Starting phenix.real_space_refine
on Tue Feb  3 16:31:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pv5_71883/02_2026/9pv5_71883.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pv5_71883/02_2026/9pv5_71883.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pv5_71883/02_2026/9pv5_71883.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pv5_71883/02_2026/9pv5_71883.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pv5_71883/02_2026/9pv5_71883.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pv5_71883/02_2026/9pv5_71883.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    3158      2.51       5
     N     824      2.21       5
     O     962      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4963
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1236
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 8, 'TRANS': 145}
    Chain: "H"
      Number of atoms: 1015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 1015
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 5, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 872
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 5, 'TRANS': 107}
    Chain: "A"
      Number of atoms: 1012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1012
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
    Chain: "B"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 814
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 8, 'TRANS': 99}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.90, per 1000 atoms: 0.18
  Number of scatterers: 4963
  At special positions: 0
  Unit cell: (65.975, 88.45, 127.6, 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     962      8.00
     N     824      7.00
     C    3158      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  98 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  87 " 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
  Links applied
    NAG-ASN
      " NAG C 201 " - " ASN C  74 "
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 213.1 milliseconds
  

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1146

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 10 sheets defined
      16.8% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'C' and resid 5 through 19
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 27 through 38
    Processing helix  chain 'C' and resid 97 through 113
    Processing helix  chain 'C' and resid 114 through 124
    Processing helix  chain 'C' and resid 125 through 140
      removed outlier: 3.716A  pdb=" N   ALA C 140 " --> pdb=" O   ARG C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 153
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.993A  pdb=" N   GLY H  32 " --> pdb=" O   ILE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.523A  pdb=" N   THR H  91 " --> pdb=" O   THR H  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 53 through 57
    Processing helix  chain 'A' and resid 89 through 93
    Processing helix  chain 'B' and resid 91 through 95
    Processing sheet with id=AA1, first strand: chain 'C' and resid 64 through 65
    Processing sheet with id=AA2, first strand: chain 'H' and resid 5 through 7
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.737A  pdb=" N   VAL H 123 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 59
      removed outlier: 5.678A  pdb=" N   TRP H  48 " --> pdb=" O   ARG H  39 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ARG H  39 " --> pdb=" O   TRP H  48 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   GLY H  50 " --> pdb=" O   TRP H  37 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TRP H  37 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL H 116 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA6, first strand: chain 'L' and resid 39 through 40
    Processing sheet with id=AA7, first strand: chain 'A' and resid 5 through 7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 11
      removed outlier: 3.511A  pdb=" N   GLY A  10 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   THR A 127 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 9.469A  pdb=" N   MET A  34 " --> pdb=" O   PHE A  50 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   PHE A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 9 through 11
      removed outlier: 3.605A  pdb=" N   THR B 106 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLY B 102 " --> pdb=" O   TYR B  85 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   TYR B  85 " --> pdb=" O   GLY B 102 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TRP B  34 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 21 through 22
      removed outlier: 3.684A  pdb=" N   ALA B  70 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)

    152 hydrogen bonds defined for protein.
    366 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: 0.41

