Starting phenix.real_space_refine
on Sat May 10 01:44:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z6t_39804/05_2025/8z6t_39804.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z6t_39804/05_2025/8z6t_39804.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z6t_39804/05_2025/8z6t_39804.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z6t_39804/05_2025/8z6t_39804.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z6t_39804/05_2025/8z6t_39804.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z6t_39804/05_2025/8z6t_39804.cif"
  }
  resolution = 2.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
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      23      5.16       5
     C    2888      2.51       5
     N     750      2.21       5
     O     865      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4526
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1558
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 14, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 1424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1424
          Classifications: {'peptide': 191}
          Link IDs: {'PTRANS': 13, 'TRANS': 177}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 1544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1544
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 10, 'TRANS': 191}
          Chain breaks: 3
  Time building chain proxies: 3.60, per 1000 atoms: 0.80
  Number of scatterers: 4526
  At special positions: 0
  Unit cell: (96.928, 71.764, 114.636, 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      23     16.00
     O     865      8.00
     N     750      7.00
     C    2888      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 155 " - pdb=" SG  CYS C 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 155 " - pdb=" SG  CYS B 211 " distance=2.03

  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: 0.97
  Conformation dependent library (CDL) restraints added in 517.9 milliseconds
  

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 14 sheets defined
      10.2% alpha, 36.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.551A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.781A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASN A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 365 through 370'
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 5.390A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'C' and resid 95 through 99
    Processing helix  chain 'C' and resid 142 through 148
    Processing helix  chain 'C' and resid 202 through 209
      removed outlier: 4.055A  pdb=" N   HIS C 209 " --> pdb=" O   GLN C 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 72
      removed outlier: 4.017A  pdb=" N   GLN B  72 " --> pdb=" O   PRO B  69 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 69 through 72'
    Processing helix  chain 'B' and resid 95 through 99
      removed outlier: 3.721A  pdb=" N   THR B  99 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 173
      No H-bonds generated for 'chain 'B' and resid 171 through 173'
    Processing helix  chain 'B' and resid 216 through 219
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.564A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 356 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.391A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 14
      removed outlier: 3.893A  pdb=" N   GLY C  13 " --> pdb=" O   THR C 125 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   VAL C  39 " --> pdb=" O   TYR C  55 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   TYR C  55 " --> pdb=" O   VAL C  39 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   TRP C  41 " --> pdb=" O   MET C  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 14
      removed outlier: 3.893A  pdb=" N   GLY C  13 " --> pdb=" O   THR C 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 20 through 24
      removed outlier: 3.522A  pdb=" N   LEU C  89 " --> pdb=" O   ILE C  21 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 135 through 139
      removed outlier: 3.514A  pdb=" N   VAL C 154 " --> pdb=" O   PHE C 139 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   TYR C 193 " --> pdb=" O   ASP C 159 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLU C 181 " --> pdb=" O   TYR C 198 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 166 through 170
      removed outlier: 3.665A  pdb=" N   SER C 213 " --> pdb=" O   LYS C 170 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.560A  pdb=" N   THR B  77 " --> pdb=" O   HIS B  90 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.359A  pdb=" N   ILE B  39 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   ILE B  55 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   TRP B  41 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   ASP B  64 " --> pdb=" O   TYR B  57 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.852A  pdb=" N   TYR B 117 " --> pdb=" O   ARG B 106 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 135 through 138
      removed outlier: 3.875A  pdb=" N   SER B 195 " --> pdb=" O   CYS B 155 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP B 159 " --> pdb=" O   TYR B 191 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   TYR B 191 " --> pdb=" O   ASP B 159 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 166 through 169
      removed outlier: 3.576A  pdb=" N   THR B 166 " --> pdb=" O   ASN B 214 " (cutoff:3.500A)

    151 hydrogen bonds defined for protein.
