Starting phenix.real_space_refine
on Mon Nov 17 23:34:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d7w_7826/11_2025/6d7w_7826.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d7w_7826/11_2025/6d7w_7826.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6d7w_7826/11_2025/6d7w_7826.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d7w_7826/11_2025/6d7w_7826.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d7w_7826/11_2025/6d7w_7826.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d7w_7826/11_2025/6d7w_7826.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 464 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      20      5.16       5
     C    5749      2.51       5
     N    1560      2.21       5
     O    1616      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8946
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2264
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 11, 'TRANS': 263}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2213
          Classifications: {'peptide': 269}
          Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 256}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2255
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 11, 'TRANS': 262}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2213
          Classifications: {'peptide': 269}
          Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 255}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.98, per 1000 atoms: 0.22
  Number of scatterers: 8946
  At special positions: 0
  Unit cell: (86.52, 84.84, 148.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      20     16.00
     O    1616      8.00
     N    1560      7.00
     C    5749      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 313.0 milliseconds
  

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2062

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 4 sheets defined
      55.8% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 164 through 175
      removed outlier: 3.694A  pdb=" N   LEU A 168 " --> pdb=" O   PRO A 164 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 280
      removed outlier: 3.756A  pdb=" N   PHE A 272 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 363
      removed outlier: 4.029A  pdb=" N   PHE A 309 " --> pdb=" O   GLU A 305 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LEU A 310 " --> pdb=" O   ARG A 306 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ARG A 313 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU A 363 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 370
      removed outlier: 3.676A  pdb=" N   THR A 370 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 367 through 370'
    Processing helix  chain 'A' and resid 371 through 390
    Processing helix  chain 'A' and resid 413 through 418
      removed outlier: 3.640A  pdb=" N   LYS A 418 " --> pdb=" O   LEU A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 446
      removed outlier: 3.924A  pdb=" N   ALA A 434 " --> pdb=" O   ASP A 430 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   ILE A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ARG A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ARG A 437 " --> pdb=" O   ASN A 433 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLU A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 459
      removed outlier: 4.450A  pdb=" N   GLN A 457 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A 459 " --> pdb=" O   GLU A 456 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 175
      removed outlier: 3.989A  pdb=" N   LEU C 168 " --> pdb=" O   PRO C 164 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU C 175 " --> pdb=" O   LEU C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 280
    Processing helix  chain 'C' and resid 302 through 307
    Processing helix  chain 'C' and resid 307 through 362
      removed outlier: 5.012A  pdb=" N   ARG C 313 " --> pdb=" O   PHE C 309 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   HIS C 336 " --> pdb=" O   ASP C 332 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY C 338 " --> pdb=" O   LEU C 334 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL C 357 " --> pdb=" O   TRP C 353 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   THR C 361 " --> pdb=" O   VAL C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 370
    Processing helix  chain 'C' and resid 371 through 392
      removed outlier: 3.692A  pdb=" N   GLY C 385 " --> pdb=" O   SER C 381 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 419
      removed outlier: 3.704A  pdb=" N   GLN C 411 " --> pdb=" O   ILE C 407 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   GLN C 416 " --> pdb=" O   LYS C 412 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   MET C 417 " --> pdb=" O   LYS C 413 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 447
      removed outlier: 3.688A  pdb=" N   TRP C 425 " --> pdb=" O   ASP C 421 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLU C 438 " --> pdb=" O   ALA C 434 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 457
      removed outlier: 3.905A  pdb=" N   GLU C 456 " --> pdb=" O   GLU C 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 175
      removed outlier: 3.582A  pdb=" N   LEU B 168 " --> pdb=" O   PRO B 164 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLU B 175 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 280
      removed outlier: 3.688A  pdb=" N   PHE B 272 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 363
      removed outlier: 4.514A  pdb=" N   LEU B 324 " --> pdb=" O   ARG B 320 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   VAL B 342 " --> pdb=" O   GLY B 338 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU B 363 " --> pdb=" O   LYS B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 389
      removed outlier: 3.812A  pdb=" N   MET B 371 " --> pdb=" O   GLY B 367 " (cutoff:3.500A)
      Proline residue:  B 373  - end of helix
      removed outlier: 3.788A  pdb=" N   TRP B 389 " --> pdb=" O   GLY B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 418
    Processing helix  chain 'B' and resid 422 through 447
      removed outlier: 4.031A  pdb=" N   ALA B 434 " --> pdb=" O   ASP B 430 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ILE B 435 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ARG B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ARG B 437 " --> pdb=" O   ASN B 433 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASP B 447 " --> pdb=" O   ALA B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 459
      removed outlier: 3.531A  pdb=" N   ASP B 459 " --> pdb=" O   GLU B 456 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 174
    Processing helix  chain 'D' and resid 268 through 280
    Processing helix  chain 'D' and resid 302 through 364
      removed outlier: 3.580A  pdb=" N   PHE D 309 " --> pdb=" O   GLU D 305 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU D 310 " --> pdb=" O   ARG D 306 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG D 313 " --> pdb=" O   PHE D 309 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LEU D 324 " --> pdb=" O   ARG D 320 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   THR D 364 " --> pdb=" O   LEU D 360 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 371 through 386
    Processing helix  chain 'D' and resid 387 through 391
    Processing helix  chain 'D' and resid 406 through 415
      removed outlier: 3.764A  pdb=" N   GLN D 411 " --> pdb=" O   ILE D 407 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 421 through 446
      removed outlier: 3.799A  pdb=" N   TRP D 425 " --> pdb=" O   ASP D 421 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU D 438 " --> pdb=" O   ALA D 434 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 452 through 457
      removed outlier: 3.951A  pdb=" N   GLU D 456 " --> pdb=" O   GLU D 452 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 132
      removed outlier: 3.572A  pdb=" N   LYS A 129 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS A 139 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE A 142 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 153 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 196
      removed outlier: 3.518A  pdb=" N   ILE A 261 " --> pdb=" O   ALA A 195 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   PHE A 260 " --> pdb=" O   GLN C 154 " (cutoff:3.500A)
      removed outlier: 8.907A  pdb=" N   ALA C 156 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   ARG A 262 " --> pdb=" O   ALA C 156 " (cutoff:3.500A)
      removed outlier: 8.996A  pdb=" N   LEU C 158 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE C 142 " --> pdb=" O   ILE C 155 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 283 through 284
    Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 159
      removed outlier: 3.855A  pdb=" N   GLU B 153 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU B 144 " --> pdb=" O   GLU B 153 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LYS B 139 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS B 129 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   ALA B 127 " --> pdb=" O   PRO B 143 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   GLY B 128 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   PHE B 282 " --> pdb=" O   VAL B 298 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   PHE B 193 " --> pdb=" O   TRP B 263 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   ARG B 262 " --> pdb=" O   ALA D 156 " (cutoff:3.500A)
      removed outlier: 8.873A  pdb=" N   LEU D 158 " --> pdb=" O   ARG B 262 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ALA D 127 " --> pdb=" O   PRO D 143 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU D 130 " --> pdb=" O   ALA D 299 " (cutoff:3.500A)