  Time building geometry restraints manager: 0.39 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: 1556
        1.34 -     1.46: 1280
        1.46 -     1.58: 2222
        1.58 -     1.70: 0
        1.70 -     1.82: 30
  Bond restraints: 5088
  Sorted by residual:
  bond pdb=" CG  PRO B  43 "
       pdb=" CD  PRO B  43 "
    ideal  model  delta    sigma   weight residual
    1.503  1.273  0.230 3.40e-02 8.65e+02 4.56e+01
  bond pdb=" SD  MET C 124 "
       pdb=" CE  MET C 124 "
    ideal  model  delta    sigma   weight residual
    1.791  1.708  0.083 2.50e-02 1.60e+03 1.09e+01
  bond pdb=" CB  PHE L  77 "
       pdb=" CG  PHE L  77 "
    ideal  model  delta    sigma   weight residual
    1.502  1.445  0.057 2.30e-02 1.89e+03 6.16e+00
  bond pdb=" CG1 ILE C 133 "
       pdb=" CD1 ILE C 133 "
    ideal  model  delta    sigma   weight residual
    1.513  1.420  0.093 3.90e-02 6.57e+02 5.66e+00
  bond pdb=" N   PRO B  43 "
       pdb=" CD  PRO B  43 "
    ideal  model  delta    sigma   weight residual
    1.473  1.503 -0.030 1.40e-02 5.10e+03 4.57e+00
  ... (remaining 5083 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.08: 6555
        3.08 -     6.16: 303
        6.16 -     9.23: 50
        9.23 -    12.31: 2
       12.31 -    15.39: 2
  Bond angle restraints: 6912
  Sorted by residual:
  angle pdb=" N   PRO B  43 "
        pdb=" CD  PRO B  43 "
        pdb=" CG  PRO B  43 "
      ideal   model   delta    sigma   weight residual
     103.20   87.81   15.39 1.50e+00 4.44e-01 1.05e+02
  angle pdb=" CA  PRO B  43 "
        pdb=" CB  PRO B  43 "
        pdb=" CG  PRO B  43 "
      ideal   model   delta    sigma   weight residual
     104.50   91.52   12.98 1.90e+00 2.77e-01 4.67e+01
  angle pdb=" CA  PRO L  46 "
        pdb=" N   PRO L  46 "
        pdb=" CD  PRO L  46 "
      ideal   model   delta    sigma   weight residual
     112.00  102.70    9.30 1.40e+00 5.10e-01 4.41e+01
  angle pdb=" N   MET C 124 "
        pdb=" CA  MET C 124 "
        pdb=" CB  MET C 124 "
      ideal   model   delta    sigma   weight residual
     110.36  102.18    8.18 1.43e+00 4.89e-01 3.27e+01
  angle pdb=" N   SER L  22 "
        pdb=" CA  SER L  22 "
        pdb=" C   SER L  22 "
      ideal   model   delta    sigma   weight residual
     108.26  117.04   -8.78 1.66e+00 3.63e-01 2.80e+01
  ... (remaining 6907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.68: 2774
       16.68 -    33.36: 153
       33.36 -    50.04: 53
       50.04 -    66.72: 13
       66.72 -    83.40: 5
  Dihedral angle restraints: 2998
    sinusoidal: 1186
      harmonic: 1812
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  87 "
           pdb=" CB  CYS B  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.74   40.74     1      1.00e+01 1.00e-02 2.33e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  94 "
           pdb=" CB  CYS L  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.30   35.30     1      1.00e+01 1.00e-02 1.76e+01
  dihedral pdb=" CA  TYR H  51 "
           pdb=" C   TYR H  51 "
           pdb=" N   ILE H  52 "
           pdb=" CA  ILE H  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.83   20.17     0      5.00e+00 4.00e-02 1.63e+01
  ... (remaining 2995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 561
       0.078 -    0.156: 159
       0.156 -    0.234: 18
       0.234 -    0.312: 2
       0.312 -    0.390: 2
  Chirality restraints: 742
  Sorted by residual:
  chirality pdb=" CB  ILE C 129 "
            pdb=" CA  ILE C 129 "
            pdb=" CG1 ILE C 129 "
            pdb=" CG2 ILE C 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CB  VAL C  59 "
            pdb=" CA  VAL C  59 "
            pdb=" CG1 VAL C  59 "
            pdb=" CG2 VAL C  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.08e+00
  chirality pdb=" CB  ILE C 137 "
            pdb=" CA  ILE C 137 "
            pdb=" CG1 ILE C 137 "
            pdb=" CG2 ILE C 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.23e+00
  ... (remaining 739 not shown)

  Planarity restraints: 884
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS L  45 "   -0.106 5.00e-02 4.00e+02   1.54e-01 3.78e+01
        pdb=" N   PRO L  46 "    0.266 5.00e-02 4.00e+02
        pdb=" CA  PRO L  46 "   -0.080 5.00e-02 4.00e+02
        pdb=" CD  PRO L  46 "   -0.080 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 125 "    0.024 2.00e-02 2.50e+03   4.78e-02 2.28e+01
        pdb=" C   SER C 125 "   -0.083 2.00e-02 2.50e+03
        pdb=" O   SER C 125 "    0.032 2.00e-02 2.50e+03
        pdb=" N   ASP C 126 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP H  55 "    0.019 2.00e-02 2.50e+03   3.83e-02 1.46e+01
        pdb=" CG  ASP H  55 "   -0.066 2.00e-02 2.50e+03
        pdb=" OD1 ASP H  55 "    0.024 2.00e-02 2.50e+03
        pdb=" OD2 ASP H  55 "    0.023 2.00e-02 2.50e+03
  ... (remaining 881 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 58
