Starting phenix.real_space_refine
on Tue Jan 13 14:33:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i8c_35247/01_2026/8i8c_35247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i8c_35247/01_2026/8i8c_35247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i8c_35247/01_2026/8i8c_35247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i8c_35247/01_2026/8i8c_35247.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i8c_35247/01_2026/8i8c_35247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i8c_35247/01_2026/8i8c_35247.map"
  }
  resolution = 4.93
  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=   0.023
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      50      5.16       5
     C    4604      2.51       5
     N    1188      2.21       5
     O    1369      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7211
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "K"
      Number of atoms: 1878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1878
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 7, 'TRANS': 219}
    Chain: "L"
      Number of atoms: 1878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1878
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 7, 'TRANS': 219}
    Chain: "M"
      Number of atoms: 1846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1846
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 5, 'TRANS': 221}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 1609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1609
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 5, 'TRANS': 192}
          Chain breaks: 1
  Time building chain proxies: 1.51, per 1000 atoms: 0.21
  Number of scatterers: 7211
  At special positions: 0
  Unit cell: (102.6, 81, 126.9, 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      50     16.00
     O    1369      8.00
     N    1188      7.00
     C    4604      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: 0.63
  Conformation dependent library (CDL) restraints added in 252.6 milliseconds
  

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1738

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 4 sheets defined
      58.9% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'K' and resid 115 through 132
      removed outlier: 3.674A  pdb=" N   TYR K 119 " --> pdb=" O   ASN K 115 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS K 125 " --> pdb=" O   ASN K 121 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 141 through 155
      removed outlier: 3.573A  pdb=" N   VAL K 145 " --> pdb=" O   LYS K 141 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   SER K 155 " --> pdb=" O   PHE K 151 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 158 through 167
      removed outlier: 4.147A  pdb=" N   THR K 167 " --> pdb=" O   LYS K 163 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 179 through 195
    Processing helix  chain 'K' and resid 202 through 218
    Processing helix  chain 'K' and resid 243 through 255
      removed outlier: 3.767A  pdb=" N   LYS K 253 " --> pdb=" O   GLU K 249 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 274 through 285
      removed outlier: 3.788A  pdb=" N   LEU K 278 " --> pdb=" O   ASP K 274 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 290 through 313
    Processing helix  chain 'K' and resid 320 through 335
    Processing helix  chain 'L' and resid 115 through 131
    Processing helix  chain 'L' and resid 141 through 155
      removed outlier: 3.661A  pdb=" N   VAL L 145 " --> pdb=" O   LYS L 141 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 158 through 169
    Processing helix  chain 'L' and resid 179 through 195
    Processing helix  chain 'L' and resid 197 through 200
      removed outlier: 3.575A  pdb=" N   THR L 200 " --> pdb=" O   PRO L 197 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 197 through 200'
    Processing helix  chain 'L' and resid 201 through 218
    Processing helix  chain 'L' and resid 242 through 255
    Processing helix  chain 'L' and resid 274 through 286
    Processing helix  chain 'L' and resid 289 through 313
    Processing helix  chain 'L' and resid 320 through 335
    Processing helix  chain 'M' and resid 28 through 39
    Processing helix  chain 'M' and resid 39 through 61
      removed outlier: 3.724A  pdb=" N   GLU M  43 " --> pdb=" O   LEU M  39 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 66 through 73
      removed outlier: 3.881A  pdb=" N   ASN M  73 " --> pdb=" O   GLU M  69 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 77 through 96
    Processing helix  chain 'M' and resid 138 through 145
    Processing helix  chain 'M' and resid 202 through 229
    Processing helix  chain 'M' and resid 230 through 241
    Processing helix  chain 'M' and resid 242 through 246
    Processing helix  chain 'M' and resid 260 through 264
    Processing helix  chain 'N' and resid 40 through 61
    Processing helix  chain 'N' and resid 66 through 73
    Processing helix  chain 'N' and resid 77 through 96
    Processing helix  chain 'N' and resid 138 through 145
    Processing helix  chain 'N' and resid 202 through 229
    Processing helix  chain 'N' and resid 230 through 241
    Processing helix  chain 'N' and resid 242 through 247
      removed outlier: 3.929A  pdb=" N   THR N 245 " --> pdb=" O   SER N 242 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LYS N 247 " --> pdb=" O   PHE N 244 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 261 through 263
      removed outlier: 3.834A  pdb=" N   ILE K 263 " --> pdb=" O   MET N 106 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   MET N 106 " --> pdb=" O   ILE K 263 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU N 107 " --> pdb=" O   CYS N 134 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   VAL N 136 " --> pdb=" O   GLU N 107 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 261 through 263
      removed outlier: 3.834A  pdb=" N   ILE K 263 " --> pdb=" O   MET N 106 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   MET N 106 " --> pdb=" O   ILE K 263 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU N 107 " --> pdb=" O   CYS N 134 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   VAL N 136 " --> pdb=" O   GLU N 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'M' and resid 9 through 13
