Starting phenix.real_space_refine
on Sat Dec 28 16:34:39 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t8e_41097/12_2024/8t8e_41097.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t8e_41097/12_2024/8t8e_41097.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t8e_41097/12_2024/8t8e_41097.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t8e_41097/12_2024/8t8e_41097.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t8e_41097/12_2024/8t8e_41097.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t8e_41097/12_2024/8t8e_41097.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.062
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      45      5.16       5
     C    5634      2.51       5
     N    1463      2.21       5
     O    1613      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8755
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2703
          Classifications: {'peptide': 348}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 341}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 3966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 488, 3966
          Classifications: {'peptide': 488}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 467}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2086
          Classifications: {'peptide': 249}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 243}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 28
  Time building chain proxies: 5.73, per 1000 atoms: 0.65
  Number of scatterers: 8755
  At special positions: 0
  Unit cell: (92.568, 81.928, 148.96, 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      45     16.00
     O    1613      8.00
     N    1463      7.00
     C    5634      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: 2.34
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 3 sheets defined
      50.1% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 114 through 125
      removed outlier: 3.780A  pdb=" N   LEU A 119 " --> pdb=" O   LYS A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
      removed outlier: 3.922A  pdb=" N   PHE A 169 " --> pdb=" O   GLN A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 211
      removed outlier: 3.582A  pdb=" N   ILE A 204 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 231
      removed outlier: 3.725A  pdb=" N   PHE A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 247
      removed outlier: 3.618A  pdb=" N   LYS A 239 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   TYR A 240 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   SER A 241 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 256
    Processing helix  chain 'A' and resid 258 through 263
    Processing helix  chain 'A' and resid 951 through 959
    Processing helix  chain 'A' and resid 960 through 966
      removed outlier: 3.527A  pdb=" N   TYR A 964 " --> pdb=" O   ARG A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 981
      removed outlier: 3.639A  pdb=" N   ASP A 978 " --> pdb=" O   ASP A 974 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   PHE A 979 " --> pdb=" O   ALA A 975 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ARG A 980 " --> pdb=" O   ASP A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1020 through 1037
      removed outlier: 3.622A  pdb=" N   LYS A1024 " --> pdb=" O   SER A1020 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   TRP A1036 " --> pdb=" O   LEU A1032 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LYS A1037 " --> pdb=" O   LEU A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1071
      removed outlier: 3.975A  pdb=" N   ILE A1060 " --> pdb=" O   VAL A1056 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ASP A1071 " --> pdb=" O   LYS A1067 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 41
      removed outlier: 3.505A  pdb=" N   LEU C  30 " --> pdb=" O   GLU C  26 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ALA C  31 " --> pdb=" O   LYS C  27 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASN C  36 " --> pdb=" O   PHE C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 53
      removed outlier: 3.605A  pdb=" N   VAL C  47 " --> pdb=" O   ASN C  43 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU C  51 " --> pdb=" O   VAL C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 76
    Processing helix  chain 'C' and resid 84 through 91
      removed outlier: 4.456A  pdb=" N   ASP C  91 " --> pdb=" O   LEU C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 109
      removed outlier: 3.531A  pdb=" N   ARG C 103 " --> pdb=" O   THR C  99 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU C 105 " --> pdb=" O   SER C 101 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS C 106 " --> pdb=" O   ARG C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 116
      removed outlier: 3.682A  pdb=" N   LEU C 115 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 124 through 140
      removed outlier: 3.566A  pdb=" N   ARG C 132 " --> pdb=" O   LEU C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 209
      removed outlier: 3.765A  pdb=" N   ASN C 209 " --> pdb=" O   ASN C 205 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 224
    Processing helix  chain 'C' and resid 229 through 234
    Processing helix  chain 'C' and resid 235 through 237