        2.59 -     3.17: 4224
        3.17 -     3.75: 7495
        3.75 -     4.32: 10452
        4.32 -     4.90: 16913
  Nonbonded interactions: 39142
  Sorted by model distance:
  nonbonded pdb=" OG1 THR H  91 "
            pdb=" OG1 THR H 124 "
     model   vdw
     2.016 3.040
  nonbonded pdb=" OH  TYR L  42 "
            pdb=" OH  TYR L  97 "
     model   vdw
     2.111 3.040
  nonbonded pdb=" OE2 GLU C 151 "
            pdb=" OG  SER L  32 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" O   LEU B  27 "
            pdb=" NZ  LYS B  65 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" NH2 ARG C 131 "
            pdb=" OH  TYR H 112 "
     model   vdw
     2.252 3.120
  ... (remaining 39137 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:             3.950
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.980
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5726
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      :  0.008   0.230   5093  Z= 0.359
  Angle     :  1.468  15.388   6923  Z= 0.844
  Chirality :  0.073   0.390    742
  Planarity :  0.010   0.154    883
  Dihedral  : 12.473  83.395   1840
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.81 %
    Favored  : 90.19 %
  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: -0.25 (0.33), residues: 620
  helix:  0.17 (0.53), residues: 69
  sheet: -0.14 (0.35), residues: 191
  loop : -0.14 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.002   ARG C 131 
 TYR   0.055   0.005   TYR H  27 
 PHE   0.045   0.006   PHE C  91 
 TRP   0.028   0.006   TRP L  56 
 HIS   0.005   0.002   HIS B  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00816 ( 5088)
  covalent geometry    : angle       1.46099 ( 6912)
  SS BOND              : bond        0.01046 (    4)
  SS BOND              : angle       4.40233 (    8)
  hydrogen bonds       : bond        0.16875 (  152)
  hydrogen bonds       : angle       8.68245 (  366)
  link_NAG-ASN         : bond        0.00319 (    1)
  link_NAG-ASN         : angle       0.90697 (    3)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   30 TYR cc_start: 0.6222 (t80) cc_final: 0.5926 (t80)
REVERT: C  131 ARG cc_start: 0.7493 (tpp80) cc_final: 0.6036 (mmt180)
REVERT: B   74 ILE cc_start: 0.5023 (pt) cc_final: 0.4341 (pt)
REVERT: B   75 SER cc_start: 0.6159 (p) cc_final: 0.5535 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0661
  time to fit residues: 11.6308
Evaluate side-chains
  101 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0970
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 147 ASN
H  77 ASN
L  34 ASN
B  96 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.192832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.173518 restraints weight = 9725.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.176209 restraints weight = 6267.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.177845 restraints weight = 4421.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.179249 restraints weight = 3394.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.180019 restraints weight = 2731.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5945
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   5093  Z= 0.171
  Angle     :  0.780   8.172   6923  Z= 0.415
  Chirality :  0.048   0.154    742
  Planarity :  0.006   0.060    883
  Dihedral  :  5.929  28.201    715
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.41 %
    Favored  : 85.19 %
  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: -0.51 (0.33), residues: 620
  helix: -0.23 (0.53), residues: 71
  sheet: -0.03 (0.35), residues: 191
  loop : -0.46 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  37 
 TYR   0.027   0.002   TYR C 130 
 PHE   0.023   0.003   PHE B  99 
 TRP   0.032   0.002   TRP A  33 
 HIS   0.004   0.002   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5088)
  covalent geometry    : angle       0.77880 ( 6912)
  SS BOND              : bond        0.00597 (    4)
  SS BOND              : angle       1.48274 (    8)
  hydrogen bonds       : bond        0.05002 (  152)
  hydrogen bonds       : angle       7.68425 (  366)
  link_NAG-ASN         : bond        0.00032 (    1)
  link_NAG-ASN         : angle       0.74066 (    3)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.129 
Fit side-chains
REVERT: L   94 CYS cc_start: 0.4674 (m) cc_final: 0.4460 (m)
REVERT: B   74 ILE cc_start: 0.4981 (pt) cc_final: 0.4729 (pt)
  outliers start: 13
  outliers final: 9
  residues processed: 119
  average time/residue: 0.0579
  time to fit residues: 8.9262
Evaluate side-chains
  102 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  102 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0060
