Starting phenix.real_space_refine
on Fri Oct 10 22:31:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j5d_35985/10_2025/8j5d_35985.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j5d_35985/10_2025/8j5d_35985.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j5d_35985/10_2025/8j5d_35985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j5d_35985/10_2025/8j5d_35985.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j5d_35985/10_2025/8j5d_35985.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j5d_35985/10_2025/8j5d_35985.cif"
  }
  resolution = 3.0
  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=   0.084
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      39      5.16       5
     C    6088      2.51       5
     N    1599      2.21       5
     O    1805      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9531
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3340
          Classifications: {'peptide': 422}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 398}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2356
          Classifications: {'peptide': 316}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 300}
    Chain: "D"
      Number of atoms: 1488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1488
          Classifications: {'peptide': 191}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 182}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2347
          Classifications: {'peptide': 315}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 299}
  Time building chain proxies: 2.43, per 1000 atoms: 0.25
  Number of scatterers: 9531
  At special positions: 0
  Unit cell: (70.62, 92.02, 146.59, 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      39     16.00
     O    1805      8.00
     N    1599      7.00
     C    6088      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: 0.92
  Conformation dependent library (CDL) restraints added in 395.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2288

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      47.0% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 125 through 139
    Processing helix  chain 'A' and resid 163 through 176
    Processing helix  chain 'A' and resid 202 through 212
    Processing helix  chain 'A' and resid 243 through 259
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 287 through 291
    Processing helix  chain 'A' and resid 304 through 318
      removed outlier: 4.452A  pdb=" N   SER A 310 " --> pdb=" O   TYR A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 341
      removed outlier: 3.530A  pdb=" N   THR A 341 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 352
    Processing helix  chain 'A' and resid 353 through 382
    Processing helix  chain 'A' and resid 405 through 411
    Processing helix  chain 'A' and resid 421 through 433
      removed outlier: 4.251A  pdb=" N   ILE A 425 " --> pdb=" O   GLY A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 471
    Processing helix  chain 'A' and resid 484 through 497
    Processing helix  chain 'A' and resid 519 through 523
    Processing helix  chain 'A' and resid 524 through 539
    Processing helix  chain 'B' and resid 94 through 104
    Processing helix  chain 'B' and resid 119 through 128
      removed outlier: 3.789A  pdb=" N   HIS B 128 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 148
      removed outlier: 3.634A  pdb=" N   ALA B 145 " --> pdb=" O   PRO B 141 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ASP B 146 " --> pdb=" O   SER B 142 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU B 148 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 190
      removed outlier: 4.165A  pdb=" N   GLU B 188 " --> pdb=" O   GLU B 184 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASN B 189 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 215
      Proline residue:  B 207  - end of helix
    Processing helix  chain 'B' and resid 220 through 222
      No H-bonds generated for 'chain 'B' and resid 220 through 222'
    Processing helix  chain 'B' and resid 228 through 244
      removed outlier: 3.663A  pdb=" N   VAL B 232 " --> pdb=" O   THR B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 270
    Processing helix  chain 'B' and resid 277 through 282
    Processing helix  chain 'B' and resid 283 through 299
      removed outlier: 5.363A  pdb=" N   GLY B 292 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   THR B 293 " --> pdb=" O   GLN B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 325
    Processing helix  chain 'B' and resid 362 through 366
    Processing helix  chain 'B' and resid 369 through 396
      removed outlier: 4.590A  pdb=" N   VAL B 381 " --> pdb=" O   GLU B 377 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   GLU B 382 " --> pdb=" O   ALA B 378 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 111
    Processing helix  chain 'D' and resid 136 through 146
      removed outlier: 3.773A  pdb=" N   THR D 140 " --> pdb=" O   ASP D 136 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LYS D 142 " --> pdb=" O   GLY D 138 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   MET D 143 " --> pdb=" O   ASP D 139 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU D 146 " --> pdb=" O   LYS D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 163 through 170
      removed outlier: 4.080A  pdb=" N   LEU D 167 " --> pdb=" O   PRO D 163 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 212 through 216
      removed outlier: 3.642A  pdb=" N   PHE D 215 " --> pdb=" O   SER D 212 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   PHE D 216 " --> pdb=" O   SER D 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 212 through 216'
    Processing helix  chain 'D' and resid 217 through 225
    Processing helix  chain 'D' and resid 267 through 280
    Processing helix  chain 'C' and resid 94 through 104
    Processing helix  chain 'C' and resid 118 through 127
    Processing helix  chain 'C' and resid 140 through 148
