Starting phenix.real_space_refine
on Fri Aug 22 14:57:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nt5_0502/08_2025/6nt5_0502_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nt5_0502/08_2025/6nt5_0502.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nt5_0502/08_2025/6nt5_0502_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nt5_0502/08_2025/6nt5_0502_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nt5_0502/08_2025/6nt5_0502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nt5_0502/08_2025/6nt5_0502.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    2952      2.51       5
     N     798      2.21       5
     O     812      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4586
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2293
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 278}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 18
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.03, per 1000 atoms: 0.22
  Number of scatterers: 4586
  At special positions: 0
  Unit cell: (78.12, 73.08, 104.16, 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      24     16.00
     O     812      8.00
     N     798      7.00
     C    2952      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.24
  Conformation dependent library (CDL) restraints added in 202.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1100

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      60.6% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 33
      removed outlier: 3.846A  pdb=" N   LEU A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 70
      removed outlier: 3.763A  pdb=" N   GLU A  68 " --> pdb=" O   CYS A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 89
    Processing helix  chain 'A' and resid 91 through 105
      removed outlier: 3.612A  pdb=" N   ARG A  95 " --> pdb=" O   CYS A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 134
      removed outlier: 3.765A  pdb=" N   LEU A 123 " --> pdb=" O   TRP A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 149
    Processing helix  chain 'A' and resid 156 through 167
      removed outlier: 3.684A  pdb=" N   ALA A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR A 167 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 174 through 183
    Processing helix  chain 'A' and resid 183 through 188
      removed outlier: 4.134A  pdb=" N   ASN A 188 " --> pdb=" O   GLN A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 273
      removed outlier: 4.179A  pdb=" N   THR A 267 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
      removed outlier: 3.528A  pdb=" N   ALA A 277 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY A 278 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 274 through 278'
    Processing helix  chain 'A' and resid 280 through 301
      removed outlier: 3.746A  pdb=" N   ASP A 301 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 336
      removed outlier: 3.699A  pdb=" N   GLU A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 33
      removed outlier: 3.846A  pdb=" N   LEU B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 70
      removed outlier: 3.762A  pdb=" N   GLU B  68 " --> pdb=" O   CYS B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 89
    Processing helix  chain 'B' and resid 91 through 105
      removed outlier: 3.612A  pdb=" N   ARG B  95 " --> pdb=" O   CYS B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 134
      removed outlier: 3.766A  pdb=" N   LEU B 123 " --> pdb=" O   TRP B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 149
    Processing helix  chain 'B' and resid 156 through 167
      removed outlier: 3.683A  pdb=" N   ALA B 160 " --> pdb=" O   ALA B 156 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR B 167 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 172
    Processing helix  chain 'B' and resid 174 through 183
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 4.134A  pdb=" N   ASN B 188 " --> pdb=" O   GLN B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 273
      removed outlier: 4.179A  pdb=" N   THR B 267 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 278
      removed outlier: 3.529A  pdb=" N   ALA B 277 " --> pdb=" O   TYR B 274 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLY B 278 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 274 through 278'
    Processing helix  chain 'B' and resid 280 through 301
      removed outlier: 3.748A  pdb=" N   ASP B 301 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 336
      removed outlier: 3.699A  pdb=" N   GLU B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 223
      removed outlier: 5.944A  pdb=" N   PHE A 221 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   GLU A 246 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   GLY A 255 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   LEU A 198 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ILE A 312 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   ILE A 200 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   TYR A 314 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LEU A 202 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 219 through 223
      removed outlier: 5.945A  pdb=" N   PHE B 221 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   GLU B 246 " --> pdb=" O   PHE B 221 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   GLY B 255 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LEU B 198 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ILE B 312 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   TYR B 314 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B 202 " --> pdb=" O   TYR B 314 " (cutoff:3.500A)

    236 hydrogen bonds defined for protein.
