826)
  hydrogen bonds       : bond        0.04208 (  456)
  hydrogen bonds       : angle       3.76717 ( 1341)
  Misc. bond           : bond        0.00012 (    3)

*********************** 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
  67 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 45
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7635 (pt0)
REVERT: A  200 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7562 (t80)
REVERT: A  203 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8122 (tm)
REVERT: B  200 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7568 (t80)
REVERT: B  203 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8154 (tm)
REVERT: C  200 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7616 (t80)
REVERT: C  203 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8160 (tm)
  outliers start: 22
  outliers final: 12
  residues processed: 59
  average time/residue: 0.3284
  time to fit residues: 21.0355
Evaluate side-chains
  61 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
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  168 LEU
Chi-restraints excluded: chain B residue  182 SER
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  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  203 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3656 r_free = 0.3656 target = 0.139673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.113971 restraints weight = 5873.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.31
r_work: 0.3182 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.5333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6468  Z= 0.138
  Angle     :  0.543  12.140   8826  Z= 0.263
  Chirality :  0.039   0.127    954
  Planarity :  0.005   0.046   1095
  Dihedral  :  7.986  85.625    882
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.95 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 24.57 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.25 (0.30), residues: 780
  helix:  2.74 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.46 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  51 
 TYR   0.013   0.001   TYR C  86 
 PHE   0.009   0.001   PHE B 194 
 TRP   0.009   0.001   TRP B 184 
 HIS   0.005   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6465)
  covalent geometry    : angle       0.54298 ( 8826)
  hydrogen bonds       : bond        0.04185 (  456)
  hydrogen bonds       : angle       3.77396 ( 1341)
  Misc. bond           : bond        0.00008 (    3)

*********************** 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
  63 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7544 (pt0)
REVERT: A  200 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7460 (t80)
REVERT: A  203 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8023 (tm)
REVERT: B  200 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7452 (t80)
REVERT: B  203 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8035 (tm)
REVERT: C  200 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7505 (t80)
REVERT: C  203 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8039 (tm)
  outliers start: 19
  outliers final: 12
  residues processed: 54
  average time/residue: 0.3801
  time to fit residues: 22.1207
Evaluate side-chains
  62 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 44
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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  168 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 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  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   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 = 0.3638 r_free = 0.3638 target = 0.138146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.112999 restraints weight = 5777.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.23
r_work: 0.3187 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.5347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6468  Z= 0.155
  Angle     :  0.564  12.903   8826  Z= 0.273
  Chirality :  0.039   0.132    954
  Planarity :  0.005   0.045   1095
  Dihedral  :  7.995  86.299    880
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.21 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 24.73 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.19 (0.29), residues: 780
  helix:  2.69 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.48 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 176 
 TYR   0.013   0.001   TYR C  86 
 PHE   0.009   0.001   PHE B 194 
 TRP   0.010   0.001   TRP B 184 
 HIS   0.005   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6465)
  covalent geometry    : angle       0.56438 ( 8826)
  hydrogen bonds       : bond        0.04354 (  456)
  hydrogen bonds       : angle       3.79239 ( 1341)
  Misc. bond           : bond        0.00015 (    3)

********************** 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
  64 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7656 (pt0)
REVERT: A  200 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7555 (t80)
REVERT: A  203 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8145 (tm)
REVERT: B  200 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7559 (t80)
REVERT: B  203 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8163 (tm)
REVERT: C  200 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7596 (t80)
REVERT: C  203 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8163 (tm)
  outliers start: 18
  outliers final: 12
  residues processed: 56
  average time/residue: 0.3497
  time to fit residues: 21.1854
Evaluate side-chains
  64 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
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  168 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 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  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0970
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.141246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.115906 restraints weight = 5888.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.29
r_work: 0.3207 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.5416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6468  Z= 0.119
  Angle     :  0.526  11.373   8826  Z= 0.256
  Chirality :  0.038   0.122    954
  Planarity :  0.005   0.046   1095
  Dihedral  :  7.732  85.194    880
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.69 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 25.04 %
    Favored  : 72.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.32 (0.29), residues: 780
  helix:  2.79 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.52 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 176 
 TYR   0.012   0.001   TYR C  86 
 PHE   0.010   0.001   PHE B 194 
 TRP   0.009   0.001   TRP B 184 
 HIS   0.004   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6465)
  covalent geometry    : angle       0.52550 ( 8826)
  hydrogen bonds       : bond        0.04010 (  456)
  hydrogen bonds       : angle       3.76956 ( 1341)
  Misc. bond           : bond        0.00003 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2271.39 seconds
wall clock time: 39 minutes 32.55 seconds (2372.55 seconds total)