Starting phenix.real_space_refine
on Tue Mar  3 13:30:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r1d_14239/03_2026/7r1d_14239.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r1d_14239/03_2026/7r1d_14239.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r1d_14239/03_2026/7r1d_14239.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r1d_14239/03_2026/7r1d_14239.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r1d_14239/03_2026/7r1d_14239.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r1d_14239/03_2026/7r1d_14239.map"
  }
  resolution = 3.5
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    3279      2.51       5
     N     904      2.21       5
     O     981      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5183
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1549
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 180}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 3206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 405, 3206
          Classifications: {'peptide': 405}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 22, 'TRANS': 382}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 428
          Classifications: {'peptide': 56}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 7, 'TRANS': 48}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 1.30, per 1000 atoms: 0.25
  Number of scatterers: 5183
  At special positions: 0
  Unit cell: (68.04, 85.05, 99.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O     981      8.00
     N     904      7.00
     C    3279      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 403.7 milliseconds
  

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1234

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 12 sheets defined
      21.4% alpha, 24.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'C' and resid 96 through 114
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.608A  pdb=" N   TRP C 126 " --> pdb=" O   CYS C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 140 through 150
    Processing helix  chain 'C' and resid 159 through 169
      removed outlier: 3.717A  pdb=" N   LYS C 165 " --> pdb=" O   VAL C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 199
    Processing helix  chain 'C' and resid 281 through 286
      removed outlier: 3.548A  pdb=" N   PHE C 285 " --> pdb=" O   PRO C 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 9 through 27
    Processing helix  chain 'A' and resid 27 through 31
      removed outlier: 4.253A  pdb=" N   LEU A  31 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 27 through 31'
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'A' and resid 356 through 360
      removed outlier: 3.892A  pdb=" N   ALA A 359 " --> pdb=" O   PRO A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 409
    Processing helix  chain 'B' and resid 107 through 109
      No H-bonds generated for 'chain 'B' and resid 107 through 109'
    Processing helix  chain 'B' and resid 114 through 125
      removed outlier: 4.116A  pdb=" N   ILE B 118 " --> pdb=" O   PRO B 114 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 157 through 158
      removed outlier: 3.856A  pdb=" N   PHE A  93 " --> pdb=" O   LEU C 158 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 216 through 217
      removed outlier: 3.769A  pdb=" N   MET C 280 " --> pdb=" O   ILE C 216 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 263 through 267
      removed outlier: 6.958A  pdb=" N   THR C 251 " --> pdb=" O   VAL C 245 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   VAL C 245 " --> pdb=" O   THR C 251 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ARG C 253 " --> pdb=" O   ASP C 243 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 39
      removed outlier: 3.982A  pdb=" N   ILE A 398 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP A 379 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 49
      removed outlier: 3.660A  pdb=" N   GLN A  48 " --> pdb=" O   VAL A  67 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASN A  77 " --> pdb=" O   HIS A 123 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   HIS A 123 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 119 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   SER A  83 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   ILE A 117 " --> pdb=" O   SER A  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 63
    Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 133
      removed outlier: 5.561A  pdb=" N   ILE A 139 " --> pdb=" O   MET A 133 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ARG A 172 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 183 through 185
    Processing sheet with id=AA9, first strand: chain 'A' and resid 230 through 235
      removed outlier: 3.737A  pdb=" N   ALA A 247 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LYS A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 276 through 281