    369 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.27

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 757
        1.32 -     1.44: 1328
        1.44 -     1.57: 2532
        1.57 -     1.69: 0
        1.69 -     1.81: 29
  Bond restraints: 4646
  Sorted by residual:
  bond pdb=" CA  SER A 443 "
       pdb=" C   SER A 443 "
    ideal  model  delta    sigma   weight residual
    1.529  1.469  0.060 1.04e-02 9.25e+03 3.31e+01
  bond pdb=" CA  LEU B 110 "
       pdb=" C   LEU B 110 "
    ideal  model  delta    sigma   weight residual
    1.527  1.472  0.055 1.21e-02 6.83e+03 2.05e+01
  bond pdb=" CA  SER A 443 "
       pdb=" CB  SER A 443 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 1.48e-02 4.57e+03 1.98e+01
  bond pdb=" CA  THR A 346 "
       pdb=" C   THR A 346 "
    ideal  model  delta    sigma   weight residual
    1.522  1.471  0.051 1.21e-02 6.83e+03 1.77e+01
  bond pdb=" CA  PHE A 347 "
       pdb=" CB  PHE A 347 "
    ideal  model  delta    sigma   weight residual
    1.532  1.461  0.070 1.69e-02 3.50e+03 1.73e+01
  ... (remaining 4641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 6151
        1.64 -     3.28: 118
        3.28 -     4.92: 38
        4.92 -     6.56: 8
        6.56 -     8.20: 5
  Bond angle restraints: 6320
  Sorted by residual:
  angle pdb=" C   SER A 443 "
        pdb=" CA  SER A 443 "
        pdb=" CB  SER A 443 "
      ideal   model   delta    sigma   weight residual
     111.43  104.78    6.65 1.24e+00 6.50e-01 2.88e+01
  angle pdb=" N   PHE A 347 "
        pdb=" CA  PHE A 347 "
        pdb=" C   PHE A 347 "
      ideal   model   delta    sigma   weight residual
     109.80  101.60    8.20 1.70e+00 3.46e-01 2.33e+01
  angle pdb=" N   SER A 443 "
        pdb=" CA  SER A 443 "
        pdb=" C   SER A 443 "
      ideal   model   delta    sigma   weight residual
     107.20  114.04   -6.84 1.70e+00 3.46e-01 1.62e+01
  angle pdb=" C   ARG C   8 "
        pdb=" N   SER C   9 "
        pdb=" CA  SER C   9 "
      ideal   model   delta    sigma   weight residual
     122.62  116.52    6.10 1.56e+00 4.11e-01 1.53e+01
  angle pdb=" N   THR A 346 "
        pdb=" CA  THR A 346 "
        pdb=" C   THR A 346 "
      ideal   model   delta    sigma   weight residual
     109.50  103.78    5.72 1.58e+00 4.01e-01 1.31e+01
  ... (remaining 6315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.92: 2580
       11.92 -    23.84: 105
       23.84 -    35.76: 29
       35.76 -    47.68: 17
       47.68 -    59.60: 9
  Dihedral angle restraints: 2740
    sinusoidal: 1044
      harmonic: 1696
  Sorted by residual:
  dihedral pdb=" CA  ASP C  56 "
           pdb=" C   ASP C  56 "
           pdb=" N   VAL C  57 "
           pdb=" CA  VAL C  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.20  -20.80     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" N   PHE A 347 "
           pdb=" C   PHE A 347 "
           pdb=" CA  PHE A 347 "
           pdb=" CB  PHE A 347 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.00    8.80     0      2.50e+00 1.60e-01 1.24e+01
  dihedral pdb=" C   PHE A 347 "
           pdb=" N   PHE A 347 "
           pdb=" CA  PHE A 347 "
           pdb=" CB  PHE A 347 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.30   -8.30     0      2.50e+00 1.60e-01 1.10e+01
  ... (remaining 2737 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 561
       0.048 -    0.097: 71
       0.097 -    0.145: 52
       0.145 -    0.193: 4
       0.193 -    0.241: 3
  Chirality restraints: 691
  Sorted by residual:
  chirality pdb=" CA  GLN B 107 "
            pdb=" N   GLN B 107 "
            pdb=" C   GLN B 107 "
            pdb=" CB  GLN B 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  THR A 345 "
            pdb=" N   THR A 345 "
            pdb=" C   THR A 345 "
            pdb=" CB  THR A 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  ASP B 112A"
            pdb=" N   ASP B 112A"
            pdb=" C   ASP B 112A"
            pdb=" CB  ASP B 112A"
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 688 not shown)

  Planarity restraints: 802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 344 "    0.011 2.00e-02 2.50e+03   2.25e-02 5.05e+00
        pdb=" C   ALA A 344 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 344 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 345 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 105 "   -0.008 2.00e-02 2.50e+03   1.62e-02 2.62e+00
