Starting phenix.real_space_refine
on Fri Aug 22 21:07:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ti8_41281/08_2025/8ti8_41281.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ti8_41281/08_2025/8ti8_41281.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ti8_41281/08_2025/8ti8_41281.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ti8_41281/08_2025/8ti8_41281.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ti8_41281/08_2025/8ti8_41281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ti8_41281/08_2025/8ti8_41281.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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      16      5.16       5
     C    5053      2.51       5
     N    1281      2.21       5
     O    1537      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 7887
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1901
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 7, 'TRANS': 227}
    Chain: "C"
      Number of atoms: 2093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2093
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 7, 'TRANS': 251}
    Chain: "D"
      Number of atoms: 2052
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 2052
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1841
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 7, 'TRANS': 220}
          Chain breaks: 1
  Time building chain proxies: 2.21, per 1000 atoms: 0.28
  Number of scatterers: 7887
  At special positions: 0
  Unit cell: (79.8, 82.32, 146.16, 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      16     16.00
     O    1537      8.00
     N    1281      7.00
     C    5053      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: 0.79
  Conformation dependent library (CDL) restraints added in 464.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1880

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 6 sheets defined
      62.5% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 147 through 156
    Processing helix  chain 'A' and resid 159 through 169
      removed outlier: 4.281A  pdb=" N   ILE A 163 " --> pdb=" O   ASN A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 197
    Processing helix  chain 'A' and resid 203 through 213
      removed outlier: 3.578A  pdb=" N   TRP A 207 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 223
    Processing helix  chain 'A' and resid 246 through 253
      removed outlier: 3.624A  pdb=" N   PHE A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 318
    Processing helix  chain 'A' and resid 342 through 354
      removed outlier: 3.508A  pdb=" N   ARG A 346 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 379
    Processing helix  chain 'C' and resid 123 through 130
      removed outlier: 3.643A  pdb=" N   SER C 130 " --> pdb=" O   GLU C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 141
    Processing helix  chain 'C' and resid 145 through 157
    Processing helix  chain 'C' and resid 159 through 169
      removed outlier: 3.543A  pdb=" N   ILE C 163 " --> pdb=" O   ASN C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 171 through 198
    Processing helix  chain 'C' and resid 203 through 213
      removed outlier: 3.532A  pdb=" N   TRP C 207 " --> pdb=" O   SER C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 223
    Processing helix  chain 'C' and resid 246 through 253
      removed outlier: 3.937A  pdb=" N   PHE C 250 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 317
      removed outlier: 3.571A  pdb=" N   GLN C 317 " --> pdb=" O   ASN C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 336 through 340
      removed outlier: 3.651A  pdb=" N   THR C 339 " --> pdb=" O   MET C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 342 through 354
      removed outlier: 3.525A  pdb=" N   ARG C 346 " --> pdb=" O   ASP C 342 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 380
    Processing helix  chain 'D' and resid 121 through 131
    Processing helix  chain 'D' and resid 131 through 141
      removed outlier: 3.953A  pdb=" N   LEU D 135 " --> pdb=" O   ASN D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 145 through 156
    Processing helix  chain 'D' and resid 159 through 168
      removed outlier: 3.839A  pdb=" N   ILE D 163 " --> pdb=" O   ASN D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 198
    Processing helix  chain 'D' and resid 203 through 213
    Processing helix  chain 'D' and resid 214 through 223
      removed outlier: 3.826A  pdb=" N   LEU D 218 " --> pdb=" O   ASN D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 246 through 253
      removed outlier: 3.856A  pdb=" N   PHE D 250 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 318
      removed outlier: 3.556A  pdb=" N   THR D 290 " --> pdb=" O   HIS D 286 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY D 318 " --> pdb=" O   ASN D 314 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 342 through 356
    Processing helix  chain 'D' and resid 364 through 379
    Processing helix  chain 'B' and resid 148 through 156
    Processing helix  chain 'B' and resid 159 through 168
    Processing helix  chain 'B' and resid 171 through 197
    Processing helix  chain 'B' and resid 203 through 213
      removed outlier: 3.631A  pdb=" N   TRP B 207 " --> pdb=" O   SER B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 223
      removed outlier: 3.798A  pdb=" N   LEU B 218 " --> pdb=" O   ASN B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 253
      removed outlier: 3.772A  pdb=" N   PHE B 250 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 316
      removed outlier: 3.538A  pdb=" N   THR B 290 " --> pdb=" O   HIS B 286 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA B 292 " --> pdb=" O   ASP B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 356
    Processing helix  chain 'B' and resid 363 through 380
    Processing sheet with id=AA1, first strand: chain 'A' and resid 238 through 239
      removed outlier: 3.852A  pdb=" N   LYS A 238 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   CYS A 330 " --> pdb=" O   THR A 360 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   ILE A 362 " --> pdb=" O   CYS A 330 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   VAL A 332 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 238 through 239
    Processing sheet with id=AA3, first strand: chain 'D' and resid 238 through 239
    Processing sheet with id=AA4, first strand: chain 'D' and resid 273 through 274
      removed outlier: 4.389A  pdb=" N   SER D 284 " --> pdb=" O   THR D 274 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 238 through 240
      removed outlier: 4.760A  pdb=" N   ALA B 233 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 273 through 274
      removed outlier: 3.939A  pdb=" N   SER B 284 " --> pdb=" O   THR B 274 " (cutoff:3.500A)