      removed outlier: 3.608A  pdb=" N   CYS A 278 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   HIS A 311 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 322 through 325
      removed outlier: 6.664A  pdb=" N   ASP A 346 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   LEU A 366 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 99
      removed outlier: 3.792A  pdb=" N   ILE B  97 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   VAL B 104 " --> pdb=" O   ILE B  97 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    495 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: 0.68

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1664
        1.34 -     1.45: 788
        1.45 -     1.57: 2838
        1.57 -     1.69: 0
        1.69 -     1.81: 27
  Bond restraints: 5317
  Sorted by residual:
  bond pdb=" CA  GLU A 286 "
       pdb=" C   GLU A 286 "
    ideal  model  delta    sigma   weight residual
    1.523  1.497  0.027 1.80e-02 3.09e+03 2.20e+00
  bond pdb=" CB  PRO C 173 "
       pdb=" CG  PRO C 173 "
    ideal  model  delta    sigma   weight residual
    1.492  1.565 -0.073 5.00e-02 4.00e+02 2.13e+00
  bond pdb=" CD1 TYR A  98 "
       pdb=" CE1 TYR A  98 "
    ideal  model  delta    sigma   weight residual
    1.382  1.342  0.040 3.00e-02 1.11e+03 1.79e+00
  bond pdb=" CB  TYR A  98 "
       pdb=" CG  TYR A  98 "
    ideal  model  delta    sigma   weight residual
    1.512  1.485  0.027 2.20e-02 2.07e+03 1.49e+00
  bond pdb=" CA  ILE A  81 "
       pdb=" C   ILE A  81 "
    ideal  model  delta    sigma   weight residual
    1.527  1.518  0.009 8.50e-03 1.38e+04 1.11e+00
  ... (remaining 5312 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 7080
        2.40 -     4.81: 121
        4.81 -     7.21: 17
        7.21 -     9.61: 2
        9.61 -    12.02: 2
  Bond angle restraints: 7222
  Sorted by residual:
  angle pdb=" C   HIS A  97 "
        pdb=" N   TYR A  98 "
        pdb=" CA  TYR A  98 "
      ideal   model   delta    sigma   weight residual
     121.54  111.77    9.77 1.91e+00 2.74e-01 2.62e+01
  angle pdb=" C   LEU C 198 "
        pdb=" N   GLN C 199 "
        pdb=" CA  GLN C 199 "
      ideal   model   delta    sigma   weight residual
     122.56  114.04    8.52 1.72e+00 3.38e-01 2.45e+01
  angle pdb=" C   GLY A 107 "
        pdb=" N   PHE A 108 "
        pdb=" CA  PHE A 108 "
      ideal   model   delta    sigma   weight residual
     122.41  131.60   -9.19 2.09e+00 2.29e-01 1.93e+01
  angle pdb=" CA  PRO C 173 "
        pdb=" N   PRO C 173 "
        pdb=" CD  PRO C 173 "
      ideal   model   delta    sigma   weight residual
     112.00  106.57    5.43 1.40e+00 5.10e-01 1.51e+01
  angle pdb=" CA  LEU C 212 "
        pdb=" CB  LEU C 212 "
        pdb=" CG  LEU C 212 "
      ideal   model   delta    sigma   weight residual
     116.30  128.32  -12.02 3.50e+00 8.16e-02 1.18e+01
  ... (remaining 7217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.09: 2844
       16.09 -    32.18: 270
       32.18 -    48.26: 50
       48.26 -    64.35: 18
       64.35 -    80.44: 3
  Dihedral angle restraints: 3185
    sinusoidal: 1288
      harmonic: 1897
  Sorted by residual:
  dihedral pdb=" CA  GLY A 107 "
           pdb=" C   GLY A 107 "
           pdb=" N   PHE A 108 "
           pdb=" CA  PHE A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.22   27.78     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  SER A 315 "
           pdb=" C   SER A 315 "
           pdb=" N   HIS A 316 "
           pdb=" CA  HIS A 316 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.42   22.58     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  HIS A  78 "
           pdb=" C   HIS A  78 "
           pdb=" N   LEU A  79 "
           pdb=" CA  LEU A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.10   21.90     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 3182 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 449
       0.033 -    0.067: 194
       0.067 -    0.100: 93
       0.100 -    0.133: 44
       0.133 -    0.167: 3
  Chirality restraints: 783
  Sorted by residual:
  chirality pdb=" CA  GLN C 199 "
            pdb=" N   GLN C 199 "
            pdb=" C   GLN C 199 "
            pdb=" CB  GLN C 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.95e-01
  chirality pdb=" CA  THR A  28 "
            pdb=" N   THR A  28 "
            pdb=" C   THR A  28 "
            pdb=" CB  THR A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.06e-01
  chirality pdb=" CG  LEU C 212 "
            pdb=" CB  LEU C 212 "
            pdb=" CD1 LEU C 212 "
            pdb=" CD2 LEU C 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.47e-01
  ... (remaining 780 not shown)

  Planarity restraints: 940
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 172 "    0.084 5.00e-02 4.00e+02   1.24e-01 2.47e+01