        pdb=" C   ALA B 105 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ALA B 105 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG B 106 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 444 "    0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO A 445 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 445 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 445 "    0.019 5.00e-02 4.00e+02
  ... (remaining 799 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 346
        2.74 -     3.28: 4369
        3.28 -     3.82: 7167
        3.82 -     4.36: 8706
        4.36 -     4.90: 15100
  Nonbonded interactions: 35688
  Sorted by model distance:
  nonbonded pdb=" O   VAL C 126 "
            pdb=" OH  TYR C 161 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER C 186 "
            pdb=" N   ALA C 194 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" ND1 HIS B 215 "
            pdb=" OG  SER B 218 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OH  TYR A 369 "
            pdb=" O   PRO A 384 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   ASP C  56 "
            pdb=" N   LYS C  66 "
     model   vdw
     2.235 3.120
  ... (remaining 35683 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.960
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
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   0.070   4653  Z= 0.322
  Angle     :  0.627   8.199   6334  Z= 0.360
  Chirality :  0.048   0.241    691
  Planarity :  0.003   0.035    802
  Dihedral  :  8.846  59.602   1639
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.27 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  :  4.38 %
    Favored  : 91.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.32), residues: 569
  helix: -3.03 (0.59), residues: 47
  sheet: -0.96 (0.38), residues: 185
  loop : -2.40 (0.29), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 169 
 HIS   0.002   0.000   HIS A 339 
 PHE   0.016   0.001   PHE A 347 
 TYR   0.006   0.001   TYR B  57 
 ARG   0.001   0.000   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27842 (  139)
  hydrogen bonds       : angle      10.32319 (  369)
  SS BOND              : bond        0.00134 (    7)
  SS BOND              : angle       0.46125 (   14)
  covalent geometry    : bond        0.00473 ( 4646)
  covalent geometry    : angle       0.62694 ( 6320)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.512 
Fit side-chains
REVERT: A  346 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7753 (p)
REVERT: A  360 ASN cc_start: 0.7887 (m110) cc_final: 0.7660 (m110)
REVERT: A  362 VAL cc_start: 0.7998 (m) cc_final: 0.7797 (p)
REVERT: A  399 SER cc_start: 0.8104 (m) cc_final: 0.7858 (p)
REVERT: A  406 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6557 (pp20)
REVERT: A  439 ASN cc_start: 0.7743 (t0) cc_final: 0.7253 (t0)
REVERT: A  442 ASP cc_start: 0.7741 (m-30) cc_final: 0.7279 (m-30)
REVERT: A  443 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.7795 (p)
REVERT: A  455 LEU cc_start: 0.7720 (tp) cc_final: 0.7313 (tp)
REVERT: A  456 PHE cc_start: 0.7775 (m-10) cc_final: 0.7494 (m-10)
REVERT: A  494 SER cc_start: 0.7968 (t) cc_final: 0.7759 (p)
REVERT: C   30 VAL cc_start: 0.8024 (t) cc_final: 0.7778 (m)
REVERT: B  117 TYR cc_start: 0.7726 (m-80) cc_final: 0.6957 (m-80)
REVERT: B  184 VAL cc_start: 0.7654 (t) cc_final: 0.7422 (m)
REVERT: B  193 LEU cc_start: 0.7741 (pt) cc_final: 0.7449 (pt)
  outliers start: 19
  outliers final: 4
  residues processed: 148
  average time/residue: 0.6097
  time to fit residues: 96.3717
Evaluate side-chains
  121 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain B residue   21 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 24 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    0.3980
   chunk 27 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 52 optimal weight:    0.0670
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
A 343 ASN
A 388 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 ASN
A 450 ASN
A 474 GLN
C  95 GLN
B   3 GLN
B   6 GLN
B 107 GLN
B 120 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.144642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.122629 restraints weight = 6450.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.05
