Starting phenix.real_space_refine
on Tue Mar 11 18:29:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rsb_24668/03_2025/7rsb_24668.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rsb_24668/03_2025/7rsb_24668.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rsb_24668/03_2025/7rsb_24668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rsb_24668/03_2025/7rsb_24668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rsb_24668/03_2025/7rsb_24668.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rsb_24668/03_2025/7rsb_24668.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.033
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      40      5.16       5
     C    4362      2.51       5
     N    1104      2.21       5
     O    1124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6630
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3315
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 3315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3315
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 4.56, per 1000 atoms: 0.69
  Number of scatterers: 6630
  At special positions: 0
  Unit cell: (72.312, 96.416, 114.232, 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      40     16.00
     O    1124      8.00
     N    1104      7.00
     C    4362      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.70
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      76.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 29
      removed outlier: 4.405A  pdb=" N   GLU A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ARG A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ASP A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 46
      removed outlier: 3.637A  pdb=" N   LEU A  33 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 59
    Processing helix  chain 'A' and resid 61 through 71
      removed outlier: 3.984A  pdb=" N   THR A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 85
      removed outlier: 3.686A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 99
      removed outlier: 3.554A  pdb=" N   PHE A  95 " --> pdb=" O   MET A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 123 through 140
      Proline residue:  A 129  - end of helix
      removed outlier: 3.600A  pdb=" N   PHE A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   PHE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 167
      removed outlier: 4.453A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 191
      removed outlier: 3.724A  pdb=" N   HIS A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 179 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 198
      removed outlier: 4.090A  pdb=" N   ILE A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 224
      removed outlier: 3.637A  pdb=" N   ILE A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LYS A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 231
    Processing helix  chain 'A' and resid 251 through 266
      removed outlier: 3.844A  pdb=" N   TYR A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 285
      removed outlier: 3.816A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
      removed outlier: 3.589A  pdb=" N   ALA A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLY A 306 " --> pdb=" O   CYS A 302 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 325
    Processing helix  chain 'A' and resid 329 through 349
      removed outlier: 3.678A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 379
      removed outlier: 3.523A  pdb=" N   MET A 360 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   PHE A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 395
      removed outlier: 3.958A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
      removed outlier: 3.709A  pdb=" N   ILE A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LEU A 413 " --> pdb=" O   ILE A 409 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   MET A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 439
      removed outlier: 3.619A  pdb=" N   ILE A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 460
      removed outlier: 3.674A  pdb=" N   GLN A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 29
      removed outlier: 3.686A  pdb=" N   GLU B  27 " --> pdb=" O   ARG B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 59