        pdb=" N   PRO C 173 "   -0.215 5.00e-02 4.00e+02
        pdb=" CA  PRO C 173 "    0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO C 173 "    0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 107 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   GLY A 107 "    0.039 2.00e-02 2.50e+03
        pdb=" O   GLY A 107 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PHE A 108 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  24 "   -0.017 2.00e-02 2.50e+03   1.31e-02 4.31e+00
        pdb=" CG  TRP A  24 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  24 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  24 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  24 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  24 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  24 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  24 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  24 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  24 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 937 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 107
        2.66 -     3.22: 5036
        3.22 -     3.78: 8356
        3.78 -     4.34: 11320
        4.34 -     4.90: 18569
  Nonbonded interactions: 43388
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 227 "
            pdb=" OD1 ASN C 274 "
     model   vdw
     2.097 3.040
  nonbonded pdb=" NE2 GLN A  76 "
            pdb=" OD1 ASN A 122 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" OD1 ASP A 379 "
            pdb=" N   PHE A 380 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" O   GLU A 275 "
            pdb=" OG  SER A 293 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OH  TYR A 284 "
            pdb=" O   PRO A 327 "
     model   vdw
     2.190 3.040
  ... (remaining 43383 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
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:             0.340
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.570
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
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      :  0.005   0.073   5317  Z= 0.217
  Angle     :  0.795  12.018   7222  Z= 0.432
  Chirality :  0.048   0.167    783
  Planarity :  0.006   0.124    940
  Dihedral  : 13.608  80.437   1951
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 18.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.32), residues: 645
  helix:  0.41 (0.49), residues: 121
  sheet: -1.10 (0.34), residues: 193
  loop : -1.14 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 172 
 TYR   0.021   0.002   TYR A 409 
 PHE   0.010   0.001   PHE A 243 
 TRP   0.033   0.003   TRP A  24 
 HIS   0.005   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 5317)
  covalent geometry    : angle       0.79536 ( 7222)
  hydrogen bonds       : bond        0.21431 (  180)
  hydrogen bonds       : angle       8.72972 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.189 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9293 (tp) cc_final: 0.9038 (tp)
REVERT: C  111 ASN cc_start: 0.8693 (m-40) cc_final: 0.8381 (m-40)
REVERT: C  183 GLU cc_start: 0.8659 (tt0) cc_final: 0.8353 (tt0)
REVERT: C  252 TYR cc_start: 0.8183 (m-80) cc_final: 0.7965 (m-80)
REVERT: A   33 ASP cc_start: 0.7141 (m-30) cc_final: 0.6819 (m-30)
REVERT: A   40 LEU cc_start: 0.9024 (mt) cc_final: 0.8779 (mt)
REVERT: A   72 THR cc_start: 0.8702 (m) cc_final: 0.8492 (m)
REVERT: A   79 LEU cc_start: 0.8577 (tp) cc_final: 0.8311 (tp)
REVERT: A  102 LYS cc_start: 0.7214 (mttt) cc_final: 0.6846 (mttt)
REVERT: A  282 ASN cc_start: 0.8648 (t0) cc_final: 0.7842 (t0)
REVERT: A  319 GLU cc_start: 0.7109 (tt0) cc_final: 0.6851 (mt-10)
REVERT: A  395 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7381 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0900
  time to fit residues: 15.9749
Evaluate side-chains
  118 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0020
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 HIS
A 322 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.139150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108004 restraints weight = 9375.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.111730 restraints weight = 4817.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.114168 restraints weight = 3228.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.115738 restraints weight = 2545.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.116694 restraints weight = 2202.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5317  Z= 0.162
  Angle     :  0.705  10.115   7222  Z= 0.357
  Chirality :  0.048   0.163    783
  Planarity :  0.005   0.080    940
  Dihedral  :  5.559  23.353    695
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  9.84 %
    Favored  : 88.05 %
  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 are not related in a simple way.