      removed outlier: 3.839A  pdb=" N   THR M  13 " --> pdb=" O   ILE M  22 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE M  22 " --> pdb=" O   THR M  13 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'M' and resid 106 through 111
      removed outlier: 6.415A  pdb=" N   GLU M 107 " --> pdb=" O   CYS M 134 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   VAL M 136 " --> pdb=" O   GLU M 107 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   VAL M 109 " --> pdb=" O   VAL M 136 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1134 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1402
        1.33 -     1.45: 1739
        1.45 -     1.57: 4116
        1.57 -     1.69: 1
        1.69 -     1.81: 87
  Bond restraints: 7345
  Sorted by residual:
  bond pdb=" C   TYR K 224 "
       pdb=" N   ALA K 225 "
    ideal  model  delta    sigma   weight residual
    1.332  1.411 -0.078 1.40e-02 5.10e+03 3.14e+01
  bond pdb=" CA  THR N 251 "
       pdb=" CB  THR N 251 "
    ideal  model  delta    sigma   weight residual
    1.534  1.608 -0.074 1.77e-02 3.19e+03 1.73e+01
  bond pdb=" N   PRO L 259 "
       pdb=" CD  PRO L 259 "
    ideal  model  delta    sigma   weight residual
    1.473  1.517 -0.044 1.40e-02 5.10e+03 9.93e+00
  bond pdb=" N   PRO K 220 "
       pdb=" CD  PRO K 220 "
    ideal  model  delta    sigma   weight residual
    1.473  1.431  0.042 1.40e-02 5.10e+03 9.11e+00
  bond pdb=" N   PRO K 259 "
       pdb=" CD  PRO K 259 "
    ideal  model  delta    sigma   weight residual
    1.473  1.511 -0.038 1.40e-02 5.10e+03 7.54e+00
  ... (remaining 7340 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 9542
        1.54 -     3.08: 320
        3.08 -     4.63: 48
        4.63 -     6.17: 10
        6.17 -     7.71: 6
  Bond angle restraints: 9926
  Sorted by residual:
  angle pdb=" C   ASP N 195 "
        pdb=" CA  ASP N 195 "
        pdb=" CB  ASP N 195 "
      ideal   model   delta    sigma   weight residual
     117.23  110.32    6.91 1.36e+00 5.41e-01 2.58e+01
  angle pdb=" C   LEU N 196 "
        pdb=" CA  LEU N 196 "
        pdb=" CB  LEU N 196 "
      ideal   model   delta    sigma   weight residual
     115.89  110.28    5.61 1.32e+00 5.74e-01 1.81e+01
  angle pdb=" CA  PRO L 259 "
        pdb=" N   PRO L 259 "
        pdb=" CD  PRO L 259 "
      ideal   model   delta    sigma   weight residual
     112.00  106.43    5.57 1.40e+00 5.10e-01 1.58e+01
  angle pdb=" CA  TYR K 224 "
        pdb=" CB  TYR K 224 "
        pdb=" CG  TYR K 224 "
      ideal   model   delta    sigma   weight residual
     113.90  120.47   -6.57 1.80e+00 3.09e-01 1.33e+01
  angle pdb=" C   TYR K 224 "
        pdb=" N   ALA K 225 "
        pdb=" CA  ALA K 225 "
      ideal   model   delta    sigma   weight residual
     121.54  128.28   -6.74 1.91e+00 2.74e-01 1.24e+01
  ... (remaining 9921 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.77: 4191
       15.77 -    31.53: 239
       31.53 -    47.30: 35
       47.30 -    63.07: 22
       63.07 -    78.84: 8
  Dihedral angle restraints: 4495
    sinusoidal: 1841
      harmonic: 2654
  Sorted by residual:
  dihedral pdb=" CA  GLN L 258 "
           pdb=" C   GLN L 258 "
           pdb=" N   PRO L 259 "
           pdb=" CA  PRO L 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.51   22.49     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  MET L 256 "
           pdb=" C   MET L 256 "
           pdb=" N   LEU L 257 "
           pdb=" CA  LEU L 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.95  -22.05     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  PRO L 259 "
           pdb=" C   PRO L 259 "
           pdb=" N   GLN L 260 "
           pdb=" CA  GLN L 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.48  -19.52     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 4492 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 800
       0.039 -    0.077: 140
       0.077 -    0.116: 160
       0.116 -    0.154: 45
       0.154 -    0.193: 12
  Chirality restraints: 1157
  Sorted by residual:
  chirality pdb=" CA  VAL K 228 "
            pdb=" N   VAL K 228 "
            pdb=" C   VAL K 228 "
            pdb=" CB  VAL K 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.28e-01
  chirality pdb=" CA  ILE K 263 "
            pdb=" N   ILE K 263 "
            pdb=" C   ILE K 263 "
            pdb=" CB  ILE K 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.92e-01
  chirality pdb=" CA  VAL M 109 "
            pdb=" N   VAL M 109 "
            pdb=" C   VAL M 109 "
            pdb=" CB  VAL M 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.17 2.00e-01 2.50e+01 7.64e-01
  ... (remaining 1154 not shown)

  Planarity restraints: 1247
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR N 251 "   -0.014 2.00e-02 2.50e+03   2.73e-02 7.47e+00
        pdb=" C   THR N 251 "    0.047 2.00e-02 2.50e+03
        pdb=" O   THR N 251 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   MET N 252 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR K 224 "   -0.010 2.00e-02 2.50e+03   2.09e-02 4.37e+00
        pdb=" C   TYR K 224 "    0.036 2.00e-02 2.50e+03
        pdb=" O   TYR K 224 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ALA K 225 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR K 224 "    0.020 2.00e-02 2.50e+03   1.27e-02 3.23e+00
        pdb=" CG  TYR K 224 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR K 224 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR K 224 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR K 224 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR K 224 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR K 224 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR K 224 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1244 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1247
        2.77 -     3.30: 7363
        3.30 -     3.83: 11314
        3.83 -     4.37: 13354
        4.37 -     4.90: 22193
  Nonbonded interactions: 55471
  Sorted by model distance:
  nonbonded pdb=" O   ASN N 258 "
            pdb=" OG  SER N 262 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG1 THR N 256 "
            pdb=" N   SER N 257 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" NE2 GLN K 261 "
            pdb=" OG1 THR N  77 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OG1 THR N 251 "
