Starting phenix.real_space_refine
on Sun May 11 10:49:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ti8_41281/05_2025/8ti8_41281.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ti8_41281/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ti8_41281/05_2025/8ti8_41281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ti8_41281/05_2025/8ti8_41281.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ti8_41281/05_2025/8ti8_41281.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ti8_41281/05_2025/8ti8_41281.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.52, per 1000 atoms: 0.70
  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: 1.80
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.76
  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: 2.06

  Time building geometry restraints manager: 2.12 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:             2.850
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.510
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.030
  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:11.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.530
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (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
 TRP   0.006   0.001   TRP C 207 
 HIS   0.002   0.000   HIS A 347 
 PHE   0.016   0.001   PHE B 368 
 TYR   0.007   0.001   TYR D 307 
 ARG   0.001   0.000   ARG A 370 

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

*********************** 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  : 0.900 
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: 1.6427
  time to fit residues: 166.8050
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  : 1.014 
-------------------------------------------------------------------------------
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 80 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0970
   chunk 48 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 55 optimal weight:    0.3980
   chunk 86 optimal weight:    0.0470
   overall best weight:    0.4076

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
C 177 GLN
D 242 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.099191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.066412 restraints weight = 15884.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 3.01
r_work: 0.2834 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8025  Z= 0.102
  Angle     :  0.429   7.505  10891  Z= 0.226
  Chirality :  0.039   0.135   1299
  Planarity :  0.003   0.033   1363
  Dihedral  :  3.385  14.755   1034
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  6.53 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.29), residues: 964
  helix:  2.75 (0.21), residues: 621
  sheet:  1.69 (0.87), residues: 56
  loop : -0.96 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 207 
 HIS   0.001   0.001   HIS C 286 
 PHE   0.014   0.001   PHE B 368 
 TYR   0.013   0.001   TYR C 315 
 ARG   0.007   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04665 (  481)
  hydrogen bonds       : angle       3.46744 ( 1419)
  covalent geometry    : bond        0.00221 ( 8025)
  covalent geometry    : angle       0.42912 (10891)

*********************** 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
  62 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6991 (m110)
REVERT: A  316 ARG cc_start: 0.8328 (ttp80) cc_final: 0.7939 (mtt90)
REVERT: A  322 ASP cc_start: 0.8587 (m-30) cc_final: 0.7952 (p0)
REVERT: D  134 LEU cc_start: 0.8713 (mt) cc_final: 0.8447 (tt)
REVERT: D  144 SER cc_start: 0.8866 (t) cc_final: 0.8510 (p)
REVERT: B  347 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.8294 (t70)
  outliers start: 10
  outliers final: 0
  residues processed: 59
  average time/residue: 1.3831
  time to fit residues: 86.6915
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  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain B residue  347 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
C 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.094477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.062724 restraints weight = 15619.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 2.93
r_work: 0.2726 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8025  Z= 0.128
  Angle     :  0.420   7.258  10891  Z= 0.227
  Chirality :  0.039   0.137   1299
  Planarity :  0.003   0.029   1363
  Dihedral  :  3.372  14.485   1030
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.63 %
    Favored  : 91.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.28), residues: 964
  helix:  2.72 (0.21), residues: 622
  sheet:  1.46 (0.85), residues: 56
  loop : -0.96 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 207 
 HIS   0.002   0.000   HIS C 347 
 PHE   0.017   0.001   PHE B 368 
 TYR   0.011   0.001   TYR B 307 
 ARG   0.006   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05280 (  481)
  hydrogen bonds       : angle       3.47304 ( 1419)
  covalent geometry    : bond        0.00300 ( 8025)
  covalent geometry    : angle       0.41985 (10891)

*********************** 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
  53 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.7080 (m110)
REVERT: A  316 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7841 (mtt90)
REVERT: A  322 ASP cc_start: 0.8639 (m-30) cc_final: 0.7878 (p0)
REVERT: C  322 ASP cc_start: 0.8477 (m-30) cc_final: 0.7977 (p0)
REVERT: D  134 LEU cc_start: 0.8703 (mt) cc_final: 0.8423 (tt)
REVERT: B  347 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.8349 (t70)
REVERT: B  351 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8821 (mm)
  outliers start: 9
  outliers final: 2
  residues processed: 49
  average time/residue: 1.1924
  time to fit residues: 62.9760
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  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain D residue  317 GLN
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain B residue  347 HIS
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 46 optimal weight:    0.1980
   chunk 64 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
C 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.097081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.064334 restraints weight = 15789.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.98
r_work: 0.2728 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.1875