      removed outlier: 4.029A  pdb=" N   ASP C 146 " --> pdb=" O   SER C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 190
    Processing helix  chain 'C' and resid 201 through 217
      Proline residue:  C 207  - end of helix
    Processing helix  chain 'C' and resid 220 through 224
      removed outlier: 3.883A  pdb=" N   LEU C 224 " --> pdb=" O   PRO C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 243
      removed outlier: 3.636A  pdb=" N   VAL C 232 " --> pdb=" O   THR C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 270
    Processing helix  chain 'C' and resid 277 through 289
    Processing helix  chain 'C' and resid 291 through 299
    Processing helix  chain 'C' and resid 306 through 325
    Processing helix  chain 'C' and resid 362 through 366
    Processing helix  chain 'C' and resid 369 through 395
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111
      removed outlier: 6.273A  pdb=" N   VAL A 108 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   MET A 145 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL A 110 " --> pdb=" O   MET A 145 " (cutoff:3.500A)
      removed outlier: 8.553A  pdb=" N   ASP A 147 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ILE A 144 " --> pdb=" O   GLN A 181 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   VAL A 183 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ILE A 146 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   SER A 185 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 185 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   VAL A 180 " --> pdb=" O   ILE A 267 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLU A 269 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL A 268 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   SER A 390 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ILE A 270 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   LYS A 392 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   VAL A 272 " --> pdb=" O   LYS A 392 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   ALA A 475 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   PHE A 436 " --> pdb=" O   ALA A 475 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   GLU A 477 " --> pdb=" O   PHE A 436 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   PHE A 438 " --> pdb=" O   GLU A 477 " (cutoff:3.500A)
      removed outlier: 9.100A  pdb=" N   THR A 514 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   GLY A 476 " --> pdb=" O   THR A 514 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 218
      removed outlier: 3.737A  pdb=" N   TYR A 217 " --> pdb=" O   ASN A 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138
      removed outlier: 6.543A  pdb=" N   SER B 109 " --> pdb=" O   GLN B 134 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   ARG B 136 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU B 111 " --> pdb=" O   ARG B 136 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   PHE B 138 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   LEU B 113 " --> pdb=" O   PHE B 138 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   TYR B  83 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR B 110 " --> pdb=" O   TYR B  83 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL B 154 " --> pdb=" O   HIS B 196 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ILE B 195 " --> pdb=" O   PHE B 225 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL B 227 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ILE B 197 " --> pdb=" O   VAL B 227 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   ARG B 349 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      removed outlier: 5.728A  pdb=" N   VAL B 360 " --> pdb=" O   ARG B 349 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   LYS B 351 " --> pdb=" O   GLU B 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 254 through 256
    Processing sheet with id=AA5, first strand: chain 'D' and resid 76 through 82
      removed outlier: 6.395A  pdb=" N   SER D 152 " --> pdb=" O   ALA D 123 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ALA D 123 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL D 154 " --> pdb=" O   LYS D 121 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 247 through 251
      removed outlier: 6.582A  pdb=" N   ARG D  88 " --> pdb=" O   HIS D 100 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 186
    Processing sheet with id=AA8, first strand: chain 'C' and resid 134 through 139
      removed outlier: 6.455A  pdb=" N   SER C 109 " --> pdb=" O   GLN C 134 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   ARG C 136 " --> pdb=" O   SER C 109 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LEU C 111 " --> pdb=" O   ARG C 136 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   PHE C 138 " --> pdb=" O   LEU C 111 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   LEU C 113 " --> pdb=" O   PHE C 138 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR C  83 " --> pdb=" O   SER C 109 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   LEU C 111 " --> pdb=" O   TYR C  83 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL C  85 " --> pdb=" O   LEU C 111 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   LEU C 113 " --> pdb=" O   VAL C  85 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL C  87 " --> pdb=" O   LEU C 113 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   ASP C 115 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   ILE C 195 " --> pdb=" O   PHE C 225 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   VAL C 227 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ILE C 197 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   ARG C 349 " --> pdb=" O   VAL C 360 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   VAL C 360 " --> pdb=" O   ARG C 349 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   LYS C 351 " --> pdb=" O   GLU C 358 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 254 through 256

    451 hydrogen bonds defined for protein.