      removed outlier: 3.897A  pdb=" N   ALA B  34 " --> pdb=" O   LYS B  30 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ILE B  35 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU B  36 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL B  41 " --> pdb=" O   PHE B  37 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   GLY B  47 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   ALA B  50 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL B  51 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 66
    Processing helix  chain 'B' and resid 74 through 99
      removed outlier: 3.566A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   LEU B  89 " --> pdb=" O   CYS B  85 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 114
    Processing helix  chain 'B' and resid 123 through 140
      Proline residue:  B 129  - end of helix
      removed outlier: 3.660A  pdb=" N   PHE B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 166
      removed outlier: 3.987A  pdb=" N   THR B 151 " --> pdb=" O   ARG B 147 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLN B 153 " --> pdb=" O   GLY B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 187
      removed outlier: 4.085A  pdb=" N   ALA B 179 " --> pdb=" O   HIS B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 3.763A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 208
      removed outlier: 3.879A  pdb=" N   GLN B 207 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 233
      removed outlier: 3.721A  pdb=" N   ALA B 217 " --> pdb=" O   ILE B 213 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ILE B 227 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 269
      Proline residue:  B 267  - end of helix
    Processing helix  chain 'B' and resid 270 through 283
      removed outlier: 3.698A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   HIS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 309
      removed outlier: 4.270A  pdb=" N   MET B 294 " --> pdb=" O   LYS B 290 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY B 306 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   VAL B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 324
    Processing helix  chain 'B' and resid 329 through 349
      removed outlier: 4.017A  pdb=" N   ILE B 342 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR B 343 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 379
      removed outlier: 3.562A  pdb=" N   ALA B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 401
      removed outlier: 4.120A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ALA B 396 " --> pdb=" O   ALA B 392 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU B 397 " --> pdb=" O   GLY B 393 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU B 398 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   ALA B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER B 401 " --> pdb=" O   LEU B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 417
      removed outlier: 3.638A  pdb=" N   ILE B 410 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL B 412 " --> pdb=" O   GLY B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 439
      removed outlier: 3.642A  pdb=" N   MET B 425 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE B 427 " --> pdb=" O   LEU B 423 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA B 432 " --> pdb=" O   THR B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 460
      removed outlier: 3.580A  pdb=" N   GLN B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1197 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: 1.99

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2067
        1.34 -     1.46: 1160
        1.46 -     1.57: 3473
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6774
  Sorted by residual:
  bond pdb=" CB  ASN B 270 "
       pdb=" CG  ASN B 270 "
    ideal  model  delta    sigma   weight residual
    1.516  1.570 -0.054 2.50e-02 1.60e+03 4.59e+00
  bond pdb=" CA  ASN B 270 "
       pdb=" CB  ASN B 270 "
    ideal  model  delta    sigma   weight residual
    1.530  1.566 -0.036 1.69e-02 3.50e+03 4.57e+00
  bond pdb=" CA  ASN A 270 "
       pdb=" CB  ASN A 270 "
    ideal  model  delta    sigma   weight residual
    1.530  1.566 -0.036 1.69e-02 3.50e+03 4.57e+00
  bond pdb=" C   THR B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.377 -0.043 2.34e-02 1.83e+03 3.44e+00
  bond pdb=" CB  ASN A 270 "
       pdb=" CG  ASN A 270 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.38e+00
  ... (remaining 6769 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 9026