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= 0.118
  Angle     :  0.408   7.841  10891  Z= 0.220
  Chirality :  0.039   0.134   1299
  Planarity :  0.003   0.029   1363
  Dihedral  :  3.351  14.568   1030
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.28), residues: 964
  helix:  2.72 (0.21), residues: 622
  sheet:  1.28 (0.83), residues: 56
  loop : -0.92 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 207 
 HIS   0.001   0.000   HIS A 347 
 PHE   0.016   0.001   PHE B 368 
 TYR   0.010   0.001   TYR D 283 
 ARG   0.005   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05025 (  481)
  hydrogen bonds       : angle       3.38878 ( 1419)
  covalent geometry    : bond        0.00275 ( 8025)
  covalent geometry    : angle       0.40850 (10891)

*********************** 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
  52 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.7106 (m110)
REVERT: A  322 ASP cc_start: 0.8630 (m-30) cc_final: 0.7833 (p0)
REVERT: C  322 ASP cc_start: 0.8470 (m-30) cc_final: 0.7986 (p0)
REVERT: D  134 LEU cc_start: 0.8725 (mt) cc_final: 0.8449 (tt)
REVERT: B  316 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7905 (mtp85)
  outliers start: 8
  outliers final: 2
  residues processed: 48
  average time/residue: 1.3015
  time to fit residues: 67.1283
Evaluate side-chains
  47 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain D residue  127 MET
Chi-restraints excluded: chain B residue  267 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 23 optimal weight:    9.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
C 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.096531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.063869 restraints weight = 15886.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.98
r_work: 0.2710 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1934

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= 0.134
  Angle     :  0.425   8.267  10891  Z= 0.229
  Chirality :  0.039   0.137   1299
  Planarity :  0.003   0.030   1363
  Dihedral  :  3.370  14.668   1030
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.30 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.28), residues: 964
  helix:  2.69 (0.21), residues: 622
  sheet:  1.18 (0.81), residues: 56
  loop : -0.91 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 207 
 HIS   0.002   0.000   HIS B 286 
 PHE   0.016   0.001   PHE B 368 
 TYR   0.011   0.001   TYR B 307 
 ARG   0.004   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05283 (  481)
  hydrogen bonds       : angle       3.41088 ( 1419)
  covalent geometry    : bond        0.00318 ( 8025)
  covalent geometry    : angle       0.42512 (10891)

*********************** 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
  52 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8640 (m-30) cc_final: 0.7828 (p0)
REVERT: C  322 ASP cc_start: 0.8517 (m-30) cc_final: 0.8013 (p0)
REVERT: D  134 LEU cc_start: 0.8721 (mt) cc_final: 0.8431 (tt)
REVERT: D  317 GLN cc_start: 0.7986 (tp40) cc_final: 0.7672 (mp10)
REVERT: B  316 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7960 (mtp85)
REVERT: B  347 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8296 (t70)
  outliers start: 8
  outliers final: 2
  residues processed: 49
  average time/residue: 1.2692
  time to fit residues: 66.6046
Evaluate side-chains
  46 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 80 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.4980
   chunk 22 optimal weight:    0.5980
   chunk 83 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.095329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.064066 restraints weight = 15356.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 2.90
r_work: 0.2783 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8025  Z= 0.107
  Angle     :  0.406   8.714  10891  Z= 0.216
  Chirality :  0.039   0.132   1299
  Planarity :  0.003   0.028   1363
  Dihedral  :  3.329  15.036   1030
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.19 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.28), residues: 964
  helix:  2.78 (0.21), residues: 620
  sheet:  1.27 (0.81), residues: 56
  loop : -0.84 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 207 
 HIS   0.002   0.000   HIS B 286 
 PHE   0.015   0.001   PHE C 368 
 TYR   0.010   0.001   TYR D 283 
 ARG   0.004   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04664 (  481)
  hydrogen bonds       : angle       3.29119 ( 1419)
  covalent geometry    : bond        0.00244 ( 8025)
  covalent geometry    : angle       0.40603 (10891)