      No H-bonds generated for 'chain 'C' and resid 235 through 237'
    Processing helix  chain 'C' and resid 240 through 259
      removed outlier: 3.618A  pdb=" N   ILE C 246 " --> pdb=" O   PRO C 242 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   CYS C 253 " --> pdb=" O   ASP C 249 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN C 255 " --> pdb=" O   PHE C 251 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASP C 256 " --> pdb=" O   SER C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 273
    Processing helix  chain 'C' and resid 274 through 276
      No H-bonds generated for 'chain 'C' and resid 274 through 276'
    Processing helix  chain 'C' and resid 279 through 287
      removed outlier: 3.632A  pdb=" N   PHE C 285 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER C 287 " --> pdb=" O   VAL C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 296 through 301
      removed outlier: 3.665A  pdb=" N   VAL C 301 " --> pdb=" O   PHE C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 347
      removed outlier: 3.529A  pdb=" N   LYS C 346 " --> pdb=" O   TYR C 342 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 356
      removed outlier: 3.587A  pdb=" N   ARG C 351 " --> pdb=" O   SER C 347 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LYS C 353 " --> pdb=" O   ALA C 349 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 388 through 392
      removed outlier: 3.592A  pdb=" N   PHE C 392 " --> pdb=" O   LEU C 389 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 394 through 403
    Processing helix  chain 'C' and resid 413 through 430
      removed outlier: 5.145A  pdb=" N   GLU C 419 " --> pdb=" O   PRO C 415 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLU C 424 " --> pdb=" O   GLY C 420 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LYS C 427 " --> pdb=" O   SER C 423 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   ASP C 428 " --> pdb=" O   GLU C 424 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 438 through 442
    Processing helix  chain 'C' and resid 444 through 458
    Processing helix  chain 'C' and resid 471 through 497
      removed outlier: 3.925A  pdb=" N   LEU C 477 " --> pdb=" O   GLU C 473 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP C 483 " --> pdb=" O   ILE C 479 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   VAL C 484 " --> pdb=" O   GLU C 480 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   CYS C 485 " --> pdb=" O   LYS C 481 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU C 486 " --> pdb=" O   CYS C 482 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 506 through 528
    Processing helix  chain 'C' and resid 538 through 547
      removed outlier: 4.033A  pdb=" N   VAL C 542 " --> pdb=" O   LEU C 538 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   GLN C 544 " --> pdb=" O   PRO C 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 220
    Processing helix  chain 'B' and resid 245 through 254
    Processing helix  chain 'B' and resid 270 through 274
      removed outlier: 3.842A  pdb=" N   ARG B 274 " --> pdb=" O   GLU B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 292
      removed outlier: 3.508A  pdb=" N   LYS B 289 " --> pdb=" O   ASN B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 295
      No H-bonds generated for 'chain 'B' and resid 293 through 295'
    Processing helix  chain 'B' and resid 300 through 316
    Processing helix  chain 'B' and resid 317 through 322
    Processing helix  chain 'B' and resid 329 through 337
      removed outlier: 3.795A  pdb=" N   LEU B 337 " --> pdb=" O   LYS B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 346
      removed outlier: 3.524A  pdb=" N   SER B 346 " --> pdb=" O   HIS B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 363
      removed outlier: 3.783A  pdb=" N   TYR B 360 " --> pdb=" O   PHE B 356 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG B 361 " --> pdb=" O   PHE B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 365
      No H-bonds generated for 'chain 'B' and resid 364 through 365'
    Processing helix  chain 'B' and resid 366 through 368
      No H-bonds generated for 'chain 'B' and resid 366 through 368'
    Processing helix  chain 'B' and resid 369 through 378
      removed outlier: 3.905A  pdb=" N   LEU B 374 " --> pdb=" O   GLN B 370 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ARG B 375 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ARG B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 398
      removed outlier: 3.741A  pdb=" N   ILE B 393 " --> pdb=" O   GLN B 389 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLU B 398 " --> pdb=" O   LYS B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 416
      removed outlier: 3.560A  pdb=" N   MET B 415 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 440
      removed outlier: 4.070A  pdb=" N   ILE B 440 " --> pdb=" O   CYS B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 460
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 99
      removed outlier: 6.737A  pdb=" N   HIS A 155 " --> pdb=" O   LYS A  83 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   VAL A  85 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   ILE A 153 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   LEU A  87 " --> pdb=" O   LYS A 151 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   LYS A 151 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A 154 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 989 through 995