        3.20 -     6.41: 138
        6.41 -     9.61: 30
        9.61 -    12.81: 3
       12.81 -    16.02: 3
  Bond angle restraints: 9200
  Sorted by residual:
  angle pdb=" C   PHE B 269 "
        pdb=" N   ASN B 270 "
        pdb=" CA  ASN B 270 "
      ideal   model   delta    sigma   weight residual
     121.54  131.23   -9.69 1.91e+00 2.74e-01 2.57e+01
  angle pdb=" CA  ASN A 270 "
        pdb=" CB  ASN A 270 "
        pdb=" CG  ASN A 270 "
      ideal   model   delta    sigma   weight residual
     112.60  117.45   -4.85 1.00e+00 1.00e+00 2.35e+01
  angle pdb=" C   ASN B 318 "
        pdb=" N   LEU B 319 "
        pdb=" CA  LEU B 319 "
      ideal   model   delta    sigma   weight residual
     121.54  130.52   -8.98 1.91e+00 2.74e-01 2.21e+01
  angle pdb=" CA  ASN B 270 "
        pdb=" CB  ASN B 270 "
        pdb=" CG  ASN B 270 "
      ideal   model   delta    sigma   weight residual
     112.60  117.21   -4.61 1.00e+00 1.00e+00 2.13e+01
  angle pdb=" CA  LEU A  60 "
        pdb=" CB  LEU A  60 "
        pdb=" CG  LEU A  60 "
      ideal   model   delta    sigma   weight residual
     116.30  132.32  -16.02 3.50e+00 8.16e-02 2.09e+01
  ... (remaining 9195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3471
       17.95 -    35.90: 370
       35.90 -    53.86: 67
       53.86 -    71.81: 9
       71.81 -    89.76: 5
  Dihedral angle restraints: 3922
    sinusoidal: 1476
      harmonic: 2446
  Sorted by residual:
  dihedral pdb=" CA  SER A  86 "
           pdb=" C   SER A  86 "
           pdb=" N   ALA A  87 "
           pdb=" CA  ALA A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.48   29.52     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  GLY A  47 "
           pdb=" C   GLY A  47 "
           pdb=" N   LEU A  48 "
           pdb=" CA  LEU A  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.78   28.22     0      5.00e+00 4.00e-02 3.19e+01
  dihedral pdb=" CA  ASN A 270 "
           pdb=" C   ASN A 270 "
           pdb=" N   LYS A 271 "
           pdb=" CA  LYS A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.38   25.62     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 3919 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 742
       0.055 -    0.111: 281
       0.111 -    0.166: 52
       0.166 -    0.222: 7
       0.222 -    0.277: 4
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CB  VAL B 273 "
            pdb=" CA  VAL B 273 "
            pdb=" CG1 VAL B 273 "
            pdb=" CG2 VAL B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CB  ILE A 356 "
            pdb=" CA  ILE A 356 "
            pdb=" CG1 ILE A 356 "
            pdb=" CG2 ILE A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CA  THR A  31 "
            pdb=" N   THR A  31 "
            pdb=" C   THR A  31 "
            pdb=" CB  THR A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1083 not shown)

  Planarity restraints: 1154
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 266 "    0.050 5.00e-02 4.00e+02   7.57e-02 9.18e+00
        pdb=" N   PRO B 267 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO B 267 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 267 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 149 "    0.046 5.00e-02 4.00e+02   6.90e-02 7.61e+00
        pdb=" N   PRO B 150 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 150 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 150 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 270 "   -0.014 2.00e-02 2.50e+03   2.75e-02 7.55e+00
        pdb=" C   ASN B 270 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ASN B 270 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LYS B 271 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1151 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1801
        2.80 -     3.32: 6254
        3.32 -     3.85: 11297
        3.85 -     4.37: 13005
        4.37 -     4.90: 22154
  Nonbonded interactions: 54511
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  94 "
            pdb=" OG  SER B 350 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ARG A 340 "
            pdb=" OG1 THR A 344 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OH  TYR A  94 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OE2 GLU A 414 "
            pdb=" OH  TYR A 419 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   VAL A 412 "
            pdb=" OG1 THR A 416 "
     model   vdw
     2.341 3.040