    1281 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: 1.69

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 3109
        1.35 -     1.47: 2180
        1.47 -     1.59: 4374
        1.59 -     1.71: 0
        1.71 -     1.83: 64
  Bond restraints: 9727
  Sorted by residual:
  bond pdb=" C   MET A 111 "
       pdb=" N   MET A 112 "
    ideal  model  delta    sigma   weight residual
    1.328  1.360 -0.032 1.44e-02 4.82e+03 4.79e+00
  bond pdb=" CG  PRO B 207 "
       pdb=" CD  PRO B 207 "
    ideal  model  delta    sigma   weight residual
    1.503  1.447  0.056 3.40e-02 8.65e+02 2.73e+00
  bond pdb=" C   MET A 112 "
       pdb=" N   PRO A 113 "
    ideal  model  delta    sigma   weight residual
    1.331  1.350 -0.019 1.21e-02 6.83e+03 2.36e+00
  bond pdb=" C   CYS A 189 "
       pdb=" N   GLY A 190 "
    ideal  model  delta    sigma   weight residual
    1.335  1.324  0.011 7.50e-03 1.78e+04 2.07e+00
  bond pdb=" CB  ASP B 342 "
       pdb=" CG  ASP B 342 "
    ideal  model  delta    sigma   weight residual
    1.516  1.552 -0.036 2.50e-02 1.60e+03 2.04e+00
  ... (remaining 9722 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.00: 13084
        3.00 -     6.00: 93
        6.00 -     9.01: 7
        9.01 -    12.01: 3
       12.01 -    15.01: 4
  Bond angle restraints: 13191
  Sorted by residual:
  angle pdb=" N   PRO B 207 "
        pdb=" CD  PRO B 207 "
        pdb=" CG  PRO B 207 "
      ideal   model   delta    sigma   weight residual
     103.20   95.04    8.16 1.50e+00 4.44e-01 2.96e+01
  angle pdb=" C   SER A 196 "
        pdb=" CA  SER A 196 "
        pdb=" CB  SER A 196 "
      ideal   model   delta    sigma   weight residual
     116.54  110.70    5.84 1.15e+00 7.56e-01 2.58e+01
  angle pdb=" CA  PRO B 207 "
        pdb=" N   PRO B 207 "
        pdb=" CD  PRO B 207 "
      ideal   model   delta    sigma   weight residual
     112.00  104.99    7.01 1.40e+00 5.10e-01 2.51e+01
  angle pdb=" CB  MET A 112 "
        pdb=" CG  MET A 112 "
        pdb=" SD  MET A 112 "
      ideal   model   delta    sigma   weight residual
     112.70  127.71  -15.01 3.00e+00 1.11e-01 2.50e+01
  angle pdb=" CB  PRO B 207 "
        pdb=" CG  PRO B 207 "
        pdb=" CD  PRO B 207 "
      ideal   model   delta    sigma   weight residual
     106.10   92.52   13.58 3.20e+00 9.77e-02 1.80e+01
  ... (remaining 13186 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 5185
       17.19 -    34.38: 454
       34.38 -    51.57: 140
       51.57 -    68.76: 43
       68.76 -    85.96: 12
  Dihedral angle restraints: 5834
    sinusoidal: 2270
      harmonic: 3564
  Sorted by residual:
  dihedral pdb=" CA  ALA D 198 "
           pdb=" C   ALA D 198 "
           pdb=" N   SER D 199 "
           pdb=" CA  SER D 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  ARG D 179 "
           pdb=" C   ARG D 179 "
           pdb=" N   GLY D 180 "
           pdb=" CA  GLY D 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.48   16.52     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  SER D 194 "
           pdb=" C   SER D 194 "
           pdb=" N   ASN D 195 "
           pdb=" CA  ASN D 195 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.49   16.51     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 5831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1052
       0.039 -    0.077: 308
       0.077 -    0.116: 122
       0.116 -    0.154: 15
       0.154 -    0.193: 4
  Chirality restraints: 1501
  Sorted by residual:
  chirality pdb=" CB  VAL B 286 "
            pdb=" CA  VAL B 286 "
            pdb=" CG1 VAL B 286 "
            pdb=" CG2 VAL B 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.27e-01
  chirality pdb=" CB  THR B 285 "
            pdb=" CA  THR B 285 "
            pdb=" OG1 THR B 285 "
            pdb=" CG2 THR B 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.56e-01
  chirality pdb=" CB  VAL B 391 "
            pdb=" CA  VAL B 391 "
            pdb=" CG1 VAL B 391 "
            pdb=" CG2 VAL B 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.16 2.00e-01 2.50e+01 6.77e-01
  ... (remaining 1498 not shown)

  Planarity restraints: 1699
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 283 "   -0.020 2.00e-02 2.50e+03   4.01e-02 1.61e+01
        pdb=" C   GLU B 283 "    0.069 2.00e-02 2.50e+03
        pdb=" O   GLU B 283 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   LEU B 284 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 266 "   -0.043 5.00e-02 4.00e+02   6.60e-02 6.96e+00
        pdb=" N   PRO D 267 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO D 267 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO D 267 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 200 "    0.034 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO C 201 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C 201 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 201 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1696 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 254
        2.69 -     3.25: 9598