            pdb=" OG1 THR N 254 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   VAL L 145 "
            pdb=" OG1 THR L 148 "
     model   vdw
     2.315 3.040
  ... (remaining 55466 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
Found NCS groups:
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}
ncs_group {
  reference = (chain 'M' and (resid 39 through 157 or resid 198 through 271))
  selection = (chain 'N' and (resid 39 through 157 or resid 198 through 271))
}

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:             20.260
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.540
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5556
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.078   7345  Z= 0.487
  Angle     :  0.711   7.712   9926  Z= 0.433
  Chirality :  0.052   0.193   1157
  Planarity :  0.003   0.044   1247
  Dihedral  : 11.572  78.836   2757
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  2.05 %
    Favored  : 97.11 %
  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:  0.30 (0.29), residues: 867
  helix:  1.59 (0.23), residues: 491
  sheet:  0.26 (0.82), residues: 42
  loop : -2.05 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L 210 
 TYR   0.028   0.001   TYR K 224 
 PHE   0.015   0.001   PHE N 266 
 HIS   0.002   0.000   HIS N 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00893 ( 7345)
  covalent geometry    : angle       0.71106 ( 9926)
  hydrogen bonds       : bond        0.15166 (  386)
  hydrogen bonds       : angle       5.60421 ( 1134)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  523 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 516
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  151 PHE cc_start: 0.5999 (t80) cc_final: 0.5545 (t80)
REVERT: K  169 PHE cc_start: 0.7295 (m-10) cc_final: 0.6422 (m-10)
REVERT: K  186 LEU cc_start: 0.8911 (mt) cc_final: 0.8363 (mt)
REVERT: K  202 ASP cc_start: 0.7878 (p0) cc_final: 0.7427 (p0)
REVERT: K  246 LEU cc_start: 0.8786 (tp) cc_final: 0.7731 (tp)
REVERT: K  254 ILE cc_start: 0.8238 (mt) cc_final: 0.8006 (mt)
REVERT: K  285 ILE cc_start: 0.9080 (mt) cc_final: 0.8256 (mm)
REVERT: K  288 TYR cc_start: 0.8156 (m-80) cc_final: 0.6715 (m-80)
REVERT: K  290 LEU cc_start: 0.7842 (mt) cc_final: 0.7279 (mt)
REVERT: K  291 SER cc_start: 0.7952 (m) cc_final: 0.7533 (p)
REVERT: K  308 ASN cc_start: 0.6942 (m-40) cc_final: 0.6433 (m110)
REVERT: K  316 PHE cc_start: 0.6753 (t80) cc_final: 0.6493 (t80)
REVERT: L  132 LEU cc_start: 0.8071 (mt) cc_final: 0.7814 (tp)
REVERT: L  145 VAL cc_start: 0.8562 (t) cc_final: 0.8041 (m)
REVERT: L  146 VAL cc_start: 0.9266 (t) cc_final: 0.7713 (t)
REVERT: L  150 ILE cc_start: 0.9310 (mt) cc_final: 0.9010 (mt)
REVERT: L  158 TYR cc_start: 0.6068 (m-80) cc_final: 0.4738 (m-80)
REVERT: L  193 LEU cc_start: 0.7593 (tm) cc_final: 0.7280 (tm)
REVERT: L  216 CYS cc_start: 0.8056 (m) cc_final: 0.5921 (m)
REVERT: L  281 LEU cc_start: 0.9191 (mt) cc_final: 0.8433 (mt)
REVERT: L  284 HIS cc_start: 0.7171 (t70) cc_final: 0.6955 (t-170)
REVERT: L  285 ILE cc_start: 0.9257 (mt) cc_final: 0.8745 (pt)
REVERT: L  306 MET cc_start: 0.8351 (mmp) cc_final: 0.7530 (mmm)
REVERT: L  325 PHE cc_start: 0.5229 (t80) cc_final: 0.4907 (t80)
REVERT: L  326 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8122 (mtpt)
REVERT: M   32 ASP cc_start: 0.7434 (m-30) cc_final: 0.7020 (m-30)
REVERT: M   73 ASN cc_start: 0.7980 (t0) cc_final: 0.7531 (t0)
REVERT: M  110 VAL cc_start: 0.8143 (t) cc_final: 0.7918 (p)
REVERT: M  123 ILE cc_start: 0.7591 (mt) cc_final: 0.6980 (mt)
REVERT: M  140 SER cc_start: 0.8482 (t) cc_final: 0.8018 (p)
REVERT: M  211 THR cc_start: 0.8431 (m) cc_final: 0.7912 (m)
REVERT: M  216 VAL cc_start: 0.9114 (t) cc_final: 0.8843 (p)
REVERT: M  228 ASN cc_start: 0.8219 (m-40) cc_final: 0.7822 (t0)
REVERT: M  231 VAL cc_start: 0.7530 (p) cc_final: 0.7281 (m)
REVERT: M  264 PHE cc_start: 0.7948 (m-80) cc_final: 0.6443 (m-80)
REVERT: N   52 SER cc_start: 0.9399 (m) cc_final: 0.9156 (p)
REVERT: N   69 GLU cc_start: 0.5572 (mm-30) cc_final: 0.5282 (mm-30)
REVERT: N   70 ILE cc_start: 0.9654 (mt) cc_final: 0.9407 (mt)
REVERT: N   73 ASN cc_start: 0.8564 (t0) cc_final: 0.8079 (t0)
REVERT: N  123 ILE cc_start: 0.8437 (mm) cc_final: 0.7972 (mt)
REVERT: N  124 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6729 (mp)
REVERT: N  132 LEU cc_start: 0.8416 (mt) cc_final: 0.8150 (mt)
REVERT: N  133 LEU cc_start: 0.8125 (tp) cc_final: 0.7443 (tp)
REVERT: N  141 ILE cc_start: 0.8480 (mt) cc_final: 0.7945 (mt)
REVERT: N  195 ASP cc_start: 0.7177 (m-30) cc_final: 0.6952 (m-30)
REVERT: N  213 LEU cc_start: 0.7959 (mt) cc_final: 0.7538 (mt)
REVERT: N  231 VAL cc_start: 0.7780 (p) cc_final: 0.7508 (p)
  outliers start: 7
  outliers final: 0
  residues processed: 519
  average time/residue: 0.1043
  time to fit residues: 67.9179
Evaluate side-chains
  286 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 285
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
K 129 HIS
** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 128 HIS
L 334 HIS
M  92 HIS
M 222 HIS
M 241 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.092021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.069353 restraints weight = 27895.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.072112 restraints weight = 18974.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.074180 restraints weight = 14172.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.075798 restraints weight = 11216.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.077039 restraints weight = 9273.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.6613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7345  Z= 0.201
  Angle     :  0.776  14.356   9926  Z= 0.405
  Chirality :  0.046   0.210   1157
  Planarity :  0.005   0.043   1247
  Dihedral  :  5.173  23.202    961
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 19.54
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.19 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.61 %
    Favored  : 96.27 %
  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: -0.15 (0.29), residues: 867
  helix:  1.00 (0.23), residues: 502
  sheet: -0.51 (0.82), residues: 41
  loop : -1.83 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L 250 
 TYR   0.019   0.002   TYR L 294 