  ... (remaining 54506 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.440
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084   6774  Z= 0.428
  Angle     :  1.069  16.017   9200  Z= 0.549
  Chirality :  0.059   0.277   1086
  Planarity :  0.008   0.076   1154
  Dihedral  : 15.190  89.760   2378
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.86 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.18 (0.19), residues: 882
  helix: -3.05 (0.14), residues: 648
  sheet:  None (None), residues: 0
  loop : -3.92 (0.30), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 291 
 HIS   0.004   0.001   HIS B 284 
 PHE   0.019   0.002   PHE A 379 
 TYR   0.014   0.002   TYR B 210 
 ARG   0.003   0.000   ARG B 160 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 204
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.9328 (mp) cc_final: 0.9101 (mm)
REVERT: A   92 PHE cc_start: 0.8744 (t80) cc_final: 0.8525 (t80)
REVERT: A  144 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8598 (t)
REVERT: A  281 HIS cc_start: 0.7925 (t-90) cc_final: 0.7710 (t-90)
REVERT: A  336 ILE cc_start: 0.9010 (mt) cc_final: 0.8729 (mt)
REVERT: A  360 MET cc_start: 0.8408 (mtt) cc_final: 0.8163 (mtt)
REVERT: B   45 LEU cc_start: 0.8735 (mm) cc_final: 0.8305 (mm)
REVERT: B   55 LYS cc_start: 0.8880 (tttt) cc_final: 0.8657 (tttt)
REVERT: B  330 MET cc_start: 0.7701 (tpp) cc_final: 0.7112 (ptm)
REVERT: B  332 MET cc_start: 0.7835 (tpt) cc_final: 0.7490 (tpp)
REVERT: B  455 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8504 (ttpp)
  outliers start: 5
  outliers final: 2
  residues processed: 206
  average time/residue: 0.2002
  time to fit residues: 53.3445
Evaluate side-chains
  159 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain B residue  144 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
A 153 GLN
A 157 ASN
** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 GLN
B 157 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.136814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.104348 restraints weight = 9912.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.107299 restraints weight = 6234.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.109154 restraints weight = 4758.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6774  Z= 0.208
  Angle     :  0.687  10.191   9200  Z= 0.335
  Chirality :  0.042   0.139   1086
  Planarity :  0.005   0.057   1154
  Dihedral  :  5.925  43.664    944
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.72 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.24), residues: 882
  helix: -1.38 (0.18), residues: 640
  sheet:  None (None), residues: 0
  loop : -3.71 (0.30), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 291 
 HIS   0.005   0.001   HIS A 284 
 PHE   0.014   0.001   PHE B  92 
 TYR   0.014   0.001   TYR A 100 
 ARG   0.005   0.000   ARG B 282 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8289 (m-30) cc_final: 0.7940 (m-30)
REVERT: A  144 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8548 (t)
REVERT: A  227 ILE cc_start: 0.9130 (mm) cc_final: 0.8719 (mt)
REVERT: A  243 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7239 (mtpp)
REVERT: A  264 ILE cc_start: 0.8720 (pt) cc_final: 0.8440 (pt)
REVERT: A  332 MET cc_start: 0.7288 (tpp) cc_final: 0.6508 (tpp)
REVERT: A  336 ILE cc_start: 0.8924 (mt) cc_final: 0.8422 (mt)
REVERT: B   45 LEU cc_start: 0.8739 (mm) cc_final: 0.8309 (mm)
REVERT: B   55 LYS cc_start: 0.8863 (tttt) cc_final: 0.8212 (mtpt)
REVERT: B   99 LYS cc_start: 0.7666 (tptt) cc_final: 0.7431 (tptt)
REVERT: B  330 MET cc_start: 0.6986 (tpp) cc_final: 0.6621 (ptm)
REVERT: B  332 MET cc_start: 0.7427 (tpt) cc_final: 0.7174 (tpp)
  outliers start: 22
  outliers final: 10
  residues processed: 177
  average time/residue: 0.1909
  time to fit residues: 44.9753
Evaluate side-chains
  155 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  243 LYS
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.133950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.102720 restraints weight = 10126.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.104438 restraints weight = 7030.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.105483 restraints weight = 5300.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   6774  Z= 0.326
  Angle     :  0.731  10.976   9200  Z= 0.353
  Chirality :  0.045   0.215   1086
  Planarity :  0.005   0.049   1154
  Dihedral  :  5.731  49.687    943