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1043 through 1044

    295 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.16

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1759
        1.33 -     1.45: 2062
        1.45 -     1.57: 5036
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 8923
  Sorted by residual:
  bond pdb=" C   HIS B 240 "
       pdb=" O   HIS B 240 "
    ideal  model  delta    sigma   weight residual
    1.235  1.208  0.028 1.13e-02 7.83e+03 6.02e+00
  bond pdb=" CA  LEU C 538 "
       pdb=" C   LEU C 538 "
    ideal  model  delta    sigma   weight residual
    1.523  1.504  0.020 8.40e-03 1.42e+04 5.39e+00
  bond pdb=" N   HIS B 240 "
       pdb=" CA  HIS B 240 "
    ideal  model  delta    sigma   weight residual
    1.460  1.434  0.026 1.17e-02 7.31e+03 4.79e+00
  bond pdb=" C   PHE A 211 "
       pdb=" O   PHE A 211 "
    ideal  model  delta    sigma   weight residual
    1.235  1.217  0.018 1.26e-02 6.30e+03 2.10e+00
  bond pdb=" CA  TYR C 539 "
       pdb=" C   TYR C 539 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.018 1.26e-02 6.30e+03 2.09e+00
  ... (remaining 8918 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 11880
        2.58 -     5.16: 130
        5.16 -     7.74: 11
        7.74 -    10.32: 3
       10.32 -    12.90: 1
  Bond angle restraints: 12025
  Sorted by residual:
  angle pdb=" N   TYR C 539 "
        pdb=" CA  TYR C 539 "
        pdb=" C   TYR C 539 "
      ideal   model   delta    sigma   weight residual
     109.81  122.71  -12.90 2.21e+00 2.05e-01 3.41e+01
  angle pdb=" N   ILE C  68 "
        pdb=" CA  ILE C  68 "
        pdb=" C   ILE C  68 "
      ideal   model   delta    sigma   weight residual
     112.29  106.90    5.39 9.40e-01 1.13e+00 3.29e+01
  angle pdb=" N   ILE B 437 "
        pdb=" CA  ILE B 437 "
        pdb=" C   ILE B 437 "
      ideal   model   delta    sigma   weight residual
     111.91  107.25    4.66 8.90e-01 1.26e+00 2.74e+01
  angle pdb=" N   ILE B 450 "
        pdb=" CA  ILE B 450 "
        pdb=" C   ILE B 450 "
      ideal   model   delta    sigma   weight residual
     113.71  108.78    4.93 9.50e-01 1.11e+00 2.69e+01
  angle pdb=" N   GLU A 968 "
        pdb=" CA  GLU A 968 "
        pdb=" C   GLU A 968 "
      ideal   model   delta    sigma   weight residual
     112.94  107.11    5.83 1.41e+00 5.03e-01 1.71e+01
  ... (remaining 12020 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 4585
       17.05 -    34.10: 607
       34.10 -    51.15: 180
       51.15 -    68.20: 20
       68.20 -    85.26: 11
  Dihedral angle restraints: 5403
    sinusoidal: 2202
      harmonic: 3201
  Sorted by residual:
  dihedral pdb=" CA  LYS C 308 "
           pdb=" C   LYS C 308 "
           pdb=" N   LEU C 309 "
           pdb=" CA  LEU C 309 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.19  -25.81     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  TRP B 200 "
           pdb=" C   TRP B 200 "
           pdb=" N   HIS B 201 "
           pdb=" CA  HIS B 201 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.44   21.56     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  TYR B 347 "
           pdb=" C   TYR B 347 "
           pdb=" N   PHE B 348 "
           pdb=" CA  PHE B 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.75   21.25     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 5400 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1271
       0.085 -    0.169: 83
       0.169 -    0.253: 2
       0.253 -    0.338: 0
       0.338 -    0.422: 1
  Chirality restraints: 1357
  Sorted by residual:
  chirality pdb=" CA  TYR C 539 "
            pdb=" N   TYR C 539 "
            pdb=" C   TYR C 539 "
            pdb=" CB  TYR C 539 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.46e+00
  chirality pdb=" CA  SER A 212 "
            pdb=" N   SER A 212 "
            pdb=" C   SER A 212 "
            pdb=" CB  SER A 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  LYS A 987 "
            pdb=" N   LYS A 987 "
            pdb=" C   LYS A 987 "
            pdb=" CB  LYS A 987 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.95e-01
  ... (remaining 1354 not shown)

  Planarity restraints: 1525
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 210 "   -0.015 2.00e-02 2.50e+03   3.13e-02 9.77e+00
        pdb=" C   TYR A 210 "    0.054 2.00e-02 2.50e+03
        pdb=" O   TYR A 210 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PHE A 211 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  77 "   -0.036 5.00e-02 4.00e+02   5.59e-02 4.99e+00
        pdb=" N   PRO A  78 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A  78 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  78 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 444 "    0.011 2.00e-02 2.50e+03   2.10e-02 4.39e+00
        pdb=" C   THR B 444 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   THR B 444 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR B 445 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1522 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 775
        2.74 -     3.28: 8893
        3.28 -     3.82: 13661