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 52 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.192710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.174609 restraints weight = 9641.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.176947 restraints weight = 6412.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.178547 restraints weight = 4682.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.179543 restraints weight = 3643.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.180365 restraints weight = 3029.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5960
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5093  Z= 0.146
  Angle     :  0.706   8.967   6923  Z= 0.370
  Chirality :  0.047   0.180    742
  Planarity :  0.005   0.038    883
  Dihedral  :  5.619  26.781    715
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 14.63 %
    Favored  : 81.85 %
  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 (0.34), residues: 620
  helix: -0.56 (0.54), residues: 72
  sheet: -0.14 (0.37), residues: 181
  loop : -0.78 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  37 
 TYR   0.017   0.002   TYR C 130 
 PHE   0.017   0.002   PHE C  91 
 TRP   0.025   0.002   TRP A  33 
 HIS   0.003   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5088)
  covalent geometry    : angle       0.70463 ( 6912)
  SS BOND              : bond        0.00411 (    4)
  SS BOND              : angle       1.40622 (    8)
  hydrogen bonds       : bond        0.04320 (  152)
  hydrogen bonds       : angle       7.04303 (  366)
  link_NAG-ASN         : bond        0.00070 (    1)
  link_NAG-ASN         : angle       0.85637 (    3)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 11
  residues processed: 111
  average time/residue: 0.0554
  time to fit residues: 8.1436
Evaluate side-chains
  108 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  102 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0870
   chunk 28 optimal weight:    8.9990
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    0.1980
   chunk 30 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 60 optimal weight:    0.3980
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
L  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.192675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.174130 restraints weight = 9558.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.176730 restraints weight = 6319.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.178553 restraints weight = 4522.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.179712 restraints weight = 3475.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.180485 restraints weight = 2830.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.4347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5953
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5093  Z= 0.128
  Angle     :  0.681   7.967   6923  Z= 0.353
  Chirality :  0.047   0.184    742
  Planarity :  0.005   0.043    883
  Dihedral  :  5.356  24.010    715
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 16.30 %
    Favored  : 80.19 %
  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: -1.03 (0.34), residues: 620
  helix: -0.56 (0.55), residues: 72
  sheet: -0.35 (0.38), residues: 181
  loop : -0.84 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  96 
 TYR   0.023   0.002   TYR A  82 
 PHE   0.015   0.002   PHE C  91 
 TRP   0.012   0.002   TRP A  33 
 HIS   0.002   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 5088)
  covalent geometry    : angle       0.68018 ( 6912)
  SS BOND              : bond        0.00283 (    4)
  SS BOND              : angle       1.16465 (    8)
  hydrogen bonds       : bond        0.03876 (  152)
  hydrogen bonds       : angle       6.86509 (  366)
  link_NAG-ASN         : bond        0.00102 (    1)
  link_NAG-ASN         : angle       0.81477 (    3)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: B    2 TYR cc_start: 0.6899 (m-10) cc_final: 0.6542 (m-10)
REVERT: B   93 SER cc_start: 0.6539 (m) cc_final: 0.5754 (t)
  outliers start: 19
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0501
  time to fit residues: 7.3013
Evaluate side-chains
  103 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue  115 ASP
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  102 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
C 155 HIS
L  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.190600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.173569 restraints weight = 9966.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.176113 restraints weight = 6520.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.177864 restraints weight = 4678.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.179128 restraints weight = 3581.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.179960 restraints weight = 2893.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.4412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6405