 PHE   0.028   0.002   PHE L 213 
 HIS   0.007   0.002   HIS L 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7345)
  covalent geometry    : angle       0.77563 ( 9926)
  hydrogen bonds       : bond        0.05089 (  386)
  hydrogen bonds       : angle       4.86065 ( 1134)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 400
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  116 MET cc_start: 0.9393 (mmm) cc_final: 0.9057 (mmm)
REVERT: K  126 LEU cc_start: 0.9567 (tt) cc_final: 0.9256 (mt)
REVERT: K  144 ASP cc_start: 0.9196 (m-30) cc_final: 0.8929 (m-30)
REVERT: K  152 LEU cc_start: 0.9266 (pp) cc_final: 0.9000 (pp)
REVERT: K  186 LEU cc_start: 0.9288 (mt) cc_final: 0.8922 (mt)
REVERT: K  209 MET cc_start: 0.9149 (mtm) cc_final: 0.8752 (mtt)
REVERT: K  213 PHE cc_start: 0.9407 (m-10) cc_final: 0.9205 (m-80)
REVERT: K  236 GLN cc_start: 0.8617 (mm-40) cc_final: 0.7907 (mp10)
REVERT: K  261 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7191 (tm-30)
REVERT: K  276 GLU cc_start: 0.9296 (mp0) cc_final: 0.8929 (pm20)
REVERT: K  285 ILE cc_start: 0.9264 (mt) cc_final: 0.9031 (pt)
REVERT: K  303 TYR cc_start: 0.9409 (t80) cc_final: 0.9203 (t80)
REVERT: K  304 THR cc_start: 0.9010 (m) cc_final: 0.8687 (p)
REVERT: K  307 GLU cc_start: 0.9215 (pp20) cc_final: 0.8738 (pp20)
REVERT: K  316 PHE cc_start: 0.8481 (t80) cc_final: 0.8247 (t80)
REVERT: K  328 MET cc_start: 0.7005 (ptt) cc_final: 0.6424 (ptm)
REVERT: L  119 TYR cc_start: 0.9367 (m-80) cc_final: 0.9142 (m-80)
REVERT: L  128 HIS cc_start: 0.9605 (m90) cc_final: 0.9321 (m-70)
REVERT: L  209 MET cc_start: 0.9558 (tmm) cc_final: 0.9316 (tpt)
REVERT: L  210 ARG cc_start: 0.9471 (ttt-90) cc_final: 0.9241 (mmm-85)
REVERT: L  216 CYS cc_start: 0.9544 (m) cc_final: 0.8852 (m)
REVERT: L  278 LEU cc_start: 0.9686 (mp) cc_final: 0.9278 (mt)
REVERT: L  290 LEU cc_start: 0.9735 (mt) cc_final: 0.9050 (mm)
REVERT: L  293 MET cc_start: 0.9429 (ppp) cc_final: 0.9178 (ppp)
REVERT: L  294 TYR cc_start: 0.9221 (m-80) cc_final: 0.8677 (m-80)
REVERT: L  302 PHE cc_start: 0.9513 (t80) cc_final: 0.9296 (t80)
REVERT: L  328 MET cc_start: 0.7542 (ptm) cc_final: 0.7338 (ptt)
REVERT: M   14 GLU cc_start: 0.7630 (tp30) cc_final: 0.7387 (tp30)
REVERT: M   23 GLN cc_start: 0.9186 (pm20) cc_final: 0.8976 (pm20)
REVERT: M   28 LEU cc_start: 0.9063 (mm) cc_final: 0.8824 (mm)
REVERT: M   39 LEU cc_start: 0.8945 (tp) cc_final: 0.8533 (tp)
REVERT: M   42 TYR cc_start: 0.8675 (t80) cc_final: 0.8336 (t80)
REVERT: M   46 LYS cc_start: 0.9542 (mtmm) cc_final: 0.9099 (ptpt)
REVERT: M   48 LYS cc_start: 0.9572 (mttt) cc_final: 0.9199 (mttt)
REVERT: M   54 TYR cc_start: 0.9723 (t80) cc_final: 0.9356 (t80)
REVERT: M   58 LEU cc_start: 0.9558 (pp) cc_final: 0.9110 (pp)
REVERT: M   73 ASN cc_start: 0.9188 (t0) cc_final: 0.8841 (t0)
REVERT: M   76 ASP cc_start: 0.9545 (t0) cc_final: 0.9241 (t0)
REVERT: M  104 ASN cc_start: 0.8350 (t0) cc_final: 0.7924 (t0)
REVERT: M  108 PHE cc_start: 0.7255 (m-10) cc_final: 0.6671 (m-10)
REVERT: M  140 SER cc_start: 0.9552 (t) cc_final: 0.9183 (p)
REVERT: M  149 PHE cc_start: 0.8845 (m-80) cc_final: 0.7301 (m-80)
REVERT: M  228 ASN cc_start: 0.8946 (m-40) cc_final: 0.8664 (t0)
REVERT: M  244 PHE cc_start: 0.8990 (m-80) cc_final: 0.8612 (m-80)
REVERT: M  269 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8920 (tm-30)
REVERT: N   55 MET cc_start: 0.9675 (mmp) cc_final: 0.9415 (mmm)
REVERT: N   60 THR cc_start: 0.8128 (p) cc_final: 0.7915 (p)
REVERT: N   67 LEU cc_start: 0.9262 (pt) cc_final: 0.8672 (pt)
REVERT: N   73 ASN cc_start: 0.8748 (t0) cc_final: 0.8458 (t0)
REVERT: N   92 HIS cc_start: 0.9596 (t70) cc_final: 0.9159 (t70)
REVERT: N   98 LEU cc_start: 0.9600 (mt) cc_final: 0.9187 (tt)
REVERT: N  108 PHE cc_start: 0.7021 (m-80) cc_final: 0.6060 (m-80)
REVERT: N  137 ASP cc_start: 0.9000 (t0) cc_final: 0.8753 (t0)
REVERT: N  154 LEU cc_start: 0.8468 (mm) cc_final: 0.8257 (mm)
REVERT: N  195 ASP cc_start: 0.8209 (m-30) cc_final: 0.7865 (m-30)
REVERT: N  201 ILE cc_start: 0.8759 (pt) cc_final: 0.8329 (pt)
REVERT: N  220 TYR cc_start: 0.9426 (t80) cc_final: 0.8970 (t80)
REVERT: N  224 TYR cc_start: 0.9539 (t80) cc_final: 0.9173 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 401
  average time/residue: 0.0822
  time to fit residues: 43.8478
Evaluate side-chains
  285 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0010
   chunk 57 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
K 129 HIS
** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.089638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.066236 restraints weight = 28867.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.069010 restraints weight = 19568.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.071169 restraints weight = 14569.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.072826 restraints weight = 11489.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.074116 restraints weight = 9453.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.7848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7345  Z= 0.173
  Angle     :  0.719  10.664   9926  Z= 0.368
  Chirality :  0.044   0.222   1157
  Planarity :  0.004   0.031   1247
  Dihedral  :  5.053  24.581    961
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.00 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.01 %
    Favored  : 96.87 %
  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: -0.33 (0.29), residues: 867
  helix:  0.75 (0.23), residues: 503
  sheet: -0.64 (0.78), residues: 41
  loop : -1.71 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 250 
 TYR   0.016   0.002   TYR L 130 
 PHE   0.016   0.002   PHE N 125 
 HIS   0.003   0.001   HIS L 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7345)
  covalent geometry    : angle       0.71877 ( 9926)
  hydrogen bonds       : bond        0.04508 (  386)
  hydrogen bonds       : angle       4.83838 ( 1134)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 372
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  116 MET cc_start: 0.9509 (mmm) cc_final: 0.9202 (mmm)
REVERT: K  126 LEU cc_start: 0.9557 (tt) cc_final: 0.9220 (mt)
REVERT: K  144 ASP cc_start: 0.9183 (m-30) cc_final: 0.8891 (m-30)
REVERT: K  147 MET cc_start: 0.8652 (mmt) cc_final: 0.8296 (mmt)
REVERT: K  178 MET cc_start: 0.8768 (mpp) cc_final: 0.8294 (mpp)