        3.82 -     4.36: 16897
        4.36 -     4.90: 28621
  Nonbonded interactions: 68847
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C 255 "
            pdb=" OG  SER C 279 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ALA A 259 "
            pdb=" ND1 HIS A 263 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OH  TYR C  81 "
            pdb=" O   GLU C 325 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" NZ  LYS C 400 "
            pdb=" OG1 THR B 220 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" O   GLU C  23 "
            pdb=" OH  TYR C 126 "
     model   vdw
     2.247 3.040
  ... (remaining 68842 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.940
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.120
  Find NCS groups from input model:        0.090
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8923  Z= 0.199
  Angle     :  0.694  12.904  12025  Z= 0.398
  Chirality :  0.045   0.422   1357
  Planarity :  0.004   0.056   1525
  Dihedral  : 16.794  85.255   3317
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.95 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 26.77 %
    Favored  : 72.21 %
  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: -3.74 (0.24), residues: 1061
  helix: -2.29 (0.20), residues: 539
  sheet: -2.02 (0.64), residues: 75
  loop : -2.67 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 200 
 HIS   0.013   0.001   HIS C 513 
 PHE   0.014   0.001   PHE A1049 
 TYR   0.026   0.002   TYR B 295 
 ARG   0.003   0.000   ARG A 177 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7503 (m-80)
REVERT: C  545 MET cc_start: 0.8568 (ttm) cc_final: 0.8328 (mtp)
  outliers start: 10
  outliers final: 2
  residues processed: 120
  average time/residue: 0.2002
  time to fit residues: 34.7493
Evaluate side-chains
  112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  221 PHE
Chi-restraints excluded: chain C residue  273 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.0870
   chunk 80 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0010
   chunk 96 optimal weight:    0.0470
   overall best weight:    0.3062

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

Flipped N/Q/H residues before XYZ refinement:
A  93 HIS
A 954 HIS
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8923  Z= 0.158
  Angle     :  0.576   7.673  12025  Z= 0.303
  Chirality :  0.041   0.154   1357
  Planarity :  0.004   0.048   1525
  Dihedral  :  5.082  26.332   1167
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 23.79 %
    Favored  : 73.33 %
  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: -3.25 (0.24), residues: 1061
  helix: -1.75 (0.20), residues: 542
  sheet: -2.20 (0.59), residues: 75
  loop : -2.55 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 220 
 HIS   0.004   0.001   HIS C 513 
 PHE   0.011   0.001   PHE A 973 
 TYR   0.011   0.001   TYR C 539 
 ARG   0.004   0.000   ARG C 195 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  537 LEU cc_start: 0.8306 (mm) cc_final: 0.7788 (tp)
REVERT: B  210 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7616 (mm-30)
REVERT: B  328 HIS cc_start: 0.6912 (OUTLIER) cc_final: 0.6633 (m-70)
REVERT: B  361 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7822 (ttp-110)
  outliers start: 28
  outliers final: 12
  residues processed: 147
  average time/residue: 0.1860
  time to fit residues: 40.1125
Evaluate side-chains
  126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  307 TYR
Chi-restraints excluded: chain B residue  200 TRP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain B residue  361 ARG
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  456 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:    0.2980
   chunk 29 optimal weight:    0.8980
   chunk 80 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 96 optimal weight:    0.1980
   chunk 104 optimal weight:    0.3980
   chunk 85 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C 134 GLN
C 544 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8923  Z= 0.179
  Angle     :  0.574  11.496  12025  Z= 0.294
  Chirality :  0.041   0.153   1357
  Planarity :  0.003   0.044   1525
  Dihedral  :  4.882  25.376   1163
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.10 %
    Favored  : 71.79 %
  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: -2.89 (0.24), residues: 1061
  helix: -1.33 (0.21), residues: 544
  sheet: -2.20 (0.59), residues: 75
  loop : -2.54 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 220 
 HIS   0.011   0.001   HIS C 513 
 PHE   0.015   0.001   PHE C 284 
 TYR   0.017   0.001   TYR A  81 
 ARG   0.003   0.000   ARG C 195 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  508 GLN cc_start: 0.7196 (mt0) cc_final: 0.6703 (pt0)
REVERT: C  537 LEU cc_start: 0.8321 (mm) cc_final: 0.7684 (tp)
REVERT: C  544 GLN cc_start: 0.8704 (tt0) cc_final: 0.8490 (tt0)
REVERT: B  210 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7497 (mm-30)
REVERT: B  328 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6696 (m-70)
REVERT: B  361 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7859 (ttp-110)
REVERT: B  416 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7639 (t80)
  outliers start: 40
  outliers final: 21
  residues processed: 158
  average time/residue: 0.1811