  whole: -1.19 (0.32), residues: 645
  helix:  1.07 (0.48), residues: 116
  sheet: -1.40 (0.36), residues: 185
  loop : -1.03 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 185 
 TYR   0.017   0.002   TYR C 124 
 PHE   0.016   0.001   PHE C 256 
 TRP   0.024   0.002   TRP C 121 
 HIS   0.006   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 5317)
  covalent geometry    : angle       0.70530 ( 7222)
  hydrogen bonds       : bond        0.03492 (  180)
  hydrogen bonds       : angle       5.96725 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: C  109 LEU cc_start: 0.9321 (tp) cc_final: 0.9046 (tp)
REVERT: C  111 ASN cc_start: 0.8725 (m-40) cc_final: 0.8387 (m-40)
REVERT: C  163 TRP cc_start: 0.7708 (m100) cc_final: 0.7335 (m100)
REVERT: C  183 GLU cc_start: 0.8714 (tt0) cc_final: 0.8463 (tt0)
REVERT: C  192 ARG cc_start: 0.8249 (mtp-110) cc_final: 0.7886 (mtp85)
REVERT: A   24 TRP cc_start: 0.9083 (t60) cc_final: 0.8860 (t60)
REVERT: A   33 ASP cc_start: 0.7294 (m-30) cc_final: 0.6872 (m-30)
REVERT: A   79 LEU cc_start: 0.8538 (tp) cc_final: 0.8227 (tp)
REVERT: A  101 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7678 (pp20)
REVERT: A  282 ASN cc_start: 0.8680 (t0) cc_final: 0.7886 (t0)
REVERT: A  311 HIS cc_start: 0.7860 (t70) cc_final: 0.7442 (t-90)
REVERT: A  319 GLU cc_start: 0.7393 (tt0) cc_final: 0.6973 (tt0)
REVERT: A  395 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7483 (mm-30)
  outliers start: 12
  outliers final: 6
  residues processed: 125
  average time/residue: 0.0633
  time to fit residues: 10.7243
Evaluate side-chains
  117 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    0.2980
   chunk 15 optimal weight:    8.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 103 GLN
B 125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.139193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.108110 restraints weight = 9200.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.111806 restraints weight = 4754.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114232 restraints weight = 3186.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.115502 restraints weight = 2509.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.116669 restraints weight = 2196.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5317  Z= 0.154
  Angle     :  0.673  10.450   7222  Z= 0.339
  Chirality :  0.047   0.151    783
  Planarity :  0.004   0.066    940
  Dihedral  :  5.337  25.478    695
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 13.53 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.32), residues: 645
  helix:  1.04 (0.48), residues: 122
  sheet: -1.27 (0.36), residues: 184
  loop : -0.99 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 185 
 TYR   0.015   0.002   TYR A 409 
 PHE   0.015   0.001   PHE C 256 
 TRP   0.017   0.002   TRP B 122 
 HIS   0.004   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5317)
  covalent geometry    : angle       0.67320 ( 7222)
  hydrogen bonds       : bond        0.03279 (  180)
  hydrogen bonds       : angle       5.61856 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: C  109 LEU cc_start: 0.9300 (tp) cc_final: 0.9009 (tp)
REVERT: C  111 ASN cc_start: 0.8698 (m-40) cc_final: 0.8352 (m-40)
REVERT: C  125 GLU cc_start: 0.8579 (tp30) cc_final: 0.8211 (tp30)
REVERT: C  127 PHE cc_start: 0.8420 (t80) cc_final: 0.7964 (t80)
REVERT: C  163 TRP cc_start: 0.7706 (m100) cc_final: 0.7125 (m100)
REVERT: C  252 TYR cc_start: 0.8306 (m-80) cc_final: 0.8064 (m-80)
REVERT: A   24 TRP cc_start: 0.9042 (t60) cc_final: 0.8746 (t60)
REVERT: A   33 ASP cc_start: 0.7382 (m-30) cc_final: 0.6926 (m-30)
REVERT: A   79 LEU cc_start: 0.8586 (tp) cc_final: 0.8323 (tp)
REVERT: A  282 ASN cc_start: 0.8689 (t0) cc_final: 0.7871 (t0)