REVERT: K  187 LEU cc_start: 0.9513 (mt) cc_final: 0.8969 (mt)
REVERT: K  203 LEU cc_start: 0.9213 (pt) cc_final: 0.9009 (pt)
REVERT: K  207 ASP cc_start: 0.9598 (t0) cc_final: 0.9258 (p0)
REVERT: K  209 MET cc_start: 0.9173 (mtm) cc_final: 0.8925 (mtt)
REVERT: K  213 PHE cc_start: 0.9398 (m-10) cc_final: 0.9104 (m-80)
REVERT: K  236 GLN cc_start: 0.8535 (mm-40) cc_final: 0.7703 (mp10)
REVERT: K  261 GLN cc_start: 0.7751 (tm-30) cc_final: 0.6660 (tm-30)
REVERT: K  276 GLU cc_start: 0.9292 (mp0) cc_final: 0.8877 (pm20)
REVERT: K  285 ILE cc_start: 0.9479 (mt) cc_final: 0.9103 (pt)
REVERT: K  302 PHE cc_start: 0.9417 (t80) cc_final: 0.9202 (t80)
REVERT: K  303 TYR cc_start: 0.9416 (t80) cc_final: 0.9212 (t80)
REVERT: K  304 THR cc_start: 0.8961 (m) cc_final: 0.8629 (p)
REVERT: K  307 GLU cc_start: 0.9161 (pp20) cc_final: 0.8616 (pp20)
REVERT: K  316 PHE cc_start: 0.8651 (t80) cc_final: 0.8432 (t80)
REVERT: K  328 MET cc_start: 0.7191 (ptt) cc_final: 0.6364 (ptm)
REVERT: K  333 LYS cc_start: 0.6795 (tptt) cc_final: 0.6594 (pptt)
REVERT: L  128 HIS cc_start: 0.9645 (m90) cc_final: 0.9440 (m-70)
REVERT: L  146 VAL cc_start: 0.9711 (t) cc_final: 0.9222 (t)
REVERT: L  209 MET cc_start: 0.9665 (tmm) cc_final: 0.9193 (tmm)
REVERT: L  210 ARG cc_start: 0.9537 (ttt-90) cc_final: 0.9215 (mmm-85)
REVERT: L  216 CYS cc_start: 0.9462 (m) cc_final: 0.8597 (m)
REVERT: L  222 MET cc_start: 0.7091 (tpt) cc_final: 0.6525 (tpp)
REVERT: L  226 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8523 (mmtm)
REVERT: L  229 LEU cc_start: 0.8079 (mm) cc_final: 0.7613 (mm)
REVERT: L  253 LYS cc_start: 0.9104 (ptpp) cc_final: 0.8889 (pttm)
REVERT: L  290 LEU cc_start: 0.9742 (mt) cc_final: 0.9307 (mp)
REVERT: L  294 TYR cc_start: 0.9226 (m-80) cc_final: 0.8624 (m-80)
REVERT: L  303 TYR cc_start: 0.9321 (m-80) cc_final: 0.8557 (m-80)
REVERT: L  328 MET cc_start: 0.7614 (ptm) cc_final: 0.7060 (ptt)
REVERT: M   10 ARG cc_start: 0.9044 (ttm170) cc_final: 0.8836 (ttm110)
REVERT: M   14 GLU cc_start: 0.7908 (tp30) cc_final: 0.7388 (tp30)
REVERT: M   23 GLN cc_start: 0.9267 (pm20) cc_final: 0.9045 (pm20)
REVERT: M   28 LEU cc_start: 0.9188 (mm) cc_final: 0.8721 (mp)
REVERT: M   32 ASP cc_start: 0.9609 (p0) cc_final: 0.9375 (p0)
REVERT: M   46 LYS cc_start: 0.9618 (mtmm) cc_final: 0.9215 (ptpp)
REVERT: M   54 TYR cc_start: 0.9754 (t80) cc_final: 0.9385 (t80)
REVERT: M   72 ARG cc_start: 0.8847 (mmp80) cc_final: 0.8502 (mmm160)
REVERT: M   73 ASN cc_start: 0.9172 (t0) cc_final: 0.8779 (t0)
REVERT: M   76 ASP cc_start: 0.9562 (t0) cc_final: 0.9204 (t0)
REVERT: M  106 MET cc_start: 0.9022 (tpt) cc_final: 0.8807 (tpt)
REVERT: M  140 SER cc_start: 0.9639 (t) cc_final: 0.9332 (p)
REVERT: M  144 MET cc_start: 0.9220 (tpt) cc_final: 0.8910 (tpt)
REVERT: M  149 PHE cc_start: 0.8890 (m-80) cc_final: 0.7261 (m-80)
REVERT: M  150 ASP cc_start: 0.8434 (t0) cc_final: 0.8045 (t0)
REVERT: M  154 LEU cc_start: 0.9520 (mp) cc_final: 0.9289 (mp)
REVERT: M  156 ASN cc_start: 0.8579 (m110) cc_final: 0.8314 (m110)
REVERT: M  220 TYR cc_start: 0.9213 (t80) cc_final: 0.8912 (t80)
REVERT: M  225 ILE cc_start: 0.9159 (tp) cc_final: 0.8826 (tp)
REVERT: M  234 TYR cc_start: 0.9342 (t80) cc_final: 0.8663 (t80)
REVERT: N   60 THR cc_start: 0.8362 (p) cc_final: 0.8148 (p)
REVERT: N   73 ASN cc_start: 0.9177 (t0) cc_final: 0.8896 (t0)
REVERT: N   92 HIS cc_start: 0.9592 (t70) cc_final: 0.8977 (t70)
REVERT: N   98 LEU cc_start: 0.9567 (mt) cc_final: 0.9206 (tt)
REVERT: N  108 PHE cc_start: 0.6782 (m-80) cc_final: 0.6068 (m-80)
REVERT: N  137 ASP cc_start: 0.9155 (t0) cc_final: 0.8894 (t0)
REVERT: N  144 MET cc_start: 0.9126 (tpp) cc_final: 0.8738 (tpt)
REVERT: N  195 ASP cc_start: 0.8258 (m-30) cc_final: 0.7992 (m-30)
REVERT: N  201 ILE cc_start: 0.8437 (pt) cc_final: 0.7822 (pt)
REVERT: N  220 TYR cc_start: 0.9350 (t80) cc_final: 0.8706 (t80)
REVERT: N  224 TYR cc_start: 0.9553 (t80) cc_final: 0.9190 (t80)
REVERT: N  259 LEU cc_start: 0.8461 (mt) cc_final: 0.8249 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 373
  average time/residue: 0.0846
  time to fit residues: 41.6881
Evaluate side-chains
  290 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 289
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 64 optimal weight:    0.1980
   chunk 82 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0970
   chunk 61 optimal weight:    0.7980
   chunk 81 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    0.4980
   chunk 19 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
K 129 HIS
K 182 GLN
** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 296 ASN
L 129 HIS
** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 128 ASN
M 228 ASN
** N 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.089951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.066557 restraints weight = 28824.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.069342 restraints weight = 19400.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.071496 restraints weight = 14347.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.073102 restraints weight = 11297.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.074424 restraints weight = 9294.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.8542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7345  Z= 0.150
  Angle     :  0.729  10.928   9926  Z= 0.369
  Chirality :  0.044   0.228   1157
  Planarity :  0.004   0.034   1247
  Dihedral  :  4.854  21.739    961
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.07 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.13 %
    Favored  : 96.75 %
  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: -0.42 (0.29), residues: 867
  helix:  0.67 (0.23), residues: 503
  sheet: -0.41 (0.81), residues: 41
  loop : -1.77 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG M 138 
 TYR   0.025   0.001   TYR L 119 
 PHE   0.029   0.002   PHE L 217 
 HIS   0.003   0.001   HIS L 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7345)
  covalent geometry    : angle       0.72855 ( 9926)
  hydrogen bonds       : bond        0.04429 (  386)
  hydrogen bonds       : angle       4.73949 ( 1134)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 362
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  116 MET cc_start: 0.9513 (mmm) cc_final: 0.9180 (mmm)
REVERT: K  126 LEU cc_start: 0.9551 (tt) cc_final: 0.9249 (mt)