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   5093  Z= 0.257
  Angle     :  0.837   9.011   6923  Z= 0.445
  Chirality :  0.051   0.210    742
  Planarity :  0.006   0.063    883
  Dihedral  :  6.372  32.319    715
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 21.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 17.78 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -1.40 (0.34), residues: 620
  helix: -0.50 (0.53), residues: 72
  sheet: -0.89 (0.38), residues: 184
  loop : -0.99 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A  74 
 TYR   0.024   0.003   TYR H 113 
 PHE   0.031   0.003   PHE C  91 
 TRP   0.028   0.004   TRP H  37 
 HIS   0.004   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 ( 5088)
  covalent geometry    : angle       0.83615 ( 6912)
  SS BOND              : bond        0.00761 (    4)
  SS BOND              : angle       0.82045 (    8)
  hydrogen bonds       : bond        0.05250 (  152)
  hydrogen bonds       : angle       7.83574 (  366)
  link_NAG-ASN         : bond        0.00204 (    1)
  link_NAG-ASN         : angle       1.65456 (    3)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   22 MET cc_start: 0.7646 (tpp) cc_final: 0.7407 (tpp)
REVERT: C   23 VAL cc_start: 0.6983 (m) cc_final: 0.6734 (m)
REVERT: H  109 TYR cc_start: 0.6585 (t80) cc_final: 0.5978 (t80)
REVERT: L   42 TYR cc_start: 0.7676 (m-80) cc_final: 0.7413 (m-80)
REVERT: A   52 LYS cc_start: 0.7739 (mttt) cc_final: 0.7535 (mmmt)
REVERT: B    2 TYR cc_start: 0.7369 (m-10) cc_final: 0.6816 (m-10)
REVERT: B   93 SER cc_start: 0.6661 (m) cc_final: 0.5859 (t)
  outliers start: 27
  outliers final: 17
  residues processed: 117
  average time/residue: 0.0545
  time to fit residues: 8.4192
Evaluate side-chains
  113 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   51 TYR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain L residue   95 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   44 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0470
   chunk 28 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
L  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.184140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.165676 restraints weight = 9952.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.168301 restraints weight = 6553.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.170099 restraints weight = 4683.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.171412 restraints weight = 3572.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.172162 restraints weight = 2873.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6251
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5093  Z= 0.153
  Angle     :  0.711   9.004   6923  Z= 0.373
  Chirality :  0.047   0.175    742
  Planarity :  0.005   0.045    883
  Dihedral  :  5.706  27.829    715
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 19.63 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.33), residues: 620
  helix: -0.17 (0.56), residues: 72
  sheet: -0.70 (0.37), residues: 177
  loop : -1.24 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  74 
 TYR   0.022   0.002   TYR A  82 
 PHE   0.020   0.002   PHE C  91 
 TRP   0.014   0.002   TRP A  33 
 HIS   0.003   0.001   HIS B  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5088)
  covalent geometry    : angle       0.71058 ( 6912)
  SS BOND              : bond        0.00417 (    4)
  SS BOND              : angle       0.71133 (    8)
  hydrogen bonds       : bond        0.04327 (  152)
  hydrogen bonds       : angle       7.24891 (  366)
  link_NAG-ASN         : bond        0.00048 (    1)
  link_NAG-ASN         : angle       1.32426 (    3)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: C   22 MET cc_start: 0.7613 (tpp) cc_final: 0.7406 (tpp)
REVERT: C   23 VAL cc_start: 0.7032 (m) cc_final: 0.6769 (m)
REVERT: H   99 GLU cc_start: 0.5085 (OUTLIER) cc_final: 0.4233 (pt0)
REVERT: H  109 TYR cc_start: 0.5864 (t80) cc_final: 0.5465 (t80)
REVERT: A   52 LYS cc_start: 0.7859 (mttt) cc_final: 0.7520 (mmmt)
REVERT: B    2 TYR cc_start: 0.7334 (m-10) cc_final: 0.7033 (m-10)
  outliers start: 22
  outliers final: 15
  residues processed: 108
  average time/residue: 0.0533
  time to fit residues: 7.6322
Evaluate side-chains
  109 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   51 TYR
Chi-restraints excluded: chain H residue   99 GLU
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain B residue   75 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0030
   chunk 23 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
H  44 ASN