REVERT: A  311 HIS cc_start: 0.7733 (t70) cc_final: 0.7427 (t70)
REVERT: A  395 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7448 (mm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 128
  average time/residue: 0.0679
  time to fit residues: 11.4718
Evaluate side-chains
  117 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 11 optimal weight:    0.1980
   chunk 10 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0870
   chunk 49 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.140419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.109776 restraints weight = 9220.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.113425 restraints weight = 4778.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.115851 restraints weight = 3191.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.117386 restraints weight = 2504.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.118356 restraints weight = 2163.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5317  Z= 0.134
  Angle     :  0.701  14.611   7222  Z= 0.338
  Chirality :  0.047   0.188    783
  Planarity :  0.004   0.057    940
  Dihedral  :  5.161  26.138    695
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 14.41 %
    Favored  : 82.78 %
  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 are not related in a simple way.
  whole: -0.80 (0.33), residues: 645
  helix:  1.25 (0.48), residues: 122
  sheet: -0.85 (0.35), residues: 194
  loop : -0.96 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 185 
 TYR   0.017   0.002   TYR A 409 
 PHE   0.016   0.001   PHE C 256 
 TRP   0.019   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5317)
  covalent geometry    : angle       0.70146 ( 7222)
  hydrogen bonds       : bond        0.03050 (  180)
  hydrogen bonds       : angle       5.34228 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.155 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9287 (tp) cc_final: 0.8994 (tp)
REVERT: C  111 ASN cc_start: 0.8720 (m-40) cc_final: 0.8373 (m-40)
REVERT: C  127 PHE cc_start: 0.8392 (t80) cc_final: 0.8047 (t80)
REVERT: C  163 TRP cc_start: 0.7840 (m100) cc_final: 0.7377 (m100)
REVERT: C  252 TYR cc_start: 0.8286 (m-80) cc_final: 0.8034 (m-80)
REVERT: A   24 TRP cc_start: 0.9022 (t60) cc_final: 0.8709 (t60)
REVERT: A   33 ASP cc_start: 0.7388 (m-30) cc_final: 0.6954 (m-30)
REVERT: A   79 LEU cc_start: 0.8607 (tp) cc_final: 0.8366 (tp)
REVERT: A  282 ASN cc_start: 0.8661 (t0) cc_final: 0.7946 (t0)
REVERT: A  321 PHE cc_start: 0.8565 (m-80) cc_final: 0.8216 (m-80)
REVERT: A  395 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7318 (mm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 122
  average time/residue: 0.0639
  time to fit residues: 10.3382
Evaluate side-chains
  120 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   chunk 51 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.140454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.109700 restraints weight = 9443.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.113417 restraints weight = 4845.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.115861 restraints weight = 3232.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.117066 restraints weight = 2537.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.118337 restraints weight = 2221.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5317  Z= 0.139
  Angle     :  0.692  14.040   7222  Z= 0.335
  Chirality :  0.047   0.177    783
  Planarity :  0.004   0.053    940
  Dihedral  :  5.088  27.156    695
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.64 %
    Favored  : 82.25 %
  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 are not related in a simple way.