*********************** 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
  53 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8601 (m-30) cc_final: 0.7809 (p0)
REVERT: C  322 ASP cc_start: 0.8472 (m-30) cc_final: 0.8013 (p0)
REVERT: D  134 LEU cc_start: 0.8719 (mt) cc_final: 0.8433 (tt)
REVERT: D  317 GLN cc_start: 0.7891 (tp40) cc_final: 0.7580 (mp10)
REVERT: B  316 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7754 (tpt90)
  outliers start: 8
  outliers final: 3
  residues processed: 52
  average time/residue: 1.2187
  time to fit residues: 67.9025
Evaluate side-chains
  47 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  267 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3517 r_free = 0.3517 target = 0.097352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.064589 restraints weight = 16057.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 2.95
r_work: 0.2724 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8025  Z= 0.124
  Angle     :  0.422   8.849  10891  Z= 0.225
  Chirality :  0.039   0.134   1299
  Planarity :  0.003   0.029   1363
  Dihedral  :  3.337  14.656   1030
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  8.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.28), residues: 964
  helix:  2.77 (0.21), residues: 620
  sheet:  1.28 (0.81), residues: 56
  loop : -0.84 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 207 
 HIS   0.002   0.000   HIS B 286 
 PHE   0.016   0.001   PHE C 368 
 TYR   0.010   0.001   TYR B 307 
 ARG   0.003   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05023 (  481)
  hydrogen bonds       : angle       3.34313 ( 1419)
  covalent geometry    : bond        0.00293 ( 8025)
  covalent geometry    : angle       0.42203 (10891)

*********************** 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
  53 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8638 (m-30) cc_final: 0.7825 (p0)
REVERT: C  322 ASP cc_start: 0.8528 (m-30) cc_final: 0.8053 (p0)
REVERT: D  134 LEU cc_start: 0.8706 (mt) cc_final: 0.8419 (tt)
REVERT: D  317 GLN cc_start: 0.7980 (tp40) cc_final: 0.7649 (mp10)
REVERT: B  316 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7783 (tpt90)
REVERT: B  347 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.8232 (t70)
  outliers start: 9
  outliers final: 3
  residues processed: 51
  average time/residue: 1.1562
  time to fit residues: 63.5238
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  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain C residue  138 LEU
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 10 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0980
   chunk 52 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 67 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.095313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.063870 restraints weight = 15435.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 2.92
r_work: 0.2788 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8025  Z= 0.111
  Angle     :  0.414   8.613  10891  Z= 0.219
  Chirality :  0.039   0.132   1299
  Planarity :  0.003   0.030   1363
  Dihedral  :  3.307  14.611   1030
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.29 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.28), residues: 964
  helix:  2.82 (0.21), residues: 619
  sheet:  1.33 (0.81), residues: 56
  loop : -0.79 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 207 
 HIS   0.001   0.000   HIS B 286 
 PHE   0.015   0.001   PHE C 368 
 TYR   0.011   0.001   TYR B 283 
 ARG   0.003   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  481)
  hydrogen bonds       : angle       3.29294 ( 1419)
  covalent geometry    : bond        0.00258 ( 8025)
  covalent geometry    : angle       0.41386 (10891)

*********************** 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
  49 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8597 (m-30) cc_final: 0.7784 (p0)
REVERT: C  322 ASP cc_start: 0.8492 (m-30) cc_final: 0.8077 (p0)
REVERT: D  134 LEU cc_start: 0.8695 (mt) cc_final: 0.8415 (tt)
REVERT: D  317 GLN cc_start: 0.7908 (tp40) cc_final: 0.7586 (mp10)
REVERT: B  316 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7775 (tpt90)
  outliers start: 5
  outliers final: 2
  residues processed: 47
  average time/residue: 1.2560
  time to fit residues: 63.4783
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  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  267 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 20 optimal weight:    0.5980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.095503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.062523 restraints weight = 16172.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 2.99
r_work: 0.2682 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
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      :  0.004   0.032   8025  Z= 0.161
  Angle     :  0.457   8.058  10891  Z= 0.244
  Chirality :  0.040   0.144   1299
  Planarity :  0.003   0.033   1363
  Dihedral  :  3.441  15.063   1030
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.28), residues: 964
  helix:  2.73 (0.21), residues: 618
  sheet:  1.24 (0.80), residues: 56
  loop : -0.85 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 207 
 HIS   0.002   0.001   HIS A 347 
 PHE   0.017   0.001   PHE D 368 
 TYR   0.013   0.001   TYR B 307 
 ARG   0.003   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05852 (  481)
  hydrogen bonds       : angle       3.50874 ( 1419)
  covalent geometry    : bond        0.00393 ( 8025)
  covalent geometry    : angle       0.45689 (10891)