        3.25 -     3.80: 15723
        3.80 -     4.35: 21185
        4.35 -     4.90: 34873
  Nonbonded interactions: 81633
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 177 "
            pdb=" OD1 ASN D 225 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OE1 GLN A 220 "
            pdb=" OH  TYR A 303 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" OH  TYR A 400 "
            pdb=" OE1 GLN A 462 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OH  TYR D  77 "
            pdb=" OD2 ASP D 118 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OE1 GLU A 372 "
            pdb=" NE2 HIS A 432 "
     model   vdw
     2.168 3.120
  ... (remaining 81628 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 'B' and resid 81 through 395)
  selection = chain 'C'
}

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:             0.850
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.630
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
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   0.058   9727  Z= 0.151
  Angle     :  0.709  15.012  13191  Z= 0.365
  Chirality :  0.043   0.193   1501
  Planarity :  0.005   0.066   1699
  Dihedral  : 15.673  85.956   3546
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.51 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.24), residues: 1232
  helix:  1.35 (0.22), residues: 513
  sheet: -0.08 (0.45), residues: 142
  loop : -1.12 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 126 
 TYR   0.033   0.002   TYR B 219 
 PHE   0.010   0.001   PHE A 359 
 TRP   0.012   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9727)
  covalent geometry    : angle       0.70863 (13191)
  hydrogen bonds       : bond        0.05900 (  451)
  hydrogen bonds       : angle       5.22108 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  143 MET cc_start: 0.7255 (ttt) cc_final: 0.6810 (ttp)
  outliers start: 25
  outliers final: 16
  residues processed: 142
  average time/residue: 0.4855
  time to fit residues: 75.0654
Evaluate side-chains
  133 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain B residue  258 HIS
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  190 ASN
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  133 SER
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue  285 THR
Chi-restraints excluded: chain C residue  306 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.3980
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
A 427 GLN
B 241 GLN
D 205 ASN
C 128 HIS
C 196 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.182976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.144354 restraints weight = 11210.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 2.57
r_work: 0.3721 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.0680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   9727  Z= 0.129
  Angle     :  0.581  10.722  13191  Z= 0.291
  Chirality :  0.042   0.146   1501
  Planarity :  0.004   0.068   1699
  Dihedral  :  5.399  54.284   1340
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 18.08 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.24), residues: 1232
  helix:  1.54 (0.23), residues: 510
  sheet: -0.27 (0.44), residues: 144
  loop : -1.07 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 126 
 TYR   0.018   0.001   TYR A 363 
 PHE   0.019   0.001   PHE D 137 
 TRP   0.010   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9727)
  covalent geometry    : angle       0.58117 (13191)
  hydrogen bonds       : bond        0.03679 (  451)
  hydrogen bonds       : angle       4.84171 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 120
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.4780 (ppp) cc_final: 0.4538 (ppp)
REVERT: B  337 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5388 (pt0)
REVERT: B  372 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7130 (mt-10)
REVERT: D  143 MET cc_start: 0.7359 (ttt) cc_final: 0.6862 (ttp)
REVERT: C  137 ASP cc_start: 0.6913 (p0) cc_final: 0.6696 (p0)
  outliers start: 39
  outliers final: 10
  residues processed: 150
  average time/residue: 0.4877
  time to fit residues: 79.6457
Evaluate side-chains
  122 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  348 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0170
   chunk 10 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
A 271 GLN
A 427 GLN
C 173 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.182836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.144471 restraints weight = 11211.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 2.55
r_work: 0.3719 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.0881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   9727  Z= 0.126
  Angle     :  0.577  10.797  13191  Z= 0.288
  Chirality :  0.042   0.138   1501
  Planarity :  0.004   0.067   1699
  Dihedral  :  4.784  45.096   1324
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 18.85 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.24), residues: 1232
  helix:  1.57 (0.23), residues: 511