  whole: -0.74 (0.33), residues: 645
  helix:  1.26 (0.48), residues: 122
  sheet: -0.80 (0.36), residues: 193
  loop : -0.91 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 231 
 TYR   0.016   0.002   TYR A 409 
 PHE   0.022   0.001   PHE C 256 
 TRP   0.022   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 5317)
  covalent geometry    : angle       0.69196 ( 7222)
  hydrogen bonds       : bond        0.03046 (  180)
  hydrogen bonds       : angle       5.26264 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.235 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9283 (tp) cc_final: 0.8994 (tp)
REVERT: C  111 ASN cc_start: 0.8724 (m-40) cc_final: 0.8372 (m-40)
REVERT: C  127 PHE cc_start: 0.8371 (t80) cc_final: 0.8088 (t80)
REVERT: C  163 TRP cc_start: 0.7987 (m100) cc_final: 0.7633 (m100)
REVERT: A   24 TRP cc_start: 0.9019 (t60) cc_final: 0.8695 (t60)
REVERT: A   33 ASP cc_start: 0.7457 (m-30) cc_final: 0.7055 (m-30)
REVERT: A   79 LEU cc_start: 0.8636 (tp) cc_final: 0.8409 (tp)
REVERT: A  282 ASN cc_start: 0.8683 (t0) cc_final: 0.7962 (t0)
REVERT: A  321 PHE cc_start: 0.8560 (m-80) cc_final: 0.8158 (m-80)
REVERT: A  395 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7328 (mm-30)
  outliers start: 12
  outliers final: 11
  residues processed: 121
  average time/residue: 0.0647
  time to fit residues: 10.4203
Evaluate side-chains
  124 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.139783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.108895 restraints weight = 9421.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.112532 restraints weight = 4849.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114982 restraints weight = 3259.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.116562 restraints weight = 2557.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.117417 restraints weight = 2205.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5317  Z= 0.158
  Angle     :  0.711  13.761   7222  Z= 0.343
  Chirality :  0.047   0.174    783
  Planarity :  0.004   0.051    940
  Dihedral  :  5.137  26.915    695
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.34 %
    Favored  : 80.84 %
  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 are not related in a simple way.
  whole: -0.69 (0.33), residues: 645
  helix:  1.27 (0.48), residues: 122
  sheet: -0.70 (0.36), residues: 192
  loop : -0.92 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 196 
 TYR   0.015   0.002   TYR A 409 
 PHE   0.023   0.001   PHE C 256 
 TRP   0.023   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5317)
  covalent geometry    : angle       0.71093 ( 7222)
  hydrogen bonds       : bond        0.03070 (  180)
  hydrogen bonds       : angle       5.22347 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.185 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9292 (tp) cc_final: 0.9001 (tp)
REVERT: C  111 ASN cc_start: 0.8721 (m-40) cc_final: 0.8365 (m-40)
REVERT: C  127 PHE cc_start: 0.8408 (t80) cc_final: 0.8103 (t80)
REVERT: C  163 TRP cc_start: 0.8029 (m100) cc_final: 0.7625 (m100)
REVERT: C  196 ARG cc_start: 0.6856 (mtt90) cc_final: 0.6584 (ptp-170)
REVERT: A   24 TRP cc_start: 0.9035 (t60) cc_final: 0.8665 (t60)
REVERT: A   33 ASP cc_start: 0.7470 (m-30) cc_final: 0.7087 (m-30)
REVERT: A  282 ASN cc_start: 0.8730 (t0) cc_final: 0.7925 (t0)
REVERT: A  316 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7719 (m-70)
REVERT: A  321 PHE cc_start: 0.8587 (m-80) cc_final: 0.8176 (m-80)
REVERT: A  395 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7329 (mm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 127
  average time/residue: 0.0760
  time to fit residues: 12.5258
Evaluate side-chains
  126 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  231 ARG
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 47 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.4988

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.135511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.104643 restraints weight = 9435.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.108391 restraints weight = 4854.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.110768 restraints weight = 3248.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.112330 restraints weight = 2564.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.113073 restraints weight = 2216.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5317  Z= 0.257
  Angle     :  0.755  13.535   7222  Z= 0.374
  Chirality :  0.049   0.155    783
  Planarity :  0.005   0.053    940
  Dihedral  :  5.468  27.135    695
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.87 %
    Favored  : 79.96 %
  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 are not related in a simple way.