r_work: 0.3548 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3415 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4653  Z= 0.148
  Angle     :  0.605   6.528   6334  Z= 0.305
  Chirality :  0.046   0.160    691
  Planarity :  0.005   0.045    802
  Dihedral  :  5.940  55.281    644
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 14.54 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.33), residues: 569
  helix: -2.72 (0.65), residues: 42
  sheet: -0.23 (0.36), residues: 195
  loop : -1.54 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  52 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.011   0.001   PHE A 429 
 TYR   0.012   0.001   TYR B  67 
 ARG   0.003   0.001   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 (  139)
  hydrogen bonds       : angle       6.32697 (  369)
  SS BOND              : bond        0.00342 (    7)
  SS BOND              : angle       0.58623 (   14)
  covalent geometry    : bond        0.00339 ( 4646)
  covalent geometry    : angle       0.60518 ( 6320)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A  374 PHE cc_start: 0.8210 (m-80) cc_final: 0.7950 (m-80)
REVERT: A  442 ASP cc_start: 0.7945 (m-30) cc_final: 0.7575 (m-30)
REVERT: A  456 PHE cc_start: 0.8094 (m-10) cc_final: 0.7869 (m-10)
REVERT: C   29 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6532 (m-30)
REVERT: C  201 LEU cc_start: 0.7274 (mt) cc_final: 0.7002 (tm)
REVERT: B   22 SER cc_start: 0.7901 (p) cc_final: 0.7602 (t)
REVERT: B   37 TYR cc_start: 0.8306 (m-80) cc_final: 0.8105 (m-80)
REVERT: B   95 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8484 (mtpp)
REVERT: B  156 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5927 (tt)
  outliers start: 21
  outliers final: 12
  residues processed: 116
  average time/residue: 0.4642
  time to fit residues: 58.7895
Evaluate side-chains
  108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   48 LYS
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  156 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 50 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0370
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0970
   chunk 28 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 409 GLN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.142367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.120240 restraints weight = 6462.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.05
r_work: 0.3521 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3390 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4653  Z= 0.129
  Angle     :  0.570   6.051   6334  Z= 0.281
  Chirality :  0.044   0.153    691
  Planarity :  0.005   0.040    802
  Dihedral  :  5.245  47.073    639
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 14.14 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.34), residues: 569
  helix: -2.49 (0.78), residues: 35
  sheet:  0.27 (0.37), residues: 190
  loop : -1.27 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  52 
 HIS   0.003   0.001   HIS B 215 
 PHE   0.008   0.001   PHE A 429 
 TYR   0.014   0.001   TYR C  38 
 ARG   0.002   0.000   ARG B 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03387 (  139)
  hydrogen bonds       : angle       5.66601 (  369)
  SS BOND              : bond        0.00217 (    7)
  SS BOND              : angle       0.43356 (   14)
  covalent geometry    : bond        0.00292 ( 4646)
  covalent geometry    : angle       0.56998 ( 6320)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  374 PHE cc_start: 0.8192 (m-80) cc_final: 0.7875 (m-80)
REVERT: A  442 ASP cc_start: 0.8064 (m-30) cc_final: 0.7684 (m-30)
REVERT: A  492 LEU cc_start: 0.7978 (mp) cc_final: 0.7762 (mt)
REVERT: A  513 LEU cc_start: 0.8350 (mt) cc_final: 0.8142 (mp)
REVERT: A  528 LYS cc_start: 0.7710 (ttpt) cc_final: 0.6927 (tttt)
REVERT: B   21 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7682 (tt)
REVERT: B   37 TYR cc_start: 0.8341 (m-80) cc_final: 0.8082 (m-80)
  outliers start: 32
  outliers final: 15
  residues processed: 110
  average time/residue: 0.4903
  time to fit residues: 58.6641
Evaluate side-chains
  99 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  184 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 20 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0060