REVERT: K  144 ASP cc_start: 0.9192 (m-30) cc_final: 0.8933 (m-30)
REVERT: K  149 MET cc_start: 0.9209 (ptp) cc_final: 0.8767 (ptt)
REVERT: K  151 PHE cc_start: 0.9435 (t80) cc_final: 0.9220 (t80)
REVERT: K  178 MET cc_start: 0.8756 (mpp) cc_final: 0.8221 (mpp)
REVERT: K  203 LEU cc_start: 0.9189 (pt) cc_final: 0.8985 (pt)
REVERT: K  207 ASP cc_start: 0.9584 (t0) cc_final: 0.9200 (p0)
REVERT: K  209 MET cc_start: 0.9222 (mtm) cc_final: 0.8986 (mtt)
REVERT: K  213 PHE cc_start: 0.9385 (m-10) cc_final: 0.9111 (m-80)
REVERT: K  222 MET cc_start: 0.8402 (ttp) cc_final: 0.8189 (tmm)
REVERT: K  248 ILE cc_start: 0.9529 (mm) cc_final: 0.9142 (tp)
REVERT: K  261 GLN cc_start: 0.7692 (tm-30) cc_final: 0.6736 (tm-30)
REVERT: K  276 GLU cc_start: 0.9312 (mp0) cc_final: 0.8912 (pm20)
REVERT: K  285 ILE cc_start: 0.9416 (mt) cc_final: 0.9197 (pt)
REVERT: K  303 TYR cc_start: 0.9497 (t80) cc_final: 0.9218 (t80)
REVERT: K  304 THR cc_start: 0.9027 (m) cc_final: 0.8618 (p)
REVERT: K  307 GLU cc_start: 0.9051 (pp20) cc_final: 0.8641 (pp20)
REVERT: K  308 ASN cc_start: 0.9351 (m110) cc_final: 0.9035 (m110)
REVERT: K  333 LYS cc_start: 0.6818 (tptt) cc_final: 0.6513 (pptt)
REVERT: L  119 TYR cc_start: 0.9269 (m-80) cc_final: 0.9066 (m-80)
REVERT: L  128 HIS cc_start: 0.9643 (m90) cc_final: 0.9410 (m-70)
REVERT: L  149 MET cc_start: 0.9745 (tpt) cc_final: 0.9487 (tmm)
REVERT: L  191 ARG cc_start: 0.9566 (ppt170) cc_final: 0.8906 (tmm160)
REVERT: L  216 CYS cc_start: 0.9382 (m) cc_final: 0.8958 (m)
REVERT: L  217 PHE cc_start: 0.9031 (m-80) cc_final: 0.8775 (m-80)
REVERT: L  222 MET cc_start: 0.6758 (tpt) cc_final: 0.6437 (tpp)
REVERT: L  226 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8430 (mmtt)
REVERT: L  252 GLU cc_start: 0.9069 (pp20) cc_final: 0.8742 (pp20)
REVERT: L  253 LYS cc_start: 0.8900 (ptpp) cc_final: 0.8578 (pttm)
REVERT: L  281 LEU cc_start: 0.9764 (mt) cc_final: 0.9561 (mt)
REVERT: L  293 MET cc_start: 0.9583 (ppp) cc_final: 0.9262 (ppp)
REVERT: L  294 TYR cc_start: 0.9317 (m-80) cc_final: 0.8686 (m-80)
REVERT: L  303 TYR cc_start: 0.9371 (m-80) cc_final: 0.8659 (m-80)
REVERT: L  306 MET cc_start: 0.9241 (mmp) cc_final: 0.8996 (mmp)
REVERT: L  328 MET cc_start: 0.7566 (ptm) cc_final: 0.6968 (ptt)
REVERT: M   14 GLU cc_start: 0.7992 (tp30) cc_final: 0.7366 (tp30)
REVERT: M   15 ILE cc_start: 0.8864 (tt) cc_final: 0.8634 (tt)
REVERT: M   23 GLN cc_start: 0.9241 (pm20) cc_final: 0.8997 (pm20)
REVERT: M   28 LEU cc_start: 0.9224 (mm) cc_final: 0.8585 (mp)
REVERT: M   32 ASP cc_start: 0.9589 (p0) cc_final: 0.9296 (p0)
REVERT: M   46 LYS cc_start: 0.9647 (mtmm) cc_final: 0.9195 (ptpp)
REVERT: M   54 TYR cc_start: 0.9732 (t80) cc_final: 0.9324 (t80)
REVERT: M   72 ARG cc_start: 0.9105 (mmp80) cc_final: 0.8717 (mmm160)
REVERT: M   76 ASP cc_start: 0.9562 (t0) cc_final: 0.9248 (t0)
REVERT: M   85 PHE cc_start: 0.9601 (t80) cc_final: 0.9262 (t80)
REVERT: M   91 ILE cc_start: 0.9611 (mm) cc_final: 0.9333 (mm)
REVERT: M   95 PHE cc_start: 0.9357 (m-80) cc_final: 0.9053 (m-80)
REVERT: M  104 ASN cc_start: 0.8163 (t0) cc_final: 0.7908 (t0)
REVERT: M  106 MET cc_start: 0.8828 (tpt) cc_final: 0.8099 (tpt)
REVERT: M  128 ASN cc_start: 0.8664 (t0) cc_final: 0.8169 (m-40)
REVERT: M  140 SER cc_start: 0.9625 (t) cc_final: 0.9345 (p)
REVERT: M  144 MET cc_start: 0.9336 (tpt) cc_final: 0.9124 (tpt)
REVERT: M  150 ASP cc_start: 0.8376 (t0) cc_final: 0.8127 (t0)
REVERT: M  156 ASN cc_start: 0.8591 (m110) cc_final: 0.8289 (m110)
REVERT: M  218 HIS cc_start: 0.9419 (m90) cc_final: 0.9185 (m90)
REVERT: M  220 TYR cc_start: 0.9243 (t80) cc_final: 0.8757 (t80)
REVERT: M  225 ILE cc_start: 0.9126 (tp) cc_final: 0.8926 (tp)
REVERT: M  227 LYS cc_start: 0.9597 (pptt) cc_final: 0.9380 (pptt)
REVERT: M  234 TYR cc_start: 0.9339 (t80) cc_final: 0.8712 (t80)
REVERT: N   73 ASN cc_start: 0.9264 (t0) cc_final: 0.9018 (t0)
REVERT: N   98 LEU cc_start: 0.9623 (mt) cc_final: 0.9258 (tt)
REVERT: N  108 PHE cc_start: 0.6967 (m-80) cc_final: 0.6764 (m-80)
REVERT: N  137 ASP cc_start: 0.8998 (t0) cc_final: 0.8556 (t0)
REVERT: N  144 MET cc_start: 0.8818 (tpp) cc_final: 0.8570 (tpp)
REVERT: N  195 ASP cc_start: 0.8321 (m-30) cc_final: 0.8025 (m-30)
REVERT: N  201 ILE cc_start: 0.8599 (pt) cc_final: 0.7707 (pt)
REVERT: N  221 LEU cc_start: 0.9832 (mp) cc_final: 0.9628 (mp)
REVERT: N  224 TYR cc_start: 0.9585 (t80) cc_final: 0.9219 (t80)
REVERT: N  236 LYS cc_start: 0.9299 (mtmt) cc_final: 0.8998 (mtmm)
REVERT: N  244 PHE cc_start: 0.8361 (m-10) cc_final: 0.7846 (m-80)
REVERT: N  259 LEU cc_start: 0.8837 (mt) cc_final: 0.8494 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 363
  average time/residue: 0.0845
  time to fit residues: 40.7157
Evaluate side-chains
  278 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 47 optimal weight:    0.3980
   chunk 31 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0980
   chunk 37 optimal weight:    0.0040
   chunk 67 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0670
   chunk 2 optimal weight:    0.0020
   chunk 3 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 68 optimal weight:    0.1980
   overall best weight:    0.0738

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

Flipped N/Q/H residues before XYZ refinement:
K 129 HIS
** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 323 ASN
M 228 ASN
** N  93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.093811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.069823 restraints weight = 27925.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.072723 restraints weight = 18722.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.075067 restraints weight = 13849.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.076611 restraints weight = 10857.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.078033 restraints weight = 9047.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.8845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7345  Z= 0.137
  Angle     :  0.723   9.484   9926  Z= 0.363
  Chirality :  0.044   0.229   1157
  Planarity :  0.003   0.034   1247
  Dihedral  :  4.673  22.242    961
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.81 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.53 %
    Favored  : 97.35 %
  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 are not related in a simple way.