  sheet: -0.35 (0.44), residues: 143
  loop : -1.06 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 126 
 TYR   0.019   0.001   TYR A 363 
 PHE   0.012   0.001   PHE C 335 
 TRP   0.009   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9727)
  covalent geometry    : angle       0.57727 (13191)
  hydrogen bonds       : bond        0.03581 (  451)
  hydrogen bonds       : angle       4.81484 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 131
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.4735 (OUTLIER) cc_final: 0.4485 (ppp)
REVERT: A  220 GLN cc_start: 0.7182 (tp40) cc_final: 0.6522 (tp40)
REVERT: A  304 ASP cc_start: 0.5559 (OUTLIER) cc_final: 0.4413 (m-30)
REVERT: B  216 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8240 (mmmt)
REVERT: B  337 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5347 (pt0)
REVERT: B  372 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7068 (mt-10)
REVERT: D  143 MET cc_start: 0.7355 (ttt) cc_final: 0.6882 (ttp)
REVERT: C  137 ASP cc_start: 0.6887 (p0) cc_final: 0.6578 (p0)
  outliers start: 44
  outliers final: 13
  residues processed: 163
  average time/residue: 0.4498
  time to fit residues: 79.9176
Evaluate side-chains
  130 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  258 HIS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  348 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 88 optimal weight:    0.0170
   chunk 18 optimal weight:    0.1980
   chunk 85 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 119 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    1.0022

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

Flipped N/Q/H residues before XYZ refinement:
A 352 ASN
A 397 HIS
A 427 GLN
** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.179357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.141515 restraints weight = 11430.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.52
r_work: 0.3660 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.1084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086   9727  Z= 0.144
  Angle     :  0.603  12.869  13191  Z= 0.298
  Chirality :  0.043   0.157   1501
  Planarity :  0.005   0.067   1699
  Dihedral  :  4.582  37.400   1322
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 19.73 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.24), residues: 1232
  helix:  1.51 (0.23), residues: 512
  sheet: -0.46 (0.43), residues: 144
  loop : -1.10 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 126 
 TYR   0.021   0.002   TYR A 363 
 PHE   0.021   0.001   PHE D 137 
 TRP   0.008   0.001   TRP A 398 
 HIS   0.004   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9727)
  covalent geometry    : angle       0.60255 (13191)
  hydrogen bonds       : bond        0.03640 (  451)
  hydrogen bonds       : angle       4.86051 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 124
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.4845 (ppp) cc_final: 0.4582 (ppp)
REVERT: A  220 GLN cc_start: 0.7262 (tp40) cc_final: 0.6675 (tt0)
REVERT: A  304 ASP cc_start: 0.5486 (OUTLIER) cc_final: 0.4653 (m-30)
REVERT: B  337 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5276 (pt0)
REVERT: B  372 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7083 (mt-10)
REVERT: C  114 TYR cc_start: 0.7657 (t80) cc_final: 0.7415 (t80)
REVERT: C  137 ASP cc_start: 0.6701 (p0) cc_final: 0.6339 (p0)
REVERT: C  263 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7520 (mm)
  outliers start: 38
  outliers final: 16
  residues processed: 151
  average time/residue: 0.5096
  time to fit residues: 83.2856
Evaluate side-chains
  137 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  538 MET
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  339 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 21 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 93 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0970
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 352 ASN
A 427 GLN
** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.175537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.138081 restraints weight = 11502.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.49
r_work: 0.3612 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.124   9727  Z= 0.204
  Angle     :  0.666  11.923  13191  Z= 0.334
  Chirality :  0.045   0.186   1501
  Planarity :  0.005   0.069   1699
  Dihedral  :  4.813  37.991   1321
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 19.53 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.24), residues: 1232
  helix:  1.16 (0.22), residues: 513
  sheet: -0.66 (0.42), residues: 144
  loop : -1.18 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 126 
 TYR   0.025   0.002   TYR A 363 
 PHE   0.020   0.002   PHE C 335 
 TRP   0.010   0.002   TRP A 398 
 HIS   0.005   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 9727)
  covalent geometry    : angle       0.66586 (13191)
  hydrogen bonds       : bond        0.04010 (  451)