  time to fit residues: 41.7611
Evaluate side-chains
  135 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1056 VAL
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  307 TYR
Chi-restraints excluded: chain C residue  330 ASP
Chi-restraints excluded: chain C residue  361 LEU
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain C residue  478 ASN
Chi-restraints excluded: chain B residue  200 TRP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  243 CYS
Chi-restraints excluded: chain B residue  267 TYR
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain B residue  361 ARG
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  456 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 50 optimal weight:    0.4980
   chunk 10 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
C 201 ASN
C 518 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8923  Z= 0.232
  Angle     :  0.582  10.041  12025  Z= 0.301
  Chirality :  0.042   0.155   1357
  Planarity :  0.003   0.042   1525
  Dihedral  :  4.951  25.254   1163
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 24.82 %
    Favored  : 70.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.77 (0.24), residues: 1061
  helix: -1.22 (0.21), residues: 548
  sheet: -2.25 (0.57), residues: 75
  loop : -2.48 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 220 
 HIS   0.004   0.001   HIS B 201 
 PHE   0.024   0.002   PHE C 258 
 TYR   0.012   0.001   TYR A 258 
 ARG   0.003   0.000   ARG C 195 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 116
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7941 (m)
REVERT: A  256 LEU cc_start: 0.2734 (OUTLIER) cc_final: 0.2474 (mp)
REVERT: A 1078 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7928 (mm)
REVERT: C  508 GLN cc_start: 0.7092 (mt0) cc_final: 0.6629 (pt0)
REVERT: B  210 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7551 (mm-30)
REVERT: B  316 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7927 (pt)
REVERT: B  328 HIS cc_start: 0.6976 (OUTLIER) cc_final: 0.6673 (m-70)
  outliers start: 42
  outliers final: 23
  residues processed: 153
  average time/residue: 0.1882
  time to fit residues: 41.7056
Evaluate side-chains
  136 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1056 VAL
Chi-restraints excluded: chain A residue 1078 ILE
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain C residue   99 THR
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  307 TYR
Chi-restraints excluded: chain C residue  330 ASP
Chi-restraints excluded: chain C residue  361 LEU
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain C residue  478 ASN
Chi-restraints excluded: chain B residue  200 TRP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  243 CYS
Chi-restraints excluded: chain B residue  267 TYR
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  456 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    0.0010
   chunk 1 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0010
   chunk 91 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.5592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8923  Z= 0.183
  Angle     :  0.559   9.559  12025  Z= 0.288
  Chirality :  0.041   0.157   1357
  Planarity :  0.003   0.043   1525
  Dihedral  :  4.775  25.164   1163
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 24.21 %
    Favored  : 71.18 %
  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: -2.63 (0.25), residues: 1061
  helix: -1.05 (0.22), residues: 558
  sheet: -2.14 (0.58), residues: 75
  loop : -2.53 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 220 
 HIS   0.008   0.001   HIS C 513 
 PHE   0.018   0.001   PHE C 258 
 TYR   0.019   0.001   TYR A  81 
 ARG   0.002   0.000   ARG C 195 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 116
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   78 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7634 (pp)
REVERT: C  479 ILE cc_start: 0.8732 (tp) cc_final: 0.8367 (tp)
REVERT: B  241 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5710 (mm)
REVERT: B  316 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7849 (pt)
REVERT: B  317 ASP cc_start: 0.8104 (p0) cc_final: 0.7786 (p0)
REVERT: B  416 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7270 (t80)
  outliers start: 45
  outliers final: 27
  residues processed: 153
  average time/residue: 0.1952
  time to fit residues: 43.2308
Evaluate side-chains
  141 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 110
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1056 VAL
Chi-restraints excluded: chain A residue 1057 ASN
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain C residue   99 THR
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  307 TYR
Chi-restraints excluded: chain C residue  330 ASP
Chi-restraints excluded: chain C residue  361 LEU
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain B residue  200 TRP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  243 CYS
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  257 GLN
Chi-restraints excluded: chain B residue  267 TYR
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  456 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0980
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    1.0188

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 508 GLN