  whole: -0.40 (0.29), residues: 867
  helix:  0.74 (0.23), residues: 505
  sheet: -0.60 (0.80), residues: 41
  loop : -1.86 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG M 138 
 TYR   0.012   0.001   TYR M 224 
 PHE   0.022   0.002   PHE N 266 
 HIS   0.003   0.001   HIS K 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7345)
  covalent geometry    : angle       0.72333 ( 9926)
  hydrogen bonds       : bond        0.04232 (  386)
  hydrogen bonds       : angle       4.56453 ( 1134)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 356
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  116 MET cc_start: 0.9554 (mmm) cc_final: 0.9232 (mmm)
REVERT: K  126 LEU cc_start: 0.9549 (tt) cc_final: 0.9250 (mt)
REVERT: K  144 ASP cc_start: 0.9144 (m-30) cc_final: 0.8824 (m-30)
REVERT: K  147 MET cc_start: 0.8378 (mmt) cc_final: 0.8029 (mmt)
REVERT: K  169 PHE cc_start: 0.9613 (m-10) cc_final: 0.9349 (m-10)
REVERT: K  178 MET cc_start: 0.8495 (mpp) cc_final: 0.7929 (mpp)
REVERT: K  203 LEU cc_start: 0.9374 (pt) cc_final: 0.9143 (pt)
REVERT: K  207 ASP cc_start: 0.9573 (t0) cc_final: 0.9237 (p0)
REVERT: K  209 MET cc_start: 0.9235 (mtm) cc_final: 0.9012 (mtt)
REVERT: K  213 PHE cc_start: 0.9459 (m-10) cc_final: 0.9230 (m-80)
REVERT: K  222 MET cc_start: 0.8121 (ttp) cc_final: 0.7150 (tpp)
REVERT: K  239 LYS cc_start: 0.9564 (pttp) cc_final: 0.9345 (pttp)
REVERT: K  245 GLU cc_start: 0.9717 (pm20) cc_final: 0.9481 (pm20)
REVERT: K  246 LEU cc_start: 0.9844 (tp) cc_final: 0.9574 (mp)
REVERT: K  276 GLU cc_start: 0.9276 (mp0) cc_final: 0.9014 (pm20)
REVERT: K  285 ILE cc_start: 0.9629 (mt) cc_final: 0.8963 (pt)
REVERT: K  288 TYR cc_start: 0.9246 (m-80) cc_final: 0.8950 (m-80)
REVERT: K  300 THR cc_start: 0.9381 (p) cc_final: 0.9053 (p)
REVERT: K  303 TYR cc_start: 0.9462 (t80) cc_final: 0.9199 (t80)
REVERT: K  304 THR cc_start: 0.9022 (m) cc_final: 0.8632 (p)
REVERT: K  307 GLU cc_start: 0.9124 (pp20) cc_final: 0.8699 (pp20)
REVERT: K  308 ASN cc_start: 0.9359 (m110) cc_final: 0.9013 (m110)
REVERT: L  128 HIS cc_start: 0.9610 (m90) cc_final: 0.9350 (m-70)
REVERT: L  132 LEU cc_start: 0.9424 (tp) cc_final: 0.9188 (tt)
REVERT: L  139 GLU cc_start: 0.8635 (tp30) cc_final: 0.8384 (tp30)
REVERT: L  149 MET cc_start: 0.9666 (tpt) cc_final: 0.9442 (mmm)
REVERT: L  191 ARG cc_start: 0.9506 (ppt170) cc_final: 0.8814 (tmm160)
REVERT: L  216 CYS cc_start: 0.9427 (m) cc_final: 0.8711 (m)
REVERT: L  217 PHE cc_start: 0.9151 (m-80) cc_final: 0.8687 (m-80)
REVERT: L  222 MET cc_start: 0.7272 (tpt) cc_final: 0.6817 (tpp)
REVERT: L  226 LYS cc_start: 0.8734 (mmtp) cc_final: 0.7717 (mmtp)
REVERT: L  228 VAL cc_start: 0.9087 (t) cc_final: 0.8726 (m)
REVERT: L  249 GLU cc_start: 0.9182 (pt0) cc_final: 0.8831 (pt0)
REVERT: L  252 GLU cc_start: 0.9074 (pp20) cc_final: 0.8658 (pp20)
REVERT: L  253 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8570 (pttm)
REVERT: L  294 TYR cc_start: 0.9426 (m-80) cc_final: 0.8814 (m-80)
REVERT: L  302 PHE cc_start: 0.9306 (t80) cc_final: 0.8869 (t80)
REVERT: L  306 MET cc_start: 0.9260 (mmp) cc_final: 0.8893 (mmp)
REVERT: L  328 MET cc_start: 0.7066 (ptm) cc_final: 0.6540 (ptt)
REVERT: M   14 GLU cc_start: 0.8057 (tp30) cc_final: 0.7395 (tp30)
REVERT: M   23 GLN cc_start: 0.9132 (pm20) cc_final: 0.8909 (pm20)
REVERT: M   28 LEU cc_start: 0.9131 (mm) cc_final: 0.8531 (mp)
REVERT: M   32 ASP cc_start: 0.9570 (p0) cc_final: 0.9300 (p0)
REVERT: M   42 TYR cc_start: 0.8723 (t80) cc_final: 0.8509 (t80)
REVERT: M   54 TYR cc_start: 0.9705 (t80) cc_final: 0.9278 (t80)
REVERT: M   72 ARG cc_start: 0.9077 (mmp80) cc_final: 0.8695 (mmm160)
REVERT: M   73 ASN cc_start: 0.8914 (t0) cc_final: 0.8705 (t0)
REVERT: M   76 ASP cc_start: 0.9491 (t0) cc_final: 0.9232 (t0)
REVERT: M   85 PHE cc_start: 0.9572 (t80) cc_final: 0.9246 (t80)
REVERT: M   91 ILE cc_start: 0.9626 (mm) cc_final: 0.9342 (mm)
REVERT: M   95 PHE cc_start: 0.9297 (m-80) cc_final: 0.9025 (m-80)
REVERT: M  104 ASN cc_start: 0.8106 (t0) cc_final: 0.7845 (t0)
REVERT: M  106 MET cc_start: 0.8809 (tpt) cc_final: 0.8088 (tpt)
REVERT: M  128 ASN cc_start: 0.8811 (t0) cc_final: 0.7999 (m-40)
REVERT: M  140 SER cc_start: 0.9679 (t) cc_final: 0.9406 (p)