   chunk 39 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.139583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.117829 restraints weight = 6490.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 1.99
r_work: 0.3480 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4653  Z= 0.154
  Angle     :  0.616  10.174   6334  Z= 0.296
  Chirality :  0.045   0.147    691
  Planarity :  0.005   0.037    802
  Dihedral  :  5.300  48.862    639
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 18.33 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.34), residues: 569
  helix: -2.43 (0.79), residues: 35
  sheet:  0.52 (0.38), residues: 190
  loop : -1.13 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  52 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.013   0.001   PHE A 456 
 TYR   0.017   0.001   TYR C  38 
 ARG   0.003   0.000   ARG B  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03219 (  139)
  hydrogen bonds       : angle       5.53316 (  369)
  SS BOND              : bond        0.00121 (    7)
  SS BOND              : angle       0.63134 (   14)
  covalent geometry    : bond        0.00358 ( 4646)
  covalent geometry    : angle       0.61637 ( 6320)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A  374 PHE cc_start: 0.8201 (m-80) cc_final: 0.7872 (m-80)
REVERT: A  438 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7544 (t)
REVERT: A  442 ASP cc_start: 0.8073 (m-30) cc_final: 0.7651 (m-30)
REVERT: A  492 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7770 (mt)
REVERT: A  528 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7616 (ttmt)
REVERT: C   29 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6670 (m-30)
REVERT: B   23 CYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7574 (t)
REVERT: B   37 TYR cc_start: 0.8373 (m-80) cc_final: 0.8127 (m-80)
REVERT: B  126 VAL cc_start: 0.8621 (t) cc_final: 0.8290 (m)
  outliers start: 29
  outliers final: 17
  residues processed: 93
  average time/residue: 0.4361
  time to fit residues: 44.6629
Evaluate side-chains
  98 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  105 CYS
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  184 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.136394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.114517 restraints weight = 6590.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.02
r_work: 0.3425 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   4653  Z= 0.231
  Angle     :  0.662   9.514   6334  Z= 0.325
  Chirality :  0.048   0.183    691
  Planarity :  0.005   0.037    802
  Dihedral  :  5.594  46.784    638
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 18.13 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.35), residues: 569
  helix: -2.35 (0.82), residues: 35
  sheet:  0.54 (0.38), residues: 188
  loop : -1.20 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  52 
 HIS   0.006   0.001   HIS B 215 
 PHE   0.013   0.002   PHE A 429 
 TYR   0.018   0.002   TYR C  38 
 ARG   0.004   0.001   ARG B  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03534 (  139)
  hydrogen bonds       : angle       5.73207 (  369)
  SS BOND              : bond        0.00305 (    7)
  SS BOND              : angle       0.61965 (   14)
  covalent geometry    : bond        0.00536 ( 4646)
  covalent geometry    : angle       0.66257 ( 6320)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 79
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  385 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8473 (p)
REVERT: A  438 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.7541 (t)
REVERT: A  442 ASP cc_start: 0.8180 (m-30) cc_final: 0.7759 (m-30)
REVERT: A  492 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7701 (mt)
REVERT: A  517 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6764 (mp)
REVERT: A  528 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7532 (ttmt)
REVERT: C   28 SER cc_start: 0.8383 (m) cc_final: 0.8099 (p)
REVERT: C   29 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6758 (m-30)
REVERT: B   23 CYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7683 (t)
REVERT: B   37 TYR cc_start: 0.8421 (m-80) cc_final: 0.8155 (m-80)
REVERT: B  126 VAL cc_start: 0.8701 (t) cc_final: 0.8347 (m)