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.77 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.27), residues: 882
  helix: -0.79 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -3.58 (0.31), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 291 
 HIS   0.013   0.002   HIS B 284 
 PHE   0.016   0.001   PHE A  92 
 TYR   0.014   0.002   TYR B 419 
 ARG   0.004   0.000   ARG B 451 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.7744 (mtp) cc_final: 0.7365 (mtp)
REVERT: A  210 TYR cc_start: 0.7960 (t80) cc_final: 0.7746 (t80)
REVERT: A  332 MET cc_start: 0.7468 (tpp) cc_final: 0.7200 (tpp)
REVERT: A  336 ILE cc_start: 0.9030 (mt) cc_final: 0.8802 (mt)
REVERT: B   45 LEU cc_start: 0.8818 (mm) cc_final: 0.8336 (mm)
REVERT: B   55 LYS cc_start: 0.8884 (tttt) cc_final: 0.8193 (mtpt)
REVERT: B   59 TRP cc_start: 0.8587 (t-100) cc_final: 0.8292 (t-100)
REVERT: B   99 LYS cc_start: 0.7643 (tptt) cc_final: 0.7404 (tptt)
REVERT: B  330 MET cc_start: 0.7345 (tpp) cc_final: 0.6514 (ptt)
REVERT: B  332 MET cc_start: 0.7691 (tpt) cc_final: 0.7397 (tpp)
REVERT: B  419 TYR cc_start: 0.6804 (m-80) cc_final: 0.6536 (m-80)
  outliers start: 21
  outliers final: 18
  residues processed: 159
  average time/residue: 0.1859
  time to fit residues: 39.3654
Evaluate side-chains
  151 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 81 optimal weight:    0.3980
   chunk 85 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 437 GLN
A 460 GLN
B 175 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.143104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.113526 restraints weight = 9955.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.116144 restraints weight = 7195.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.116932 restraints weight = 5031.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6774  Z= 0.215
  Angle     :  0.661  10.768   9200  Z= 0.317
  Chirality :  0.043   0.162   1086
  Planarity :  0.004   0.047   1154
  Dihedral  :  5.357  47.195    942
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 22.07 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.27), residues: 882
  helix: -0.36 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -3.37 (0.32), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 291 
 HIS   0.013   0.001   HIS B 284 
 PHE   0.019   0.001   PHE B  92 
 TYR   0.011   0.001   TYR B 419 
 ARG   0.003   0.000   ARG B 282 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.7771 (mtp) cc_final: 0.7263 (mtp)
REVERT: A  144 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8670 (t)
REVERT: A  332 MET cc_start: 0.7365 (tpp) cc_final: 0.6788 (tpp)
REVERT: A  336 ILE cc_start: 0.9048 (mt) cc_final: 0.8298 (mt)
REVERT: A  455 LYS cc_start: 0.8733 (ttpp) cc_final: 0.7979 (mtmm)
REVERT: B   45 LEU cc_start: 0.8735 (mm) cc_final: 0.8228 (mm)
REVERT: B   55 LYS cc_start: 0.8857 (tttt) cc_final: 0.8204 (mtpt)
REVERT: B  330 MET cc_start: 0.7064 (tpp) cc_final: 0.6338 (ptm)
REVERT: B  332 MET cc_start: 0.7698 (tpt) cc_final: 0.7369 (tpp)
  outliers start: 28
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1946
  time to fit residues: 43.8061
Evaluate side-chains
  156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  410 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0070
   chunk 78 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0030
   overall best weight:    0.4208

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

Flipped N/Q/H residues before XYZ refinement:
B 175 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.139267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.107998 restraints weight = 9897.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.110756 restraints weight = 6534.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.112688 restraints weight = 5052.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6774  Z= 0.176
  Angle     :  0.655  10.658   9200  Z= 0.312
  Chirality :  0.042   0.196   1086
  Planarity :  0.004   0.046   1154
  Dihedral  :  5.113  46.068    942
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 23.27 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.28), residues: 882
  helix: -0.03 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -3.21 (0.32), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  59 
 HIS   0.014   0.001   HIS B 284 
 PHE   0.011   0.001   PHE A  92 
 TYR   0.015   0.002   TYR B  94 
 ARG   0.003   0.000   ARG B 282 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8611 (t)