  whole: -0.93 (0.32), residues: 645
  helix:  1.48 (0.49), residues: 116
  sheet: -1.05 (0.37), residues: 177
  loop : -1.09 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 196 
 TYR   0.022   0.002   TYR A  98 
 PHE   0.024   0.002   PHE C 256 
 TRP   0.025   0.002   TRP B 122 
 HIS   0.004   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 ( 5317)
  covalent geometry    : angle       0.75528 ( 7222)
  hydrogen bonds       : bond        0.03395 (  180)
  hydrogen bonds       : angle       5.45864 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.213 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9336 (tp) cc_final: 0.9076 (tp)
REVERT: C  111 ASN cc_start: 0.8833 (m-40) cc_final: 0.8498 (m-40)
REVERT: C  163 TRP cc_start: 0.8084 (m100) cc_final: 0.7761 (m100)
REVERT: C  231 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6429 (mtm180)
REVERT: A   33 ASP cc_start: 0.7442 (m-30) cc_final: 0.7079 (m-30)
REVERT: A  282 ASN cc_start: 0.8845 (t0) cc_final: 0.7995 (t0)
REVERT: A  316 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7888 (m-70)
REVERT: A  395 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7347 (mm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 122
  average time/residue: 0.0753
  time to fit residues: 12.0605
Evaluate side-chains
  121 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  183 GLU
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  231 ARG
Chi-restraints excluded: chain C residue  239 THR
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.137973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.106913 restraints weight = 9309.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.110654 restraints weight = 4769.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.113141 restraints weight = 3198.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.114717 restraints weight = 2509.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.115665 restraints weight = 2168.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5317  Z= 0.154
  Angle     :  0.732  13.596   7222  Z= 0.353
  Chirality :  0.048   0.149    783
  Planarity :  0.004   0.049    940
  Dihedral  :  5.224  27.642    695
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.63 %
    Favored  : 78.91 %
  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 are not related in a simple way.
  whole: -0.85 (0.33), residues: 645
  helix:  1.31 (0.49), residues: 122
  sheet: -0.94 (0.36), residues: 190
  loop : -1.00 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 185 
 TYR   0.023   0.002   TYR C 124 
 PHE   0.024   0.001   PHE C 256 
 TRP   0.022   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 5317)
  covalent geometry    : angle       0.73210 ( 7222)
  hydrogen bonds       : bond        0.03119 (  180)
  hydrogen bonds       : angle       5.29854 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.221 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9308 (tp) cc_final: 0.9030 (tp)
REVERT: C  111 ASN cc_start: 0.8784 (m-40) cc_final: 0.8416 (m-40)
REVERT: C  127 PHE cc_start: 0.8449 (t80) cc_final: 0.8201 (t80)
REVERT: C  163 TRP cc_start: 0.8025 (m100) cc_final: 0.7652 (m100)
REVERT: A   33 ASP cc_start: 0.7463 (m-30) cc_final: 0.7023 (m-30)
REVERT: A  282 ASN cc_start: 0.8725 (t0) cc_final: 0.7876 (t0)
REVERT: A  316 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7560 (m-70)
REVERT: A  395 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7348 (mm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 118
  average time/residue: 0.0663
  time to fit residues: 10.4594
Evaluate side-chains
  118 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 53 optimal weight:    0.4980
   chunk 12 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    0.1980
   chunk 15 optimal weight:    4.9990
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.138780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.107929 restraints weight = 9330.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.111681 restraints weight = 4740.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.114188 restraints weight = 3176.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.115748 restraints weight = 2485.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.116740 restraints weight = 2148.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5317  Z= 0.143
  Angle     :  0.736  14.196   7222  Z= 0.357
  Chirality :  0.048   0.162    783
  Planarity :  0.005   0.059    940
  Dihedral  :  5.264  28.551    695
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.98 %
    Favored  : 78.73 %
  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 are not related in a simple way.