    481 hydrogen bonds defined for protein.
    1419 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.27

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2526
        1.34 -     1.46: 1227
        1.46 -     1.57: 4248
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 8025
  Sorted by residual:
  bond pdb=" N   VAL C 235 "
       pdb=" CA  VAL C 235 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.034 1.17e-02 7.31e+03 8.58e+00
  bond pdb=" N   LYS D 171 "
       pdb=" CA  LYS D 171 "
    ideal  model  delta    sigma   weight residual
    1.453  1.490 -0.037 1.37e-02 5.33e+03 7.35e+00
  bond pdb=" N   LEU D 170 "
       pdb=" CA  LEU D 170 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.32e-02 5.74e+03 7.08e+00
  bond pdb=" N   LYS C 238 "
       pdb=" CA  LYS C 238 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.23e-02 6.61e+03 6.73e+00
  bond pdb=" N   LEU D 167 "
       pdb=" CA  LEU D 167 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.21e-02 6.83e+03 6.52e+00
  ... (remaining 8020 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.79: 10147
        0.79 -     1.59: 582
        1.59 -     2.38: 114
        2.38 -     3.18: 35
        3.18 -     3.97: 13
  Bond angle restraints: 10891
  Sorted by residual:
  angle pdb=" CA  LEU D 170 "
        pdb=" C   LEU D 170 "
        pdb=" O   LEU D 170 "
      ideal   model   delta    sigma   weight residual
     121.87  117.90    3.97 1.10e+00 8.26e-01 1.30e+01
  angle pdb=" CA  LYS D 171 "
        pdb=" C   LYS D 171 "
        pdb=" O   LYS D 171 "
      ideal   model   delta    sigma   weight residual
     121.99  118.15    3.84 1.14e+00 7.69e-01 1.14e+01
  angle pdb=" C   GLY A 236 "
        pdb=" N   GLY A 237 "
        pdb=" CA  GLY A 237 "
      ideal   model   delta    sigma   weight residual
     123.30  120.55    2.75 1.06e+00 8.90e-01 6.75e+00
  angle pdb=" N   GLY C 237 "
        pdb=" CA  GLY C 237 "
        pdb=" C   GLY C 237 "
      ideal   model   delta    sigma   weight residual
     115.30  111.69    3.61 1.44e+00 4.82e-01 6.27e+00
  angle pdb=" CA  LEU D 167 "
        pdb=" C   LEU D 167 "
        pdb=" O   LEU D 167 "
      ideal   model   delta    sigma   weight residual
     120.55  117.91    2.64 1.06e+00 8.90e-01 6.18e+00
  ... (remaining 10886 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.70: 4461
       11.70 -    23.40: 322
       23.40 -    35.10: 55
       35.10 -    46.80: 15
       46.80 -    58.51: 8
  Dihedral angle restraints: 4861
    sinusoidal: 1977
      harmonic: 2884
  Sorted by residual:
  dihedral pdb=" CA  PHE B 368 "
           pdb=" C   PHE B 368 "
           pdb=" N   GLU B 369 "
           pdb=" CA  GLU B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.00   16.00     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  PHE D 368 "
           pdb=" C   PHE D 368 "
           pdb=" N   GLU D 369 "
           pdb=" CA  GLU D 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.02   15.98     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  LYS B 320 "
           pdb=" CB  LYS B 320 "
           pdb=" CG  LYS B 320 "
           pdb=" CD  LYS B 320 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.51  -58.51     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 4858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 926
       0.033 -    0.067: 247
       0.067 -    0.100: 92
       0.100 -    0.134: 31
       0.134 -    0.167: 3
  Chirality restraints: 1299
  Sorted by residual:
  chirality pdb=" CA  VAL C 235 "
            pdb=" N   VAL C 235 "
            pdb=" C   VAL C 235 "
            pdb=" CB  VAL C 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.98e-01
  chirality pdb=" CA  LEU D 170 "
            pdb=" N   LEU D 170 "
            pdb=" C   LEU D 170 "
            pdb=" CB  LEU D 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  PHE A 368 "
            pdb=" N   PHE A 368 "
            pdb=" C   PHE A 368 "
            pdb=" CB  PHE A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 1296 not shown)