*********************** 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
  48 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8652 (m-30) cc_final: 0.7862 (p0)
REVERT: C  322 ASP cc_start: 0.8593 (m-30) cc_final: 0.8179 (p0)
REVERT: D  134 LEU cc_start: 0.8714 (mt) cc_final: 0.8434 (tt)
REVERT: D  317 GLN cc_start: 0.8044 (tp40) cc_final: 0.7659 (mp10)
REVERT: B  316 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.8036 (mtp85)
REVERT: B  347 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.8309 (t70)
  outliers start: 5
  outliers final: 3
  residues processed: 47
  average time/residue: 1.1867
  time to fit residues: 59.9782
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  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  347 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 21 optimal weight:    0.2980
   chunk 90 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   chunk 64 optimal weight:    3.9990
   chunk 89 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
C 137 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 = 0.3483 r_free = 0.3483 target = 0.093627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.062037 restraints weight = 15445.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 2.93
r_work: 0.2747 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8025  Z= 0.144
  Angle     :  0.447   9.496  10891  Z= 0.236
  Chirality :  0.040   0.138   1299
  Planarity :  0.003   0.033   1363
  Dihedral  :  3.420  14.825   1030
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.28), residues: 964
  helix:  2.73 (0.21), residues: 617
  sheet:  1.25 (0.81), residues: 56
  loop : -0.84 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 207 
 HIS   0.002   0.000   HIS A 347 
 PHE   0.017   0.001   PHE D 368 
 TYR   0.022   0.001   TYR C 315 
 ARG   0.003   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05485 (  481)
  hydrogen bonds       : angle       3.45747 ( 1419)
  covalent geometry    : bond        0.00347 ( 8025)
  covalent geometry    : angle       0.44665 (10891)

********************** 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: 5
    poor density    : 43
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8621 (m-30) cc_final: 0.7883 (p0)
REVERT: C  322 ASP cc_start: 0.8520 (m-30) cc_final: 0.8179 (p0)
REVERT: D  134 LEU cc_start: 0.8762 (mt) cc_final: 0.8464 (tt)
REVERT: D  317 GLN cc_start: 0.8021 (tp40) cc_final: 0.7669 (mp10)
REVERT: B  316 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7865 (tpt90)
REVERT: B  347 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.8272 (t70)
  outliers start: 5
  outliers final: 3
  residues processed: 46
  average time/residue: 1.2858
  time to fit residues: 63.3793
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  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  347 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.094474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.062933 restraints weight = 15573.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.93
r_work: 0.2766 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8025  Z= 0.124
  Angle     :  0.439   9.596  10891  Z= 0.233
  Chirality :  0.039   0.181   1299
  Planarity :  0.003   0.032   1363
  Dihedral  :  3.373  14.709   1030
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  9.62 %
    Favored  : 89.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.28), residues: 964
  helix:  2.77 (0.21), residues: 618
  sheet:  1.30 (0.81), residues: 56
  loop : -0.80 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 207 
 HIS   0.001   0.000   HIS A 347 
 PHE   0.016   0.001   PHE C 368 
 TYR   0.012   0.001   TYR D 283 
 ARG   0.003   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05023 (  481)
  hydrogen bonds       : angle       3.39862 ( 1419)
  covalent geometry    : bond        0.00293 ( 8025)
  covalent geometry    : angle       0.43870 (10891)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4310.48 seconds
wall clock time: 75 minutes 28.05 seconds (4528.05 seconds total)