REVERT: A  153 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8698 (tt0)
REVERT: A  210 TYR cc_start: 0.7730 (t80) cc_final: 0.7519 (t80)
REVERT: A  227 ILE cc_start: 0.9188 (mm) cc_final: 0.8903 (mt)
REVERT: A  332 MET cc_start: 0.7370 (tpp) cc_final: 0.6844 (tpp)
REVERT: A  336 ILE cc_start: 0.9045 (mt) cc_final: 0.8306 (mt)
REVERT: A  455 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8020 (mtmm)
REVERT: B   45 LEU cc_start: 0.8719 (mm) cc_final: 0.8232 (mm)
REVERT: B   55 LYS cc_start: 0.8806 (tttt) cc_final: 0.8165 (mtpt)
REVERT: B   92 PHE cc_start: 0.8835 (t80) cc_final: 0.8538 (t80)
REVERT: B  330 MET cc_start: 0.6987 (tpp) cc_final: 0.6336 (ptm)
REVERT: B  332 MET cc_start: 0.7716 (tpt) cc_final: 0.7395 (tpp)
REVERT: B  419 TYR cc_start: 0.6802 (m-80) cc_final: 0.6551 (m-80)
  outliers start: 27
  outliers final: 17
  residues processed: 175
  average time/residue: 0.1729
  time to fit residues: 41.0674
Evaluate side-chains
  161 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  410 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 175 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.147594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.117488 restraints weight = 9793.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.120495 restraints weight = 6262.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.122478 restraints weight = 4769.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6774  Z= 0.208
  Angle     :  0.668  10.640   9200  Z= 0.316
  Chirality :  0.043   0.170   1086
  Planarity :  0.004   0.060   1154
  Dihedral  :  5.058  45.696    942
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.32 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.28), residues: 882
  helix:  0.13 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -3.04 (0.33), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  59 
 HIS   0.009   0.001   HIS B 284 
 PHE   0.025   0.001   PHE A  92 
 TYR   0.017   0.001   TYR B 100 
 ARG   0.004   0.000   ARG B  98 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8615 (t)
REVERT: A  153 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8726 (tt0)
REVERT: A  210 TYR cc_start: 0.7874 (t80) cc_final: 0.7663 (t80)
REVERT: A  227 ILE cc_start: 0.9229 (mm) cc_final: 0.8937 (mt)
REVERT: A  332 MET cc_start: 0.7252 (tpp) cc_final: 0.6818 (tpp)
REVERT: A  336 ILE cc_start: 0.9033 (mt) cc_final: 0.8290 (mt)
REVERT: A  455 LYS cc_start: 0.8693 (ttpp) cc_final: 0.7961 (mtmm)
REVERT: B   45 LEU cc_start: 0.8752 (mm) cc_final: 0.8254 (mm)
REVERT: B   55 LYS cc_start: 0.8795 (tttt) cc_final: 0.8164 (mtpt)
REVERT: B   78 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8636 (pp)
REVERT: B   99 LYS cc_start: 0.7780 (tppp) cc_final: 0.7446 (tptt)
REVERT: B  330 MET cc_start: 0.6976 (tpp) cc_final: 0.6290 (ptm)
REVERT: B  332 MET cc_start: 0.7648 (tpt) cc_final: 0.7315 (tpp)
REVERT: B  428 THR cc_start: 0.9508 (t) cc_final: 0.9298 (m)
  outliers start: 21
  outliers final: 14
  residues processed: 167
  average time/residue: 0.1760
  time to fit residues: 39.8154
Evaluate side-chains
  155 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  435 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 65 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
B 175 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.137565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.106154 restraints weight = 9890.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.109121 restraints weight = 6280.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.111109 restraints weight = 4743.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6774  Z= 0.223
  Angle     :  0.685  10.632   9200  Z= 0.322
  Chirality :  0.044   0.163   1086
  Planarity :  0.005   0.071   1154
  Dihedral  :  5.041  44.496    942
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 25.83 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.28), residues: 882
  helix:  0.24 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -3.00 (0.33), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  59 
 HIS   0.012   0.002   HIS B 284 
 PHE   0.021   0.001   PHE B  92 
 TYR   0.017   0.002   TYR B  94 
 ARG   0.005   0.000   ARG B  64 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8515 (t)
REVERT: A  332 MET cc_start: 0.7060 (tpp) cc_final: 0.6703 (tpp)
REVERT: A  336 ILE cc_start: 0.8957 (mt) cc_final: 0.8229 (mt)
REVERT: A  455 LYS cc_start: 0.8685 (ttpp) cc_final: 0.7992 (mtmm)