  Planarity restraints: 1363
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 254 "   -0.024 5.00e-02 4.00e+02   3.70e-02 2.20e+00
        pdb=" N   PRO C 255 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO C 255 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 255 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 254 "    0.021 5.00e-02 4.00e+02   3.19e-02 1.62e+00
        pdb=" N   PRO D 255 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO D 255 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D 255 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 254 "   -0.020 5.00e-02 4.00e+02   3.00e-02 1.44e+00
        pdb=" N   PRO B 255 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B 255 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 255 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1360 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1807
        2.80 -     3.33: 7455
        3.33 -     3.85: 12300
        3.85 -     4.38: 14113
        4.38 -     4.90: 24776
  Nonbonded interactions: 60451
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 254 "
            pdb=" O   SER A 257 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" OE1 GLU A 232 "
            pdb=" OH  TYR A 234 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" NZ  LYS A 354 "
            pdb=" OD1 ASP B 324 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" ND2 ASN C 254 "
            pdb=" O   SER C 257 "
     model   vdw
     2.365 3.120
  nonbonded pdb=" O   PHE C 256 "
            pdb=" NH1 ARG D 370 "
     model   vdw
     2.386 3.120
  ... (remaining 60446 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 'A' and (resid 147 through 168 or (resid 169 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 170 through 275 or resid 282 through 379)) \ 

  selection = (chain 'B' and (resid 147 through 168 or (resid 169 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 170 through 379))
  selection = (chain 'C' and (resid 147 through 168 or (resid 169 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 170 through 275 or resid 282 through 379)) \ 