  hydrogen bonds       : angle       5.11180 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 121
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8085 (mmm)
REVERT: A  220 GLN cc_start: 0.7190 (tp40) cc_final: 0.6696 (tt0)
REVERT: A  285 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.5197 (m-80)
REVERT: B  337 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5256 (pt0)
REVERT: B  372 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7136 (mt-10)
REVERT: C  114 TYR cc_start: 0.7870 (t80) cc_final: 0.7570 (t80)
REVERT: C  137 ASP cc_start: 0.6735 (p0) cc_final: 0.6381 (p0)
REVERT: C  263 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7703 (mm)
REVERT: C  362 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6297 (pm20)
  outliers start: 50
  outliers final: 20
  residues processed: 158
  average time/residue: 0.4813
  time to fit residues: 82.5750
Evaluate side-chains
  142 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  285 TYR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  538 MET
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  133 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  258 HIS
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  348 SER
Chi-restraints excluded: chain C residue  362 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9990
   chunk 120 optimal weight:    0.4980
   chunk 39 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 121 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 352 ASN
A 427 GLN
C 134 GLN
** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.178966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.141343 restraints weight = 11288.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 2.49
r_work: 0.3653 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   9727  Z= 0.131
  Angle     :  0.624  12.522  13191  Z= 0.311
  Chirality :  0.043   0.190   1501
  Planarity :  0.005   0.068   1699
  Dihedral  :  4.568  37.924   1321
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 20.12 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.24), residues: 1232
  helix:  1.44 (0.23), residues: 515
  sheet: -0.53 (0.44), residues: 143
  loop : -1.16 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 126 
 TYR   0.020   0.001   TYR B 371 
 PHE   0.012   0.001   PHE C 335 
 TRP   0.010   0.001   TRP A 398 
 HIS   0.004   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9727)
  covalent geometry    : angle       0.62377 (13191)
  hydrogen bonds       : bond        0.03625 (  451)
  hydrogen bonds       : angle       4.91529 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 127
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.4652 (ppp) cc_final: 0.4431 (ppp)
REVERT: A  129 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.8040 (mmm)
REVERT: A  220 GLN cc_start: 0.7203 (tp40) cc_final: 0.6606 (tt0)
REVERT: A  227 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7592 (mm-30)
REVERT: A  285 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.5388 (m-80)
REVERT: A  304 ASP cc_start: 0.5768 (OUTLIER) cc_final: 0.4489 (m-30)
REVERT: B  216 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8199 (mmmt)
REVERT: B  337 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5282 (pt0)
REVERT: B  372 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7024 (mt-10)
REVERT: D  143 MET cc_start: 0.7331 (ttt) cc_final: 0.6828 (ttp)
REVERT: C  137 ASP cc_start: 0.6693 (p0) cc_final: 0.6324 (p0)
REVERT: C  263 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7600 (mm)
  outliers start: 42
  outliers final: 15
  residues processed: 155
  average time/residue: 0.4953
  time to fit residues: 83.4578
Evaluate side-chains
  141 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  285 TYR
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  133 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  339 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 15 optimal weight:    0.0370
   chunk 114 optimal weight:    8.9990
   chunk 69 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 105 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
A 352 ASN
A 427 GLN
C 196 HIS
C 236 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.180276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.142380 restraints weight = 11286.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 2.52
r_work: 0.3668 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9727  Z= 0.126
  Angle     :  0.629  12.866  13191  Z= 0.312
  Chirality :  0.043   0.186   1501
  Planarity :  0.005   0.068   1699
  Dihedral  :  4.491  37.869   1321
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.38 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.24), residues: 1232
  helix:  1.51 (0.23), residues: 515
  sheet: -0.46 (0.45), residues: 143
  loop : -1.13 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 126 
 TYR   0.020   0.001   TYR C 114 
 PHE   0.011   0.001   PHE C 335 
 TRP   0.009   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9727)
  covalent geometry    : angle       0.62860 (13191)