    702 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: 0.61

  Time building geometry restraints manager: 0.34 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: 1437
        1.34 -     1.45: 710
        1.45 -     1.57: 2501
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 4676
  Sorted by residual:
  bond pdb=" CA  GLY B  90 "
       pdb=" C   GLY B  90 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.020 1.04e-02 9.25e+03 3.67e+00
  bond pdb=" CA  GLY A  90 "
       pdb=" C   GLY A  90 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.019 1.04e-02 9.25e+03 3.50e+00
  bond pdb=" N   GLY B  90 "
       pdb=" CA  GLY B  90 "
    ideal  model  delta    sigma   weight residual
    1.464  1.447  0.018 1.12e-02 7.97e+03 2.44e+00
  bond pdb=" N   GLY A  90 "
       pdb=" CA  GLY A  90 "
    ideal  model  delta    sigma   weight residual
    1.464  1.447  0.017 1.12e-02 7.97e+03 2.36e+00
  bond pdb=" C   PRO A  11 "
       pdb=" N   CYS A  12 "
    ideal  model  delta    sigma   weight residual
    1.329  1.300  0.029 1.86e-02 2.89e+03 2.35e+00
  ... (remaining 4671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 6141
        2.26 -     4.52: 171
        4.52 -     6.79: 18
        6.79 -     9.05: 10
        9.05 -    11.31: 2
  Bond angle restraints: 6342
  Sorted by residual:
  angle pdb=" N   LEU B 172 "
        pdb=" CA  LEU B 172 "
        pdb=" C   LEU B 172 "
      ideal   model   delta    sigma   weight residual
     109.81  121.12  -11.31 2.21e+00 2.05e-01 2.62e+01
  angle pdb=" N   LEU A 172 "
        pdb=" CA  LEU A 172 "
        pdb=" C   LEU A 172 "
      ideal   model   delta    sigma   weight residual
     109.81  121.11  -11.30 2.21e+00 2.05e-01 2.62e+01
  angle pdb=" C   GLY B 151 "
        pdb=" N   ASN B 152 "
        pdb=" CA  ASN B 152 "
      ideal   model   delta    sigma   weight residual
     122.08  128.79   -6.71 1.47e+00 4.63e-01 2.09e+01
  angle pdb=" C   GLY A 151 "
        pdb=" N   ASN A 152 "
        pdb=" CA  ASN A 152 "
      ideal   model   delta    sigma   weight residual
     122.08  128.75   -6.67 1.47e+00 4.63e-01 2.06e+01
  angle pdb=" C   PRO A  11 "
        pdb=" N   CYS A  12 "
        pdb=" CA  CYS A  12 "
      ideal   model   delta    sigma   weight residual
     121.48  129.66   -8.18 2.04e+00 2.40e-01 1.61e+01
  ... (remaining 6337 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.52: 2634
       14.52 -    29.04: 108
       29.04 -    43.56: 34
       43.56 -    58.08: 3
       58.08 -    72.60: 7
  Dihedral angle restraints: 2786
    sinusoidal: 1086
      harmonic: 1700
  Sorted by residual:
  dihedral pdb=" CA  ASP B 223 "
           pdb=" C   ASP B 223 "
           pdb=" N   LYS B 224 "
           pdb=" CA  LYS B 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.02   17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ASP A 223 "
           pdb=" C   ASP A 223 "
           pdb=" N   LYS A 224 "
           pdb=" CA  LYS A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.04   17.96     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  TYR A 245 "
           pdb=" C   TYR A 245 "
           pdb=" N   GLU A 246 "
           pdb=" CA  GLU A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 2783 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 559
       0.055 -    0.109: 141
       0.109 -    0.164: 24
       0.164 -    0.218: 2
       0.218 -    0.273: 4
  Chirality restraints: 730
  Sorted by residual:
  chirality pdb=" CA  LEU A 172 "
            pdb=" N   LEU A 172 "
            pdb=" C   LEU A 172 "
            pdb=" CB  LEU A 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  LEU B 172 "
            pdb=" N   LEU B 172 "
            pdb=" C   LEU B 172 "
            pdb=" CB  LEU B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  ASN A 152 "
            pdb=" N   ASN A 152 "
            pdb=" C   ASN A 152 "
            pdb=" CB  ASN A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 727 not shown)

  Planarity restraints: 798
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 172 "   -0.036 5.00e-02 4.00e+02   5.37e-02 4.61e+00
        pdb=" N   PRO A 173 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 173 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 173 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 172 "   -0.036 5.00e-02 4.00e+02   5.34e-02 4.57e+00
        pdb=" N   PRO B 173 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 173 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 173 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A   7 "    0.032 5.00e-02 4.00e+02   4.81e-02 3.70e+00
        pdb=" N   PRO A   8 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A   8 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A   8 "    0.027 5.00e-02 4.00e+02
  ... (remaining 795 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1337
        2.82 -     3.34: 4039
        3.34 -     3.86: 7068
        3.86 -     4.38: 7543
        4.38 -     4.90: 13049
  Nonbonded interactions: 33036
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  81 "
            pdb=" OG1 THR A  84 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   TYR B  81 "
            pdb=" OG1 THR B  84 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   LEU A 124 "
            pdb=" OG  SER A 127 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" O   LEU B 124 "
            pdb=" OG  SER B 127 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" O   HIS A  50 "