  selection = (chain 'D' and resid 147 through 379)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.090
  Find NCS groups from input model:        0.150
  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:             0.010
  Load rotamer database and sin/cos tables:6.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
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      :  0.003   0.037   8025  Z= 0.159
  Angle     :  0.461   3.971  10891  Z= 0.298
  Chirality :  0.039   0.167   1299
  Planarity :  0.003   0.037   1363
  Dihedral  :  8.827  58.505   2981
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  1.88 %
    Favored  : 97.46 %
  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:  2.48 (0.29), residues: 964
  helix:  2.81 (0.21), residues: 610
  sheet:  2.37 (0.89), residues: 54
  loop : -1.12 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 370 
 TYR   0.007   0.001   TYR D 307 
 PHE   0.016   0.001   PHE B 368 
 TRP   0.006   0.001   TRP C 207 
 HIS   0.002   0.000   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8025)
  covalent geometry    : angle       0.46079 (10891)
  hydrogen bonds       : bond        0.15398 (  481)
  hydrogen bonds       : angle       4.54924 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8367 (m-30) cc_final: 0.8089 (p0)
  outliers start: 6
  outliers final: 2
  residues processed: 97
  average time/residue: 0.7631
  time to fit residues: 77.1148
Evaluate side-chains
  45 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  158 ASP
Chi-restraints excluded: chain D residue  231 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0470
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
C 177 GLN
D 242 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.097399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.064463 restraints weight = 15906.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 3.00
r_work: 0.2733 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   8025  Z= 0.122
  Angle     :  0.446   7.808  10891  Z= 0.237
  Chirality :  0.039   0.137   1299
  Planarity :  0.003   0.032   1363
  Dihedral  :  3.440  14.873   1034
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  6.97 %
    Favored  : 92.26 %
  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:  2.41 (0.29), residues: 964
  helix:  2.68 (0.21), residues: 621
  sheet:  1.69 (0.87), residues: 56
  loop : -0.99 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 316 
 TYR   0.013   0.001   TYR C 315 
 PHE   0.016   0.001   PHE B 368 
 TRP   0.006   0.001   TRP D 207 
 HIS   0.002   0.001   HIS C 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8025)
  covalent geometry    : angle       0.44616 (10891)
  hydrogen bonds       : bond        0.05292 (  481)
  hydrogen bonds       : angle       3.57800 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 LYS cc_start: 0.8308 (mtmt) cc_final: 0.8067 (pttm)
REVERT: A  316 ARG cc_start: 0.8368 (ttp80) cc_final: 0.7895 (mtt90)
REVERT: A  322 ASP cc_start: 0.8618 (m-30) cc_final: 0.7910 (p0)
REVERT: D  134 LEU cc_start: 0.8712 (mt) cc_final: 0.8462 (tt)
REVERT: B  347 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8300 (t70)
REVERT: B  351 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8810 (mm)
  outliers start: 7
  outliers final: 0
  residues processed: 56
  average time/residue: 0.6180
  time to fit residues: 36.4672
Evaluate side-chains
  46 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 HIS
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0870
   chunk 90 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 47 optimal weight:    0.3980
   chunk 92 optimal weight:    6.9990
   chunk 67 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0670
   chunk 25 optimal weight:    0.0770
   chunk 91 optimal weight:    0.0770
   overall best weight:    0.1412