REVERT: B   45 LEU cc_start: 0.8745 (mm) cc_final: 0.8284 (mm)
REVERT: B   55 LYS cc_start: 0.8812 (tttt) cc_final: 0.8180 (mtpt)
REVERT: B   99 LYS cc_start: 0.7891 (tppp) cc_final: 0.7623 (tptt)
REVERT: B  208 PHE cc_start: 0.7889 (t80) cc_final: 0.7660 (t80)
REVERT: B  290 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8035 (mmtp)
REVERT: B  330 MET cc_start: 0.6888 (tpp) cc_final: 0.6328 (ptm)
REVERT: B  332 MET cc_start: 0.7440 (tpt) cc_final: 0.7212 (tpp)
REVERT: B  428 THR cc_start: 0.9533 (t) cc_final: 0.9298 (m)
  outliers start: 25
  outliers final: 19
  residues processed: 162
  average time/residue: 0.1846
  time to fit residues: 39.9910
Evaluate side-chains
  162 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  435 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0170
   chunk 33 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 73 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A 153 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.143179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.112112 restraints weight = 9896.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.115074 restraints weight = 6368.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.116786 restraints weight = 4869.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6774  Z= 0.187
  Angle     :  0.672  10.599   9200  Z= 0.314
  Chirality :  0.043   0.186   1086
  Planarity :  0.005   0.071   1154
  Dihedral  :  4.929  43.182    942
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 25.83 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.28), residues: 882
  helix:  0.35 (0.21), residues: 650
  sheet:  None (None), residues: 0
  loop : -2.89 (0.34), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  59 
 HIS   0.012   0.001   HIS B 284 
 PHE   0.014   0.001   PHE A 379 
 TYR   0.016   0.002   TYR A 210 
 ARG   0.005   0.000   ARG B  64 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A  144 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8641 (t)
REVERT: A  210 TYR cc_start: 0.7866 (t80) cc_final: 0.7263 (t80)
REVERT: A  227 ILE cc_start: 0.9207 (mm) cc_final: 0.8922 (mt)
REVERT: A  332 MET cc_start: 0.7242 (tpp) cc_final: 0.6831 (tpp)
REVERT: A  336 ILE cc_start: 0.9016 (mt) cc_final: 0.8298 (mt)
REVERT: A  455 LYS cc_start: 0.8680 (ttpp) cc_final: 0.7922 (mtmm)
REVERT: B   45 LEU cc_start: 0.8744 (mm) cc_final: 0.8246 (mm)
REVERT: B   55 LYS cc_start: 0.8794 (tttt) cc_final: 0.8168 (mtpt)
REVERT: B  205 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.7120 (ttp-110)
REVERT: B  290 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8152 (mmtp)
REVERT: B  330 MET cc_start: 0.6966 (tpp) cc_final: 0.6300 (ptm)
REVERT: B  332 MET cc_start: 0.7703 (tpt) cc_final: 0.7376 (tpp)
REVERT: B  428 THR cc_start: 0.9492 (t) cc_final: 0.9270 (m)
  outliers start: 21
  outliers final: 16
  residues processed: 163
  average time/residue: 0.2016
  time to fit residues: 43.5471
Evaluate side-chains
  154 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0020
   chunk 78 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0370
   overall best weight:    0.5468

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
B 175 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.138913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.109564 restraints weight = 9710.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.112326 restraints weight = 6258.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.114213 restraints weight = 4759.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6774  Z= 0.195
  Angle     :  0.693  10.568   9200  Z= 0.321
  Chirality :  0.043   0.178   1086
  Planarity :  0.004   0.044   1154
  Dihedral  :  4.861  42.851    942
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 27.33 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.28), residues: 882
  helix:  0.36 (0.21), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.86 (0.34), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B  59 
 HIS   0.011   0.001   HIS B 284 
 PHE   0.039   0.001   PHE A  92 
 TYR   0.017   0.002   TYR B 100 
 ARG   0.003   0.000   ARG B  98 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7585 (mtt90)
REVERT: A  144 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8627 (t)
REVERT: A  210 TYR cc_start: 0.7999 (t80) cc_final: 0.7500 (t80)
REVERT: A  227 ILE cc_start: 0.9230 (mm) cc_final: 0.8977 (mt)