            pdb=" OG  SER A  53 "
     model   vdw
     2.461 3.040
  ... (remaining 33031 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.660
  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:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.270
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
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      :  0.006   0.055   4676  Z= 0.296
  Angle     :  0.931  11.310   6342  Z= 0.495
  Chirality :  0.053   0.273    730
  Planarity :  0.008   0.054    798
  Dihedral  : 10.321  72.601   1686
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  1.23 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.40 (0.29), residues: 552
  helix: -1.14 (0.24), residues: 304
  sheet: -1.41 (0.79), residues: 28
  loop : -2.13 (0.35), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 178 
 TYR   0.032   0.003   TYR B 199 
 PHE   0.019   0.003   PHE A 153 
 TRP   0.007   0.002   TRP B  82 
 HIS   0.007   0.002   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 ( 4676)
  covalent geometry    : angle       0.93095 ( 6342)
  hydrogen bonds       : bond        0.10373 (  236)
  hydrogen bonds       : angle       5.57110 (  702)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASN cc_start: 0.8973 (t0) cc_final: 0.8579 (t0)
REVERT: A   93 LEU cc_start: 0.8599 (mt) cc_final: 0.8245 (pp)
REVERT: A  119 TRP cc_start: 0.7263 (p90) cc_final: 0.7051 (p90)
REVERT: A  183 ASN cc_start: 0.7717 (m-40) cc_final: 0.6849 (p0)
REVERT: A  223 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7884 (m-30)
REVERT: B   61 ASN cc_start: 0.8981 (t0) cc_final: 0.8585 (t0)
REVERT: B   93 LEU cc_start: 0.8635 (mt) cc_final: 0.8278 (pp)
REVERT: B  104 TYR cc_start: 0.7430 (t80) cc_final: 0.7212 (t80)
REVERT: B  154 ASN cc_start: 0.8612 (t0) cc_final: 0.8310 (p0)
REVERT: B  183 ASN cc_start: 0.7659 (m-40) cc_final: 0.6804 (p0)
REVERT: B  223 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.7878 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0538
  time to fit residues: 9.1030
Evaluate side-chains
  51 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN
B 196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.080007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.066807 restraints weight = 19485.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.068595 restraints weight = 10615.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.069753 restraints weight = 7027.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.070516 restraints weight = 5302.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.071075 restraints weight = 4366.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4676  Z= 0.129
  Angle     :  0.572   6.793   6342  Z= 0.284
  Chirality :  0.041   0.139    730
  Planarity :  0.005   0.035    798
  Dihedral  :  4.657  17.123    638
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.35), residues: 552
  helix:  1.04 (0.29), residues: 318
  sheet: -0.40 (0.87), residues: 28
  loop : -1.47 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 293 
 TYR   0.016   0.001   TYR B 199 
 PHE   0.008   0.001   PHE B 117 
 TRP   0.004   0.001   TRP A 161 
 HIS   0.004   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4676)
  covalent geometry    : angle       0.57229 ( 6342)
  hydrogen bonds       : bond        0.03386 (  236)
  hydrogen bonds       : angle       3.89185 (  702)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 ASN cc_start: 0.7734 (m-40) cc_final: 0.6927 (p0)
REVERT: B  155 VAL cc_start: 0.9137 (t) cc_final: 0.8735 (p)
REVERT: B  183 ASN cc_start: 0.7566 (m-40) cc_final: 0.6753 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0451
  time to fit residues: 5.3334
Evaluate side-chains
  40 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0020
   chunk 28 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    0.7590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.081203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.068297 restraints weight = 18937.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.070056 restraints weight = 10609.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.071228 restraints weight = 7031.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.072053 restraints weight = 5263.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.072492 restraints weight = 4262.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4676  Z= 0.094
  Angle     :  0.516   6.029   6342  Z= 0.254
  Chirality :  0.039   0.180    730
  Planarity :  0.004   0.027    798
  Dihedral  :  4.164  15.469    638
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.36), residues: 552
  helix:  1.80 (0.30), residues: 318
  sheet:  0.10 (0.89), residues: 28
  loop : -1.11 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 178 
 TYR   0.012   0.001   TYR B 261 
 PHE   0.007   0.001   PHE A 279 
 TRP   0.005   0.001   TRP B 119 
 HIS   0.004   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 4676)
  covalent geometry    : angle       0.51562 ( 6342)
  hydrogen bonds       : bond        0.02637 (  236)
  hydrogen bonds       : angle       3.49211 (  702)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  155 VAL cc_start: 0.9066 (t) cc_final: 0.8657 (p)
REVERT: B  208 VAL cc_start: 0.9193 (t) cc_final: 0.8938 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0530
  time to fit residues: 4.7798
Evaluate side-chains