  whole: -0.88 (0.33), residues: 645
  helix:  1.18 (0.49), residues: 122
  sheet: -1.02 (0.35), residues: 197
  loop : -0.92 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG C 196 
 TYR   0.023   0.002   TYR C 124 
 PHE   0.011   0.001   PHE C 256 
 TRP   0.024   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5317)
  covalent geometry    : angle       0.73567 ( 7222)
  hydrogen bonds       : bond        0.03009 (  180)
  hydrogen bonds       : angle       5.26863 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.166 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9296 (tp) cc_final: 0.9001 (tp)
REVERT: C  111 ASN cc_start: 0.8744 (m-40) cc_final: 0.8373 (m-40)
REVERT: C  127 PHE cc_start: 0.8502 (t80) cc_final: 0.8214 (t80)
REVERT: C  163 TRP cc_start: 0.8007 (m100) cc_final: 0.7637 (m100)
REVERT: A   33 ASP cc_start: 0.7421 (m-30) cc_final: 0.7005 (m-30)
REVERT: A  282 ASN cc_start: 0.8670 (t0) cc_final: 0.7916 (t0)
REVERT: A  316 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7583 (m-70)
REVERT: A  395 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7342 (mm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 120
  average time/residue: 0.0567
  time to fit residues: 9.1309
Evaluate side-chains
  118 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 5 optimal weight:    0.0050
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.139154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.108362 restraints weight = 9295.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.112136 restraints weight = 4720.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.114650 restraints weight = 3153.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.116255 restraints weight = 2454.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.116867 restraints weight = 2107.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   5317  Z= 0.144
  Angle     :  0.751  14.452   7222  Z= 0.361
  Chirality :  0.048   0.210    783
  Planarity :  0.004   0.048    940
  Dihedral  :  5.203  28.500    695
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.86 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.33), residues: 645
  helix:  1.03 (0.49), residues: 123
  sheet: -0.86 (0.36), residues: 193
  loop : -0.95 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 196 
 TYR   0.023   0.002   TYR C 124 
 PHE   0.016   0.001   PHE C 256 
 TRP   0.034   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5317)
  covalent geometry    : angle       0.75106 ( 7222)
  hydrogen bonds       : bond        0.03111 (  180)
  hydrogen bonds       : angle       5.29351 (  495)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.212 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9283 (tp) cc_final: 0.8996 (tp)
REVERT: C  111 ASN cc_start: 0.8688 (m-40) cc_final: 0.8329 (m-40)
REVERT: C  127 PHE cc_start: 0.8504 (t80) cc_final: 0.8219 (t80)
REVERT: C  163 TRP cc_start: 0.8027 (m100) cc_final: 0.7723 (m100)
REVERT: C  196 ARG cc_start: 0.7152 (ptp-170) cc_final: 0.6640 (ptp-170)
REVERT: C  200 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.6148 (mt0)
REVERT: A   33 ASP cc_start: 0.7417 (m-30) cc_final: 0.6990 (m-30)
REVERT: A  282 ASN cc_start: 0.8590 (t0) cc_final: 0.7806 (t0)
REVERT: A  316 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7582 (m-70)
REVERT: A  321 PHE cc_start: 0.8697 (m-80) cc_final: 0.8316 (m-80)
REVERT: A  395 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7353 (mm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 122
  average time/residue: 0.0794
  time to fit residues: 12.4176
Evaluate side-chains
  123 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0030
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.138528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.107862 restraints weight = 9343.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.111602 restraints weight = 4771.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114106 restraints weight = 3178.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.115684 restraints weight = 2480.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.116403 restraints weight = 2138.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   5317  Z= 0.158
  Angle     :  0.758  14.347   7222  Z= 0.365
  Chirality :  0.049   0.188    783
  Planarity :  0.004   0.048    940
  Dihedral  :  5.285  28.313    695
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.68 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.32), residues: 645
  helix:  0.99 (0.48), residues: 123
  sheet: -0.79 (0.36), residues: 191
  loop : -0.97 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 185 
 TYR   0.022   0.002   TYR C 124 
 PHE   0.013   0.001   PHE A 243 
 TRP   0.036   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 5317)
  covalent geometry    : angle       0.75762 ( 7222)
  hydrogen bonds       : bond        0.03099 (  180)
  hydrogen bonds       : angle       5.28649 (  495)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1084.68 seconds
wall clock time: 19 minutes 23.01 seconds (1163.01 seconds total)