REVERT: A  332 MET cc_start: 0.7280 (tpp) cc_final: 0.6864 (tpp)
REVERT: A  336 ILE cc_start: 0.9017 (mt) cc_final: 0.8319 (mt)
REVERT: A  455 LYS cc_start: 0.8684 (ttpp) cc_final: 0.7928 (mtmm)
REVERT: B   45 LEU cc_start: 0.8733 (mm) cc_final: 0.8353 (mm)
REVERT: B   55 LYS cc_start: 0.8813 (tttt) cc_final: 0.8173 (mtpt)
REVERT: B   99 LYS cc_start: 0.7773 (tppp) cc_final: 0.7400 (tptt)
REVERT: B  290 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8079 (mmtp)
REVERT: B  330 MET cc_start: 0.6939 (tpp) cc_final: 0.6303 (ptm)
REVERT: B  332 MET cc_start: 0.7621 (tpt) cc_final: 0.7317 (tpp)
REVERT: B  338 VAL cc_start: 0.9264 (t) cc_final: 0.9027 (m)
  outliers start: 21
  outliers final: 17
  residues processed: 161
  average time/residue: 0.1901
  time to fit residues: 40.9906
Evaluate side-chains
  159 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0270
   chunk 64 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0070
   chunk 16 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 55 optimal weight:    0.1980
   chunk 5 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.2056

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.154023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.124393 restraints weight = 9898.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.127471 restraints weight = 6343.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.129239 restraints weight = 4800.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6774  Z= 0.175
  Angle     :  0.693  10.662   9200  Z= 0.325
  Chirality :  0.043   0.160   1086
  Planarity :  0.004   0.041   1154
  Dihedral  :  4.796  41.390    942
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 28.08 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.28), residues: 882
  helix:  0.47 (0.21), residues: 652
  sheet:  None (None), residues: 0
  loop : -2.79 (0.34), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B  59 
 HIS   0.012   0.001   HIS B 284 
 PHE   0.017   0.001   PHE A 379 
 TYR   0.017   0.001   TYR B 100 
 ARG   0.004   0.000   ARG B  64 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7642 (mtt90)
REVERT: A  144 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8617 (t)
REVERT: A  210 TYR cc_start: 0.7990 (t80) cc_final: 0.7520 (t80)
REVERT: A  227 ILE cc_start: 0.9161 (mm) cc_final: 0.8905 (mt)
REVERT: A  332 MET cc_start: 0.7083 (tpp) cc_final: 0.6767 (tpp)
REVERT: A  336 ILE cc_start: 0.8951 (mt) cc_final: 0.8276 (mt)
REVERT: A  455 LYS cc_start: 0.8581 (ttpp) cc_final: 0.7799 (mtmm)
REVERT: B   45 LEU cc_start: 0.8725 (mm) cc_final: 0.8262 (mm)
REVERT: B   55 LYS cc_start: 0.8798 (tttt) cc_final: 0.8196 (mtpt)
REVERT: B   64 ARG cc_start: 0.8652 (mtm110) cc_final: 0.8278 (mtm110)
REVERT: B  203 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7584 (tm-30)
REVERT: B  290 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8104 (mmtp)
REVERT: B  330 MET cc_start: 0.6887 (tpp) cc_final: 0.6382 (ptm)
REVERT: B  332 MET cc_start: 0.7628 (tpt) cc_final: 0.7350 (tpp)
REVERT: B  338 VAL cc_start: 0.9171 (t) cc_final: 0.8920 (m)
  outliers start: 15
  outliers final: 13
  residues processed: 162
  average time/residue: 0.2674
  time to fit residues: 59.3989
Evaluate side-chains
  157 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0270
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0770
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
A 233 ASN
B 175 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.149937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.119705 restraints weight = 9892.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.122663 restraints weight = 6454.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.124302 restraints weight = 4962.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6774  Z= 0.229
  Angle     :  0.736  10.500   9200  Z= 0.344
  Chirality :  0.044   0.177   1086
  Planarity :  0.004   0.040   1154
  Dihedral  :  4.834  43.048    942
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 29.58 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.28), residues: 882
  helix:  0.48 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.96 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B  59 
 HIS   0.011   0.001   HIS B 284 
 PHE   0.036   0.002   PHE B  92 
 TYR   0.017   0.002   TYR B 100 
 ARG   0.004   0.000   ARG B 209 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2366.03 seconds
wall clock time: 41 minutes 36.27 seconds (2496.27 seconds total)