  hydrogen bonds       : bond        0.03548 (  451)
  hydrogen bonds       : angle       4.85522 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 121
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.4684 (ppp) cc_final: 0.4439 (ppp)
REVERT: A  129 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7925 (mmm)
REVERT: A  184 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7111 (tpp)
REVERT: A  220 GLN cc_start: 0.7154 (tp40) cc_final: 0.6616 (tt0)
REVERT: A  227 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7565 (mm-30)
REVERT: A  285 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.5391 (m-80)
REVERT: A  304 ASP cc_start: 0.5599 (OUTLIER) cc_final: 0.4340 (m-30)
REVERT: B  216 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8186 (mmmt)
REVERT: B  337 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5278 (pt0)
REVERT: B  372 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6926 (mt-10)
REVERT: D  143 MET cc_start: 0.7347 (ttt) cc_final: 0.6837 (ttp)
REVERT: C  137 ASP cc_start: 0.6685 (p0) cc_final: 0.6309 (p0)
REVERT: C  263 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7514 (mm)
  outliers start: 35
  outliers final: 15
  residues processed: 144
  average time/residue: 0.5062
  time to fit residues: 79.1997
Evaluate side-chains
  135 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  285 TYR
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  538 MET
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  133 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  263 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 122 optimal weight:    7.9990
   chunk 109 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0070
   chunk 8 optimal weight:    0.2980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 GLN
** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.183114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.145094 restraints weight = 11198.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 2.56
r_work: 0.3731 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9727  Z= 0.122
  Angle     :  0.627  12.909  13191  Z= 0.313
  Chirality :  0.043   0.178   1501
  Planarity :  0.004   0.067   1699
  Dihedral  :  4.375  38.021   1320
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 22.25 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.24), residues: 1232
  helix:  1.54 (0.23), residues: 516
  sheet: -0.42 (0.45), residues: 143
  loop : -1.08 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 125 
 TYR   0.022   0.001   TYR B 371 
 PHE   0.010   0.001   PHE C 335 
 TRP   0.009   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9727)
  covalent geometry    : angle       0.62737 (13191)
  hydrogen bonds       : bond        0.03511 (  451)
  hydrogen bonds       : angle       4.82148 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.8022 (mmm)
REVERT: A  184 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7145 (tpp)
REVERT: A  220 GLN cc_start: 0.7151 (tp40) cc_final: 0.6586 (tt0)
REVERT: A  227 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7590 (mm-30)
REVERT: A  285 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.5332 (m-80)
REVERT: B  372 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6883 (mt-10)
REVERT: D  143 MET cc_start: 0.7273 (ttt) cc_final: 0.6755 (ttp)
REVERT: C  137 ASP cc_start: 0.6775 (p0) cc_final: 0.6408 (p0)
REVERT: C  263 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7484 (mm)
  outliers start: 32
  outliers final: 15
  residues processed: 145
  average time/residue: 0.4737
  time to fit residues: 74.8634
Evaluate side-chains
  134 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  285 TYR
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  538 MET
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  133 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  263 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 113 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 90 optimal weight:    0.8980
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 GLN
A 437 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.179068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.140735 restraints weight = 11330.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.57
r_work: 0.3670 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109   9727  Z= 0.185
  Angle     :  0.701  15.184  13191  Z= 0.349
  Chirality :  0.045   0.156   1501
  Planarity :  0.005   0.066   1699
  Dihedral  :  4.601  37.978   1319
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 22.74 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.24), residues: 1232
  helix:  1.20 (0.22), residues: 513
  sheet: -0.57 (0.44), residues: 143
  loop : -1.17 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 234 
 TYR   0.027   0.002   TYR C 114 
 PHE   0.026   0.002   PHE B 316 
 TRP   0.007   0.001   TRP A 362 
 HIS   0.004   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 9727)
  covalent geometry    : angle       0.70086 (13191)
  hydrogen bonds       : bond        0.03868 (  451)