REVERT: B  220 THR cc_start: 0.8491 (m) cc_final: 0.7704 (p)
  outliers start: 31
  outliers final: 20
  residues processed: 96
  average time/residue: 0.4557
  time to fit residues: 48.0147
Evaluate side-chains
  103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain C residue   24 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  105 CYS
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** 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 = 0.3856 r_free = 0.3856 target = 0.137506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.115645 restraints weight = 6513.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 1.99
r_work: 0.3436 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4653  Z= 0.167
  Angle     :  0.610   9.111   6334  Z= 0.298
  Chirality :  0.045   0.144    691
  Planarity :  0.005   0.035    802
  Dihedral  :  5.396  45.395    638
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 17.33 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.35), residues: 569
  helix: -2.34 (0.81), residues: 35
  sheet:  0.58 (0.39), residues: 190
  loop : -1.09 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  52 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.011   0.001   PHE A 429 
 TYR   0.016   0.001   TYR C  38 
 ARG   0.003   0.000   ARG B  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03180 (  139)
  hydrogen bonds       : angle       5.52070 (  369)
  SS BOND              : bond        0.00196 (    7)
  SS BOND              : angle       0.53634 (   14)
  covalent geometry    : bond        0.00392 ( 4646)
  covalent geometry    : angle       0.61031 ( 6320)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 84
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A  385 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8484 (p)
REVERT: A  438 SER cc_start: 0.8034 (OUTLIER) cc_final: 0.7584 (t)
REVERT: A  439 ASN cc_start: 0.8315 (t0) cc_final: 0.7985 (t0)
REVERT: A  442 ASP cc_start: 0.8077 (m-30) cc_final: 0.7728 (m-30)
REVERT: A  443 SER cc_start: 0.8440 (m) cc_final: 0.8195 (m)
REVERT: A  492 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7694 (mt)
REVERT: A  517 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6705 (mp)
REVERT: A  528 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7525 (ttmt)
REVERT: C   29 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6759 (m-30)
REVERT: C   98 ASP cc_start: 0.7785 (m-30) cc_final: 0.7510 (m-30)
REVERT: C  196 SER cc_start: 0.7742 (t) cc_final: 0.7519 (t)
REVERT: B   12 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8815 (m)
REVERT: B   23 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7655 (t)
REVERT: B   37 TYR cc_start: 0.8414 (m-80) cc_final: 0.8109 (m-80)
REVERT: B  220 THR cc_start: 0.8465 (m) cc_final: 0.7712 (p)
  outliers start: 35
  outliers final: 24
  residues processed: 102
  average time/residue: 0.4139
  time to fit residues: 46.5602
Evaluate side-chains
  114 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 83
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  105 CYS
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 1 optimal weight:    0.3980
   chunk 15 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0470
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** 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 = 0.3858 r_free = 0.3858 target = 0.137715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.115850 restraints weight = 6483.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.99
r_work: 0.3441 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4653  Z= 0.157
  Angle     :  0.610   9.015   6334  Z= 0.295
  Chirality :  0.045   0.143    691
  Planarity :  0.005   0.035    802
  Dihedral  :  5.340  44.102    638
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  7.37 %
    Allowed  : 16.93 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.36), residues: 569
  helix: -2.37 (0.82), residues: 35
  sheet:  0.67 (0.39), residues: 190
  loop : -1.02 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  52 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.010   0.001   PHE A 429 
 TYR   0.014   0.001   TYR C  38 
 ARG   0.003   0.000   ARG B  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03070 (  139)
  hydrogen bonds       : angle       5.45232 (  369)