REVERT: M  144 MET cc_start: 0.9258 (tpt) cc_final: 0.8757 (tpp)
REVERT: M  150 ASP cc_start: 0.8411 (t0) cc_final: 0.8025 (t0)
REVERT: M  156 ASN cc_start: 0.8600 (m110) cc_final: 0.8252 (m110)
REVERT: M  225 ILE cc_start: 0.9254 (tp) cc_final: 0.8824 (tp)
REVERT: M  234 TYR cc_start: 0.9359 (t80) cc_final: 0.8717 (t80)
REVERT: N   60 THR cc_start: 0.8750 (p) cc_final: 0.8544 (p)
REVERT: N   73 ASN cc_start: 0.9360 (t0) cc_final: 0.9054 (t0)
REVERT: N   74 LYS cc_start: 0.9751 (pptt) cc_final: 0.9431 (ptmm)
REVERT: N   98 LEU cc_start: 0.9639 (mt) cc_final: 0.9279 (tt)
REVERT: N  112 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8691 (mm-30)
REVERT: N  137 ASP cc_start: 0.8916 (t0) cc_final: 0.8352 (t0)
REVERT: N  195 ASP cc_start: 0.8321 (m-30) cc_final: 0.8049 (m-30)
REVERT: N  198 ASP cc_start: 0.8142 (p0) cc_final: 0.7925 (p0)
REVERT: N  201 ILE cc_start: 0.8530 (pt) cc_final: 0.8175 (pt)
REVERT: N  221 LEU cc_start: 0.9794 (mp) cc_final: 0.9566 (mp)
REVERT: N  224 TYR cc_start: 0.9521 (t80) cc_final: 0.9136 (t80)
REVERT: N  233 GLU cc_start: 0.9554 (pm20) cc_final: 0.9316 (pm20)
REVERT: N  236 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8865 (mtmm)
REVERT: N  244 PHE cc_start: 0.8255 (m-10) cc_final: 0.7814 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 356
  average time/residue: 0.0841
  time to fit residues: 39.8477
Evaluate side-chains
  286 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 286
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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: 65.3213 > 50:
  distance: 7 - 29:  28.461
  distance: 12 - 40:  11.383
  distance: 17 - 21:  28.463
  distance: 18 - 49:  17.905
  distance: 21 - 22:   4.950
  distance: 22 - 23:   6.831
  distance: 22 - 25:  44.670
  distance: 23 - 24:   6.600
  distance: 23 - 29:  13.315
  distance: 24 - 57:  45.377
  distance: 25 - 26:  35.504
  distance: 26 - 27:  33.168
  distance: 26 - 28:  46.464
  distance: 29 - 30:  17.958
  distance: 30 - 31:  33.265
  distance: 31 - 32:  26.250
  distance: 31 - 40:  18.507
  distance: 32 - 65:  34.890
  distance: 33 - 34:  11.748
  distance: 34 - 35:   3.182
  distance: 35 - 37:  10.158
  distance: 36 - 38:  11.094
  distance: 37 - 39:  10.926
  distance: 38 - 39:  11.744
  distance: 40 - 41:  19.496
  distance: 41 - 42:  12.518
  distance: 41 - 44:  13.805
  distance: 42 - 43:  12.675
  distance: 42 - 49:   9.766
  distance: 44 - 45:  24.906
  distance: 45 - 46:   9.017
  distance: 46 - 47:  15.197
  distance: 47 - 48:  21.788
  distance: 49 - 50:  13.511
  distance: 50 - 51:   7.321
  distance: 50 - 53:  32.641
  distance: 51 - 52:   4.486
  distance: 51 - 57:   4.424
  distance: 53 - 54:  21.092
  distance: 54 - 55:  23.416
  distance: 54 - 56:  31.423
  distance: 57 - 58:  17.678
  distance: 58 - 59:  25.135
  distance: 58 - 61:  25.954
  distance: 59 - 60:  27.515
  distance: 59 - 65:  27.785
  distance: 62 - 63:  18.462
  distance: 62 - 64:  16.619
  distance: 65 - 66:  39.331
  distance: 66 - 67:  22.199
  distance: 66 - 69:  15.381
  distance: 67 - 68:  24.622
  distance: 67 - 74:  25.305
  distance: 69 - 70:  37.000
  distance: 70 - 71:  35.524
  distance: 71 - 72:  29.590
  distance: 71 - 73:  11.733
  distance: 74 - 75:  43.628
  distance: 75 - 76:   9.417
  distance: 75 - 78:  24.508
  distance: 76 - 77:  28.027
  distance: 76 - 81:  50.934
  distance: 78 - 79:  19.446
  distance: 82 - 83:   5.390
  distance: 82 - 85:  38.030
  distance: 83 - 84:   7.339
  distance: 83 - 88:   7.197
  distance: 85 - 86:   3.327
  distance: 85 - 87:  59.352
  distance: 88 - 89:  15.648
  distance: 89 - 90:  16.111
  distance: 89 - 92:  19.627
  distance: 90 - 91:  40.668
  distance: 90 - 99:  28.733
  distance: 92 - 93:  15.715
  distance: 93 - 94:   7.908
  distance: 93 - 95:  36.797
  distance: 95 - 97:  15.081
  distance: 96 - 98:  33.617
  distance: 97 - 98:  11.883
  distance: 99 - 100:  10.255
  distance: 100 - 101:  22.105
  distance: 100 - 103:  41.414
  distance: 101 - 102:  30.042
  distance: 101 - 107:  19.945
  distance: 103 - 104:   8.291
  distance: 104 - 105:  18.293
  distance: 104 - 106:  41.021