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

Flipped N/Q/H residues before XYZ refinement:
C 177 GLN
B 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.099313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.068287 restraints weight = 15323.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.89
r_work: 0.2912 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   8025  Z= 0.081
  Angle     :  0.376   7.498  10891  Z= 0.201
  Chirality :  0.038   0.128   1299
  Planarity :  0.003   0.030   1363
  Dihedral  :  3.228  14.310   1030
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.52 %
    Favored  : 91.48 %
  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:  2.64 (0.29), residues: 964
  helix:  2.88 (0.21), residues: 620
  sheet:  1.83 (0.84), residues: 54
  loop : -0.91 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 316 
 TYR   0.010   0.001   TYR D 283 
 PHE   0.013   0.001   PHE C 368 
 TRP   0.005   0.001   TRP C 194 
 HIS   0.001   0.000   HIS D 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00159 ( 8025)
  covalent geometry    : angle       0.37648 (10891)
  hydrogen bonds       : bond        0.03410 (  481)
  hydrogen bonds       : angle       3.15441 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7867 (mtt90)
REVERT: A  322 ASP cc_start: 0.8567 (m-30) cc_final: 0.7860 (p0)
REVERT: C  322 ASP cc_start: 0.8412 (m-30) cc_final: 0.7981 (p0)
REVERT: D  134 LEU cc_start: 0.8704 (mt) cc_final: 0.8441 (tt)
  outliers start: 9
  outliers final: 2
  residues processed: 59
  average time/residue: 0.5314
  time to fit residues: 33.1809
Evaluate side-chains
  43 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  267 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 69 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 73 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 345 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.094839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.061855 restraints weight = 16173.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 3.01
r_work: 0.2667 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8025  Z= 0.191
  Angle     :  0.465   7.360  10891  Z= 0.252
  Chirality :  0.041   0.152   1299
  Planarity :  0.003   0.030   1363
  Dihedral  :  3.469  16.102   1030
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  8.41 %
    Favored  : 90.60 %
  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:  2.37 (0.28), residues: 964
  helix:  2.68 (0.21), residues: 619
  sheet:  1.29 (0.82), residues: 56
  loop : -0.95 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 316 
 TYR   0.015   0.001   TYR B 307 
 PHE   0.019   0.002   PHE D 368 
 TRP   0.008   0.001   TRP A 207 
 HIS   0.003   0.001   HIS B 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 8025)
  covalent geometry    : angle       0.46532 (10891)
  hydrogen bonds       : bond        0.06347 (  481)
  hydrogen bonds       : angle       3.63056 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8664 (m-30) cc_final: 0.7875 (p0)
REVERT: C  322 ASP cc_start: 0.8475 (m-30) cc_final: 0.7997 (p0)
REVERT: D  134 LEU cc_start: 0.8732 (mt) cc_final: 0.8446 (tt)
REVERT: B  347 HIS cc_start: 0.8663 (OUTLIER) cc_final: 0.8362 (t70)
  outliers start: 9
  outliers final: 1
  residues processed: 48
  average time/residue: 0.5553
  time to fit residues: 28.3900
Evaluate side-chains
  43 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain B residue  347 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 78 optimal weight:    0.0980
   chunk 33 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0570
   overall best weight:    0.3498