  SS BOND              : bond        0.00176 (    7)
  SS BOND              : angle       0.51269 (   14)
  covalent geometry    : bond        0.00367 ( 4646)
  covalent geometry    : angle       0.60997 ( 6320)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 85
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A  438 SER cc_start: 0.8026 (OUTLIER) cc_final: 0.7579 (t)
REVERT: A  439 ASN cc_start: 0.8314 (t0) cc_final: 0.7989 (t0)
REVERT: A  442 ASP cc_start: 0.8093 (m-30) cc_final: 0.7745 (m-30)
REVERT: A  443 SER cc_start: 0.8431 (m) cc_final: 0.8177 (m)
REVERT: A  474 GLN cc_start: 0.8151 (mt0) cc_final: 0.7877 (mt0)
REVERT: A  492 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7688 (mt)
REVERT: A  517 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6673 (mp)
REVERT: A  528 LYS cc_start: 0.7910 (ttpt) cc_final: 0.7545 (ttmt)
REVERT: C   29 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6688 (m-30)
REVERT: C   98 ASP cc_start: 0.7761 (m-30) cc_final: 0.7491 (m-30)
REVERT: C  196 SER cc_start: 0.7804 (t) cc_final: 0.7587 (t)
REVERT: C  201 LEU cc_start: 0.7477 (mt) cc_final: 0.7266 (tt)
REVERT: B   12 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8819 (m)
REVERT: B   21 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7843 (tp)
REVERT: B   23 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7627 (t)
REVERT: B   37 TYR cc_start: 0.8420 (m-80) cc_final: 0.8125 (m-80)
REVERT: B  220 THR cc_start: 0.8445 (m) cc_final: 0.7700 (p)
  outliers start: 37
  outliers final: 24
  residues processed: 104
  average time/residue: 0.4003
  time to fit residues: 46.0550
Evaluate side-chains
  116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  105 CYS
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   chunk 44 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** 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 = 0.3829 r_free = 0.3829 target = 0.135350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.113632 restraints weight = 6527.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.98
r_work: 0.3409 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   4653  Z= 0.241
  Angle     :  0.671  10.153   6334  Z= 0.327
  Chirality :  0.048   0.184    691
  Planarity :  0.005   0.037    802
  Dihedral  :  5.717  46.244    638
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 18.33 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.36), residues: 569
  helix: -2.36 (0.84), residues: 35
  sheet:  0.64 (0.39), residues: 190
  loop : -1.13 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  52 
 HIS   0.006   0.001   HIS B 215 
 PHE   0.014   0.002   PHE A 429 
 TYR   0.019   0.002   TYR C  38 
 ARG   0.003   0.000   ARG B  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03455 (  139)
  hydrogen bonds       : angle       5.66182 (  369)
  SS BOND              : bond        0.00238 (    7)
  SS BOND              : angle       0.54660 (   14)
  covalent geometry    : bond        0.00559 ( 4646)
  covalent geometry    : angle       0.67141 ( 6320)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 91
  time to evaluate  : 0.522 
Fit side-chains
REVERT: A  385 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8496 (p)
REVERT: A  438 SER cc_start: 0.8026 (OUTLIER) cc_final: 0.7580 (t)
REVERT: A  442 ASP cc_start: 0.8069 (m-30) cc_final: 0.7729 (m-30)
REVERT: A  443 SER cc_start: 0.8453 (m) cc_final: 0.8202 (m)
REVERT: A  474 GLN cc_start: 0.8146 (mt0) cc_final: 0.7809 (mt0)
REVERT: A  492 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7715 (mt)
REVERT: A  517 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6918 (mp)
REVERT: A  528 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7549 (ttmt)
REVERT: C   28 SER cc_start: 0.8362 (m) cc_final: 0.8145 (p)
REVERT: C   98 ASP cc_start: 0.7806 (m-30) cc_final: 0.7500 (m-30)
REVERT: C  162 PRO cc_start: 0.7553 (Cg_exo) cc_final: 0.7216 (Cg_endo)
REVERT: B   23 CYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7701 (t)
REVERT: B   37 TYR cc_start: 0.8423 (m-80) cc_final: 0.8168 (m-80)
REVERT: B  220 THR cc_start: 0.8466 (m) cc_final: 0.7685 (p)
  outliers start: 33
  outliers final: 22
  residues processed: 110
  average time/residue: 0.4202
  time to fit residues: 50.9192
Evaluate side-chains
  117 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  105 CYS