** C 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8923  Z= 0.269
  Angle     :  0.597   8.659  12025  Z= 0.306
  Chirality :  0.043   0.153   1357
  Planarity :  0.003   0.042   1525
  Dihedral  :  4.977  25.212   1163
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 24.82 %
    Favored  : 70.36 %
  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: -2.59 (0.25), residues: 1061
  helix: -1.04 (0.22), residues: 546
  sheet: -2.15 (0.57), residues: 75
  loop : -2.44 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 220 
 HIS   0.006   0.001   HIS B 201 
 PHE   0.016   0.002   PHE A 973 
 TYR   0.018   0.002   TYR A  81 
 ARG   0.002   0.000   ARG A 980 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 113
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   26 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7409 (mm-30)
REVERT: C  511 MET cc_start: 0.8651 (ttp) cc_final: 0.8438 (tmm)
REVERT: B  316 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8119 (pp)
  outliers start: 47
  outliers final: 33
  residues processed: 150
  average time/residue: 0.1816
  time to fit residues: 40.0488
Evaluate side-chains
  142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1056 VAL
Chi-restraints excluded: chain A residue 1057 ASN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain C residue   99 THR
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  307 TYR
Chi-restraints excluded: chain C residue  330 ASP
Chi-restraints excluded: chain C residue  361 LEU
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain C residue  482 CYS
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain B residue  200 TRP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  243 CYS
Chi-restraints excluded: chain B residue  257 GLN
Chi-restraints excluded: chain B residue  267 TYR
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  456 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  93 HIS
C 183 ASN
C 383 GLN
C 508 GLN
** C 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 322 ASN
B 328 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8923  Z= 0.226
  Angle     :  0.584   8.659  12025  Z= 0.300
  Chirality :  0.042   0.162   1357
  Planarity :  0.003   0.041   1525
  Dihedral  :  4.902  25.186   1163
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 25.95 %
    Favored  : 69.54 %
  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: -2.59 (0.25), residues: 1061
  helix: -1.04 (0.22), residues: 562
  sheet: -2.17 (0.58), residues: 75
  loop : -2.48 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 200 
 HIS   0.004   0.001   HIS B 201 
 PHE   0.014   0.002   PHE C 258 
 TYR   0.020   0.001   TYR A  81 
 ARG   0.004   0.000   ARG B 230 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 112
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   26 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7405 (mm-30)
REVERT: B  316 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7961 (pt)
  outliers start: 44
  outliers final: 32
  residues processed: 147
  average time/residue: 0.1867
  time to fit residues: 40.0527
Evaluate side-chains
  142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  968 GLU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1056 VAL
Chi-restraints excluded: chain A residue 1057 ASN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  307 TYR
Chi-restraints excluded: chain C residue  330 ASP
Chi-restraints excluded: chain C residue  361 LEU
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain B residue  200 TRP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  243 CYS
Chi-restraints excluded: chain B residue  257 GLN
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  456 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9990
   chunk 80 optimal weight:    9.9990
   chunk 92 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 508 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8923  Z= 0.216
  Angle     :  0.580   8.256  12025  Z= 0.299
  Chirality :  0.042   0.157   1357
  Planarity :  0.003   0.040   1525
  Dihedral  :  4.856  25.152   1163
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 26.05 %
    Favored  : 69.85 %
  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: -2.50 (0.25), residues: 1061
  helix: -0.99 (0.22), residues: 560
  sheet: -2.06 (0.59), residues: 75
  loop : -2.42 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 200 
 HIS   0.009   0.001   HIS C 513 
 PHE   0.014   0.001   PHE C 258 
 TYR   0.020   0.001   TYR A  81 
 ARG   0.005   0.000   ARG B 230 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 115
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   26 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7406 (mm-30)
REVERT: B  316 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7951 (pt)
REVERT: B  317 ASP cc_start: 0.8119 (p0) cc_final: 0.7807 (p0)
  outliers start: 40
  outliers final: 33
  residues processed: 144
  average time/residue: 0.1938
  time to fit residues: 40.2340
Evaluate side-chains
  143 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 109
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  968 GLU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1056 VAL
Chi-restraints excluded: chain A residue 1057 ASN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  145 LYS