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

Flipped N/Q/H residues before XYZ refinement:
C 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.098949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.066464 restraints weight = 16096.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.99
r_work: 0.2832 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8025  Z= 0.090
  Angle     :  0.386   8.030  10891  Z= 0.207
  Chirality :  0.038   0.130   1299
  Planarity :  0.003   0.029   1363
  Dihedral  :  3.265  14.559   1030
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  9.07 %
    Favored  : 90.27 %
  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 aren not related in a simple way.
  whole:  2.57 (0.29), residues: 964
  helix:  2.83 (0.21), residues: 620
  sheet:  1.36 (0.83), residues: 56
  loop : -0.86 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 316 
 TYR   0.010   0.001   TYR D 283 
 PHE   0.016   0.001   PHE C 368 
 TRP   0.006   0.001   TRP C 194 
 HIS   0.001   0.000   HIS B 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 8025)
  covalent geometry    : angle       0.38561 (10891)
  hydrogen bonds       : bond        0.04077 (  481)
  hydrogen bonds       : angle       3.19901 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7941 (mtt90)
REVERT: A  322 ASP cc_start: 0.8600 (m-30) cc_final: 0.7827 (p0)
REVERT: C  322 ASP cc_start: 0.8436 (m-30) cc_final: 0.8014 (p0)
REVERT: D  134 LEU cc_start: 0.8679 (mt) cc_final: 0.8398 (tt)
  outliers start: 6
  outliers final: 2
  residues processed: 48
  average time/residue: 0.6026
  time to fit residues: 30.8616
Evaluate side-chains
  45 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  267 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0970
   chunk 62 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
C 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.096731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.063875 restraints weight = 16163.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 2.97
r_work: 0.2704 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8025  Z= 0.143
  Angle     :  0.436   8.138  10891  Z= 0.232
  Chirality :  0.040   0.140   1299
  Planarity :  0.003   0.030   1363
  Dihedral  :  3.348  14.659   1030
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.18 %
    Favored  : 90.04 %
  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:  2.48 (0.28), residues: 964
  helix:  2.76 (0.21), residues: 620
  sheet:  1.22 (0.80), residues: 56
  loop : -0.88 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 316 
 TYR   0.012   0.001   TYR B 307 
 PHE   0.016   0.001   PHE D 368 
 TRP   0.007   0.001   TRP A 207 
 HIS   0.002   0.001   HIS C 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8025)
  covalent geometry    : angle       0.43644 (10891)
  hydrogen bonds       : bond        0.05425 (  481)
  hydrogen bonds       : angle       3.41978 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8444 (mttp)
REVERT: A  322 ASP cc_start: 0.8656 (m-30) cc_final: 0.7833 (p0)
REVERT: C  322 ASP cc_start: 0.8524 (m-30) cc_final: 0.8048 (p0)
REVERT: D  134 LEU cc_start: 0.8697 (mt) cc_final: 0.8404 (tt)
REVERT: B  347 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.8323 (t70)
  outliers start: 7
  outliers final: 2
  residues processed: 48
  average time/residue: 0.6339
  time to fit residues: 32.3692
Evaluate side-chains
  47 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LYS
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain B residue  347 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0870
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
C 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.094437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.062825 restraints weight = 15434.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 2.87
r_work: 0.2766 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8025  Z= 0.120
  Angle     :  0.419   7.253  10891  Z= 0.223
  Chirality :  0.039   0.134   1299
  Planarity :  0.003   0.029   1363
  Dihedral  :  3.318  14.690   1030
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.40 %
    Favored  : 89.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.28), residues: 964
  helix:  2.78 (0.21), residues: 621
  sheet:  1.24 (0.80), residues: 56
  loop : -0.84 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 316 
 TYR   0.010   0.001   TYR D 283 
 PHE   0.016   0.001   PHE C 368 
 TRP   0.006   0.001   TRP A 207 
 HIS   0.001   0.000   HIS B 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8025)
  covalent geometry    : angle       0.41944 (10891)
  hydrogen bonds       : bond        0.04960 (  481)
  hydrogen bonds       : angle       3.33935 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8448 (mttp)
REVERT: A  316 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8022 (mtt90)
REVERT: A  322 ASP cc_start: 0.8631 (m-30) cc_final: 0.7825 (p0)
REVERT: C  322 ASP cc_start: 0.8502 (m-30) cc_final: 0.8091 (p0)
REVERT: D  134 LEU cc_start: 0.8698 (mt) cc_final: 0.8414 (tt)
REVERT: B  347 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8233 (t70)
  outliers start: 7
  outliers final: 2
  residues processed: 47
  average time/residue: 0.6341
  time to fit residues: 31.7090
Evaluate side-chains
  46 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LYS
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain B residue  347 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0570
   chunk 65 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0040
   overall best weight:    0.3710

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

Flipped N/Q/H residues before XYZ refinement:
A 295 GLN
C 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.096546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.064936 restraints weight = 15623.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 2.95
r_work: 0.2839 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8025  Z= 0.092
  Angle     :  0.401   8.326  10891  Z= 0.211
  Chirality :  0.038   0.130   1299
  Planarity :  0.003   0.027   1363
  Dihedral  :  3.209  14.436   1030
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 10.07 %
    Favored  : 89.27 %
  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 aren not related in a simple way.
  whole:  2.70 (0.29), residues: 964
  helix:  2.90 (0.21), residues: 620
  sheet:  1.38 (0.81), residues: 56
  loop : -0.73 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 316 
 TYR   0.011   0.001   TYR B 283 
 PHE   0.015   0.001   PHE C 368 
 TRP   0.005   0.001   TRP C 194 
 HIS   0.001   0.000   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 8025)
  covalent geometry    : angle       0.40099 (10891)
  hydrogen bonds       : bond        0.03990 (  481)
  hydrogen bonds       : angle       3.17136 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7927 (mtt90)
REVERT: A  322 ASP cc_start: 0.8581 (m-30) cc_final: 0.7788 (p0)
REVERT: C  322 ASP cc_start: 0.8459 (m-30) cc_final: 0.8050 (p0)
REVERT: B  347 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.8161 (t70)
  outliers start: 6
  outliers final: 2
  residues processed: 48
  average time/residue: 0.5809
  time to fit residues: 29.7264
Evaluate side-chains
  45 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain B residue  347 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.9322