L  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.183811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.165746 restraints weight = 9921.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.168178 restraints weight = 6742.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.169844 restraints weight = 4918.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.171054 restraints weight = 3824.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.171609 restraints weight = 3130.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6253
moved from start:          0.5303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5093  Z= 0.155
  Angle     :  0.722   9.775   6923  Z= 0.378
  Chirality :  0.047   0.229    742
  Planarity :  0.004   0.030    883
  Dihedral  :  5.539  26.962    715
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.93 %
    Favored  : 75.00 %
  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: -1.46 (0.33), residues: 620
  helix: -0.08 (0.56), residues: 72
  sheet: -0.78 (0.39), residues: 162
  loop : -1.25 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  96 
 TYR   0.018   0.002   TYR C 130 
 PHE   0.024   0.002   PHE C  91 
 TRP   0.026   0.002   TRP H  48 
 HIS   0.002   0.001   HIS B  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5088)
  covalent geometry    : angle       0.72159 ( 6912)
  SS BOND              : bond        0.00376 (    4)
  SS BOND              : angle       0.90286 (    8)
  hydrogen bonds       : bond        0.04224 (  152)
  hydrogen bonds       : angle       7.11845 (  366)
  link_NAG-ASN         : bond        0.00087 (    1)
  link_NAG-ASN         : angle       1.18483 (    3)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: C   22 MET cc_start: 0.7593 (tpp) cc_final: 0.7378 (tpp)
REVERT: C   23 VAL cc_start: 0.6976 (m) cc_final: 0.6726 (m)
REVERT: C   92 MET cc_start: 0.7185 (ppp) cc_final: 0.6828 (ppp)
REVERT: H   99 GLU cc_start: 0.4994 (OUTLIER) cc_final: 0.4266 (pt0)
REVERT: B    2 TYR cc_start: 0.7415 (m-10) cc_final: 0.7112 (m-10)
  outliers start: 22
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0643
  time to fit residues: 9.2952
Evaluate side-chains
  105 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    6 GLN
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   51 TYR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   99 GLU
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain L residue   95 GLN
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain B residue   75 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0557 > 50:
  distance: 32 - 51:  35.660
  distance: 37 - 59:  35.294
  distance: 41 - 66:  32.837
  distance: 46 - 51:  34.085
  distance: 47 - 74:  21.589
  distance: 51 - 52:  20.943
  distance: 52 - 53:  27.201
  distance: 52 - 55:  24.195
  distance: 53 - 54:  12.101
  distance: 53 - 59:  39.147
  distance: 54 - 83:  16.795
  distance: 55 - 56:  13.194
  distance: 55 - 57:  33.537
  distance: 59 - 60:  15.699
  distance: 60 - 61:  27.938
  distance: 60 - 63:  21.821
  distance: 61 - 62:   4.580
  distance: 61 - 66:  35.897
  distance: 62 - 97:  56.611
  distance: 63 - 64:  59.246
  distance: 63 - 65:  55.919
  distance: 66 - 67:   6.160
  distance: 67 - 68:  18.414
  distance: 67 - 70:  43.494
  distance: 68 - 74:  37.949
  distance: 69 - 105:  16.962
  distance: 70 - 71:  29.017
  distance: 71 - 72:  26.684
  distance: 71 - 73:  48.785
  distance: 74 - 75:  24.183
  distance: 75 - 76:  13.966
  distance: 76 - 77:  15.156
  distance: 76 - 83:  46.665
  distance: 77 - 114:  58.314
  distance: 79 - 80:  69.823
  distance: 80 - 81:  40.250
  distance: 81 - 82:  69.952
  distance: 84 - 87:  41.995
  distance: 85 - 86:  36.712
  distance: 85 - 97:   3.170
  distance: 86 - 122:   3.036
  distance: 87 - 88:  10.335
  distance: 88 - 89:  21.707
  distance: 88 - 90:  16.581
  distance: 89 - 91:  24.021
  distance: 90 - 92:  27.731
  distance: 90 - 93:  10.909
  distance: 93 - 95:  22.332
  distance: 94 - 96:   4.704
  distance: 95 - 96:   6.311
  distance: 97 - 98:  22.194
  distance: 98 - 99:  19.115
  distance: 98 - 101:  18.738
  distance: 99 - 105:  45.541
  distance: 100 - 129:  69.702
  distance: 101 - 102:  39.080
  distance: 102 - 104:   3.313
  distance: 105 - 106:  16.227
  distance: 106 - 107:  26.822
  distance: 106 - 109:  13.488
  distance: 107 - 108:   3.822
  distance: 107 - 114:  39.415
  distance: 108 - 137:  26.685
  distance: 109 - 110:  13.584
  distance: 110 - 111:  36.528
  distance: 111 - 112:   8.846
  distance: 112 - 113:  55.479
  distance: 114 - 115:  38.792
  distance: 115 - 116:  31.461
  distance: 115 - 118:  17.436
  distance: 116 - 117:  41.601
  distance: 116 - 122:  32.512
  distance: 118 - 119:  49.630
  distance: 119 - 120:  44.113
  distance: 119 - 121:  45.546
  distance: 122 - 123:  40.192
  distance: 123 - 124:  50.581
  distance: 123 - 126:  39.469
  distance: 124 - 125:  42.142
  distance: 124 - 129:  49.078
  distance: 126 - 127:  38.854
  distance: 126 - 128:  39.699
  distance: 131 - 137:  34.413
  distance: 133 - 134:  15.124
  distance: 133 - 135:  50.418
  distance: 134 - 136:  25.412