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 46 optimal weight:    0.4980
   chunk 51 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.136196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.114717 restraints weight = 6484.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.97
r_work: 0.3428 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.4238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4653  Z= 0.175
  Angle     :  0.627  10.099   6334  Z= 0.303
  Chirality :  0.046   0.150    691
  Planarity :  0.005   0.034    802
  Dihedral  :  5.256  43.439    636
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 18.92 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.36), residues: 569
  helix: -2.33 (0.84), residues: 35
  sheet:  0.73 (0.39), residues: 190
  loop : -1.08 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  52 
 HIS   0.005   0.001   HIS B 215 
 PHE   0.011   0.001   PHE A 429 
 TYR   0.016   0.002   TYR A 473 
 ARG   0.003   0.000   ARG B  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03189 (  139)
  hydrogen bonds       : angle       5.51402 (  369)
  SS BOND              : bond        0.00171 (    7)
  SS BOND              : angle       0.52761 (   14)
  covalent geometry    : bond        0.00411 ( 4646)
  covalent geometry    : angle       0.62716 ( 6320)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.473 
Fit side-chains
REVERT: A  345 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.7997 (m)
REVERT: A  385 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8447 (p)
REVERT: A  438 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7565 (t)
REVERT: A  439 ASN cc_start: 0.8312 (t0) cc_final: 0.7981 (t0)
REVERT: A  442 ASP cc_start: 0.8060 (m-30) cc_final: 0.7735 (m-30)
REVERT: A  443 SER cc_start: 0.8429 (m) cc_final: 0.8216 (m)
REVERT: A  473 TYR cc_start: 0.7611 (t80) cc_final: 0.7210 (t80)
REVERT: A  474 GLN cc_start: 0.8169 (mt0) cc_final: 0.7856 (mt0)
REVERT: A  492 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7676 (mt)
REVERT: A  517 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6850 (mp)
REVERT: A  528 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7495 (ttmt)
REVERT: C   98 ASP cc_start: 0.7840 (m-30) cc_final: 0.7543 (m-30)
REVERT: C  196 SER cc_start: 0.7808 (t) cc_final: 0.7589 (t)
REVERT: B   23 CYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7608 (t)
REVERT: B   37 TYR cc_start: 0.8429 (m-80) cc_final: 0.8153 (m-80)
  outliers start: 29
  outliers final: 21
  residues processed: 92
  average time/residue: 0.4430
  time to fit residues: 44.9835
Evaluate side-chains
  102 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  105 CYS
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2652 > 50:
  distance: 16 - 21:  34.841
  distance: 21 - 22:  56.815
  distance: 22 - 23:  39.812
  distance: 26 - 27:  40.465
  distance: 26 - 28:  39.970
  distance: 27 - 29:  55.522
  distance: 28 - 30:  38.817
  distance: 30 - 31:  39.623
  distance: 33 - 34:  38.806
  distance: 33 - 36:  40.999
  distance: 34 - 35:  34.900
  distance: 34 - 40:  39.915
  distance: 36 - 37:  57.819
  distance: 37 - 38:  40.177
  distance: 37 - 39:  55.788
  distance: 40 - 41:  56.567
  distance: 41 - 42:  40.571
  distance: 41 - 44:  40.284
  distance: 42 - 43:  55.760
  distance: 42 - 45:  40.252
  distance: 45 - 46:  38.745
  distance: 46 - 47:  56.199
  distance: 46 - 49:  58.088
  distance: 47 - 48:  40.467
  distance: 47 - 52:  57.340
  distance: 49 - 51:  41.051
  distance: 53 - 54:  57.310
  distance: 54 - 55:  56.812
  distance: 60 - 61:  40.673
  distance: 60 - 63:  56.900
  distance: 61 - 62:  40.230
  distance: 63 - 64:  40.367
  distance: 64 - 65:  56.109
  distance: 64 - 66:  39.988
  distance: 65 - 67:  40.090
  distance: 68 - 69:  57.272
  distance: 70 - 71:  39.341
  distance: 71 - 72:  56.432
  distance: 71 - 74:  40.921
  distance: 72 - 75:  56.934
  distance: 76 - 77:  40.411
  distance: 78 - 100:  33.686
  distance: 79 - 80:  41.332
  distance: 81 - 82:  39.641
  distance: 82 - 83:  39.258
  distance: 82 - 85:  56.332
  distance: 83 - 88:  40.655
  distance: 89 - 90:  40.621
  distance: 90 - 100:  34.111
  distance: 93 - 94:  39.323
  distance: 93 - 95:  40.684
  distance: 94 - 96:  57.326
  distance: 96 - 98:  40.328
  distance: 97 - 98:  68.945