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

Flipped N/Q/H residues before XYZ refinement:
C 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.096513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.063573 restraints weight = 16136.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 2.96
r_work: 0.2701 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8025  Z= 0.149
  Angle     :  0.456   8.985  10891  Z= 0.243
  Chirality :  0.040   0.163   1299
  Planarity :  0.003   0.029   1363
  Dihedral  :  3.359  14.798   1030
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 10.18 %
    Favored  : 89.27 %
  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 aren not related in a simple way.
  whole:  2.50 (0.28), residues: 964
  helix:  2.79 (0.21), residues: 619
  sheet:  1.17 (0.80), residues: 56
  loop : -0.89 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 316 
 TYR   0.013   0.001   TYR B 307 
 PHE   0.017   0.001   PHE D 368 
 TRP   0.007   0.001   TRP A 207 
 HIS   0.002   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8025)
  covalent geometry    : angle       0.45576 (10891)
  hydrogen bonds       : bond        0.05473 (  481)
  hydrogen bonds       : angle       3.43743 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8419 (mttp)
REVERT: A  322 ASP cc_start: 0.8652 (m-30) cc_final: 0.7803 (p0)
REVERT: C  322 ASP cc_start: 0.8590 (m-30) cc_final: 0.8171 (p0)
REVERT: B  316 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7833 (tpt90)
  outliers start: 5
  outliers final: 3
  residues processed: 45
  average time/residue: 0.7635
  time to fit residues: 36.3302
Evaluate side-chains
  46 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LYS
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain B residue  336 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 63 optimal weight:    0.1980
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.097505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.064664 restraints weight = 16027.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.99
r_work: 0.2721 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8025  Z= 0.122
  Angle     :  0.439   9.455  10891  Z= 0.233
  Chirality :  0.039   0.160   1299
  Planarity :  0.003   0.028   1363
  Dihedral  :  3.312  14.647   1030
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 10.18 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.28), residues: 964
  helix:  2.82 (0.21), residues: 619
  sheet:  1.24 (0.80), residues: 56
  loop : -0.86 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 316 
 TYR   0.021   0.001   TYR C 315 
 PHE   0.016   0.001   PHE C 368 
 TRP   0.006   0.001   TRP A 207 
 HIS   0.002   0.000   HIS C 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8025)
  covalent geometry    : angle       0.43869 (10891)
  hydrogen bonds       : bond        0.04916 (  481)
  hydrogen bonds       : angle       3.34209 ( 1419)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8416 (mttp)
REVERT: A  322 ASP cc_start: 0.8643 (m-30) cc_final: 0.7783 (p0)
REVERT: C  322 ASP cc_start: 0.8585 (m-30) cc_final: 0.8194 (p0)
REVERT: B  316 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7755 (tpt90)
REVERT: B  347 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8262 (t70)
  outliers start: 7
  outliers final: 4
  residues processed: 46
  average time/residue: 0.5699
  time to fit residues: 27.8269
Evaluate side-chains
  47 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LYS
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain B residue  347 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 295 GLN
C 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.094879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.063471 restraints weight = 15530.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 2.93
r_work: 0.2777 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8025  Z= 0.121
  Angle     :  0.438   9.446  10891  Z= 0.232
  Chirality :  0.039   0.170   1299
  Planarity :  0.003   0.028   1363
  Dihedral  :  3.298  14.664   1030
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 10.51 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.28), residues: 964
  helix:  2.81 (0.21), residues: 619
  sheet:  1.26 (0.80), residues: 56
  loop : -0.84 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 316 
 TYR   0.012   0.001   TYR D 283 
 PHE   0.016   0.001   PHE C 368 
 TRP   0.006   0.001   TRP A 207 
 HIS   0.001   0.000   HIS C 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8025)
  covalent geometry    : angle       0.43829 (10891)
  hydrogen bonds       : bond        0.04885 (  481)
  hydrogen bonds       : angle       3.33171 ( 1419)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2058.41 seconds
wall clock time: 35 minutes 57.68 seconds (2157.68 seconds total)