  38 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 15 optimal weight:    0.6980
   chunk 57 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    4.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.077811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.064803 restraints weight = 19066.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.066510 restraints weight = 10549.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.067671 restraints weight = 7040.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.068383 restraints weight = 5294.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.068929 restraints weight = 4363.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   4676  Z= 0.229
  Angle     :  0.645   6.043   6342  Z= 0.316
  Chirality :  0.042   0.135    730
  Planarity :  0.004   0.029    798
  Dihedral  :  4.409  15.579    638
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.37), residues: 552
  helix:  1.76 (0.30), residues: 320
  sheet: -0.14 (0.93), residues: 28
  loop : -0.89 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 197 
 TYR   0.017   0.002   TYR A 199 
 PHE   0.012   0.002   PHE B 269 
 TRP   0.006   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 4676)
  covalent geometry    : angle       0.64479 ( 6342)
  hydrogen bonds       : bond        0.03734 (  236)
  hydrogen bonds       : angle       3.93871 (  702)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  155 VAL cc_start: 0.9166 (t) cc_final: 0.8781 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0714
  time to fit residues: 4.6365
Evaluate side-chains
  29 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 57 optimal weight:    0.6980
   chunk 35 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
B  50 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.076337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.063218 restraints weight = 19538.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.064873 restraints weight = 10704.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.065957 restraints weight = 7132.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.066718 restraints weight = 5431.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.067226 restraints weight = 4471.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   4676  Z= 0.254
  Angle     :  0.688   7.368   6342  Z= 0.336
  Chirality :  0.043   0.150    730
  Planarity :  0.004   0.030    798
  Dihedral  :  4.682  15.111    638
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.37), residues: 552
  helix:  1.43 (0.29), residues: 322
  sheet: -0.76 (0.78), residues: 46
  loop : -0.98 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 169 
 TYR   0.017   0.002   TYR B 199 
 PHE   0.016   0.002   PHE A 269 
 TRP   0.010   0.002   TRP A 119 
 HIS   0.004   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 4676)
  covalent geometry    : angle       0.68804 ( 6342)
  hydrogen bonds       : bond        0.04184 (  236)
  hydrogen bonds       : angle       4.22732 (  702)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.7382 (t80) cc_final: 0.7129 (t80)
REVERT: A  149 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7735 (mt-10)
REVERT: B  155 VAL cc_start: 0.9209 (t) cc_final: 0.8854 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0473
  time to fit residues: 3.0867
Evaluate side-chains
  27 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 60.1446 > 50:
  distance: 49 - 66:  21.354
  distance: 60 - 66:  21.354
  distance: 66 - 67:   9.019
  distance: 67 - 68:  30.974
  distance: 67 - 70:   3.743
  distance: 68 - 69:  12.962
  distance: 68 - 71:  11.639
  distance: 71 - 72:  15.337
  distance: 72 - 73:  25.131
  distance: 72 - 75:  23.279
  distance: 73 - 74:   8.755
  distance: 73 - 79:  41.409
  distance: 75 - 76:  10.714
  distance: 79 - 80:  18.093
  distance: 80 - 81:  24.019
  distance: 80 - 83:  25.703
  distance: 81 - 84:  16.383
  distance: 84 - 85:   9.995
  distance: 84 - 90:  25.495
  distance: 85 - 86:   7.774
  distance: 85 - 88:  17.698
  distance: 86 - 87:  14.467
  distance: 86 - 91:  24.587
  distance: 88 - 89:  16.481
  distance: 89 - 90:   5.056
  distance: 91 - 92:  19.352
  distance: 92 - 93:  13.364
  distance: 92 - 95:  13.558
  distance: 93 - 94:  18.552
  distance: 93 - 100:   3.253
  distance: 95 - 96:  17.042
  distance: 96 - 97:  23.711
  distance: 97 - 98:  40.285
  distance: 97 - 99:  28.213
  distance: 100 - 101:   7.401
  distance: 101 - 102:   8.176
  distance: 101 - 104:  10.559
  distance: 102 - 103:   5.668
  distance: 102 - 106:  12.112
  distance: 104 - 105:  13.265
  distance: 106 - 107:  23.757
  distance: 107 - 108:  18.242
  distance: 107 - 110:  10.058
  distance: 108 - 109:  16.098
  distance: 108 - 115:  20.310
  distance: 110 - 111:  23.097
  distance: 112 - 113:   6.140
  distance: 112 - 114:  23.867
  distance: 115 - 116:  29.871
  distance: 116 - 117:   6.549
  distance: 116 - 119:  39.610
  distance: 117 - 118:  22.090
  distance: 117 - 123:   6.104
  distance: 123 - 124:  19.956
  distance: 124 - 125:   8.331
  distance: 124 - 127:  27.727
  distance: 125 - 126:  23.553
  distance: 125 - 131:  24.681
  distance: 127 - 128:  30.383
  distance: 128 - 129:  21.810
  distance: 128 - 130:   6.507
  distance: 131 - 132:  18.218
  distance: 132 - 133:  16.659
  distance: 132 - 135:  19.502
  distance: 133 - 134:  16.063
  distance: 133 - 137:   4.029
  distance: 135 - 136:  26.871