  hydrogen bonds       : angle       5.13264 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.4569 (ppp) cc_final: 0.3907 (ppp)
REVERT: A  184 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7213 (tpp)
REVERT: A  220 GLN cc_start: 0.7196 (tp40) cc_final: 0.6667 (tt0)
REVERT: A  227 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7589 (mm-30)
REVERT: A  285 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.5359 (m-80)
REVERT: A  304 ASP cc_start: 0.5935 (OUTLIER) cc_final: 0.5050 (m-30)
REVERT: B  309 MET cc_start: 0.7465 (tpp) cc_final: 0.7258 (tpp)
REVERT: B  337 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5447 (pt0)
REVERT: B  372 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7056 (mt-10)
REVERT: C  137 ASP cc_start: 0.6808 (p0) cc_final: 0.6446 (p0)
REVERT: C  263 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7715 (mm)
REVERT: C  362 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6428 (pm20)
  outliers start: 32
  outliers final: 15
  residues processed: 145
  average time/residue: 0.4874
  time to fit residues: 77.1395
Evaluate side-chains
  139 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  285 TYR
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  538 MET
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  133 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  362 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 117 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 GLN
B 189 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.177686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.139942 restraints weight = 11340.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.49
r_work: 0.3637 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.101   9727  Z= 0.173
  Angle     :  0.706  15.912  13191  Z= 0.352
  Chirality :  0.045   0.186   1501
  Planarity :  0.005   0.066   1699
  Dihedral  :  4.619  38.064   1319
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 23.81 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.24), residues: 1232
  helix:  1.11 (0.22), residues: 513
  sheet: -0.59 (0.44), residues: 143
  loop : -1.19 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 125 
 TYR   0.027   0.002   TYR C 114 
 PHE   0.022   0.002   PHE B 316 
 TRP   0.023   0.002   TRP A 163 
 HIS   0.004   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 9727)
  covalent geometry    : angle       0.70599 (13191)
  hydrogen bonds       : bond        0.03820 (  451)
  hydrogen bonds       : angle       5.12773 ( 1281)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.4512 (ppp) cc_final: 0.3857 (ppp)
REVERT: A  184 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7163 (tpp)
REVERT: A  220 GLN cc_start: 0.7160 (tp40) cc_final: 0.6617 (tt0)
REVERT: A  285 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.5323 (m-80)
REVERT: A  304 ASP cc_start: 0.5888 (OUTLIER) cc_final: 0.4976 (m-30)
REVERT: B  337 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5254 (pt0)
REVERT: B  372 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7052 (mt-10)
REVERT: D  143 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7196 (ttt)
REVERT: C  137 ASP cc_start: 0.6638 (p0) cc_final: 0.6257 (p0)
REVERT: C  263 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7724 (mm)
  outliers start: 26
  outliers final: 15
  residues processed: 138
  average time/residue: 0.5090
  time to fit residues: 76.2837
Evaluate side-chains
  139 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  285 TYR
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  538 MET
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  133 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  143 MET
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  263 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 94 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.180237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.142029 restraints weight = 11252.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3840 rms_B_bonded: 2.56
r_work: 0.3689 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   9727  Z= 0.154
  Angle     :  0.689  15.493  13191  Z= 0.342
  Chirality :  0.044   0.188   1501
  Planarity :  0.005   0.067   1699
  Dihedral  :  4.569  38.032   1319
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 24.39 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.24), residues: 1232
  helix:  1.15 (0.23), residues: 512
  sheet: -0.59 (0.44), residues: 143
  loop : -1.17 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 125 
 TYR   0.026   0.002   TYR C 114 
 PHE   0.019   0.002   PHE B 316 
 TRP   0.020   0.001   TRP A 163 
 HIS   0.004   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9727)
  covalent geometry    : angle       0.68884 (13191)
  hydrogen bonds       : bond        0.03735 (  451)
  hydrogen bonds       : angle       5.08661 ( 1281)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3024.48 seconds
wall clock time: 52 minutes 35.79 seconds (3155.79 seconds total)