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  307 TYR
Chi-restraints excluded: chain C residue  330 ASP
Chi-restraints excluded: chain C residue  361 LEU
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain B residue  200 TRP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  243 CYS
Chi-restraints excluded: chain B residue  257 GLN
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  456 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0970
   chunk 41 optimal weight:    0.0030
   chunk 74 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 94 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 508 GLN
** C 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 322 ASN
B 328 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8923  Z= 0.179
  Angle     :  0.570   9.301  12025  Z= 0.293
  Chirality :  0.041   0.158   1357
  Planarity :  0.003   0.037   1525
  Dihedral  :  4.748  24.970   1163
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 26.36 %
    Favored  : 69.74 %
  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: -2.39 (0.25), residues: 1061
  helix: -0.86 (0.22), residues: 558
  sheet: -2.09 (0.59), residues: 75
  loop : -2.40 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 200 
 HIS   0.003   0.001   HIS B 201 
 PHE   0.014   0.001   PHE C 258 
 TYR   0.022   0.001   TYR A  81 
 ARG   0.005   0.000   ARG B 230 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 113
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  316 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7863 (pt)
REVERT: B  416 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7303 (t80)
  outliers start: 38
  outliers final: 27
  residues processed: 141
  average time/residue: 0.1808
  time to fit residues: 37.4340
Evaluate side-chains
  138 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  968 GLU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1056 VAL
Chi-restraints excluded: chain A residue 1057 ASN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  307 TYR
Chi-restraints excluded: chain C residue  330 ASP
Chi-restraints excluded: chain C residue  361 LEU
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain B residue  200 TRP
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  243 CYS
Chi-restraints excluded: chain B residue  257 GLN
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  456 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0070
   chunk 69 optimal weight:    0.0030
   chunk 105 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 8 optimal weight:    9.9990
   chunk 64 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.3808

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8923  Z= 0.158
  Angle     :  0.561   9.189  12025  Z= 0.287
  Chirality :  0.041   0.164   1357
  Planarity :  0.003   0.036   1525
  Dihedral  :  4.602  24.547   1163
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 27.38 %
    Favored  : 69.85 %
  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: -2.26 (0.25), residues: 1061
  helix: -0.74 (0.22), residues: 557
  sheet: -2.01 (0.60), residues: 75
  loop : -2.35 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 200 
 HIS   0.003   0.001   HIS C 513 
 PHE   0.013   0.001   PHE C 258 
 TYR   0.021   0.001   TYR A  81 
 ARG   0.004   0.000   ARG B 230 

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 ASP cc_start: 0.8283 (p0) cc_final: 0.8059 (p0)
REVERT: B  416 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7389 (t80)
  outliers start: 27
  outliers final: 22
  residues processed: 139
  average time/residue: 0.1926
  time to fit residues: 39.3506
Evaluate side-chains
  137 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1039 MET
Chi-restraints excluded: chain A residue 1056 VAL
Chi-restraints excluded: chain A residue 1057 ASN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  307 TYR
Chi-restraints excluded: chain C residue  330 ASP
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain B residue  200 TRP
Chi-restraints excluded: chain B residue  243 CYS
Chi-restraints excluded: chain B residue  257 GLN
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 23 optimal weight:    0.4980
   chunk 84 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 73 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 508 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.175894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.133549 restraints weight = 10773.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 2.49
r_work: 0.3421 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8923  Z= 0.211
  Angle     :  0.590   9.246  12025  Z= 0.302
  Chirality :  0.042   0.160   1357
  Planarity :  0.003   0.037   1525
  Dihedral  :  4.711  23.455   1163
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 27.38 %
    Favored  : 69.74 %
  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: -2.33 (0.25), residues: 1061
  helix: -0.82 (0.22), residues: 560
  sheet: -2.02 (0.59), residues: 75
  loop : -2.37 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 220 
 HIS   0.004   0.001   HIS B 201 
 PHE   0.013   0.001   PHE A 973 
 TYR   0.021   0.001   TYR A  81 
 ARG   0.004   0.000   ARG B 230 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1898.13 seconds
wall clock time: 35 minutes 29.65 seconds (2129.65 seconds total)