    477 hydrogen bonds defined for protein.
    1380 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: 1.09

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1577
        1.32 -     1.44: 2376
        1.44 -     1.56: 5152
        1.56 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 9141
  Sorted by residual:
  bond pdb=" C   PHE D 303 "
       pdb=" O   PHE D 303 "
    ideal  model  delta    sigma   weight residual
    1.237  1.201  0.036 1.17e-02 7.31e+03 9.51e+00
  bond pdb=" CA  ASN D 183 "
       pdb=" C   ASN D 183 "
    ideal  model  delta    sigma   weight residual
    1.529  1.556 -0.027 1.26e-02 6.30e+03 4.75e+00
  bond pdb=" CG  LEU B 140 "
       pdb=" CD2 LEU B 140 "
    ideal  model  delta    sigma   weight residual
    1.521  1.451  0.070 3.30e-02 9.18e+02 4.47e+00
  bond pdb=" CA  PHE D 303 "
       pdb=" C   PHE D 303 "
    ideal  model  delta    sigma   weight residual
    1.523  1.496  0.027 1.30e-02 5.92e+03 4.26e+00
  bond pdb=" N   LEU A 293 "
       pdb=" CA  LEU A 293 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.025 1.29e-02 6.01e+03 3.88e+00
  ... (remaining 9136 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 11843
        2.67 -     5.35: 432
        5.35 -     8.02: 68
        8.02 -    10.69: 20
       10.69 -    13.37: 3
  Bond angle restraints: 12366
  Sorted by residual:
  angle pdb=" C   ALA D 289 "
        pdb=" N   PRO D 290 "
        pdb=" CA  PRO D 290 "
      ideal   model   delta    sigma   weight residual
     119.05  132.42  -13.37 1.11e+00 8.12e-01 1.45e+02
  angle pdb=" N   ASP B 365 "
        pdb=" CA  ASP B 365 "
        pdb=" C   ASP B 365 "
      ideal   model   delta    sigma   weight residual
     111.28  100.85   10.43 1.09e+00 8.42e-01 9.16e+01
  angle pdb=" N   ASN D 183 "
        pdb=" CA  ASN D 183 "
        pdb=" C   ASN D 183 "
      ideal   model   delta    sigma   weight residual
     111.24  124.20  -12.96 1.38e+00 5.25e-01 8.82e+01
  angle pdb=" N   ASN B 148 "
        pdb=" CA  ASN B 148 "
        pdb=" C   ASN B 148 "
      ideal   model   delta    sigma   weight residual
     112.34  122.75  -10.41 1.30e+00 5.92e-01 6.41e+01
  angle pdb=" C   ARG D 187 "
        pdb=" N   PRO D 188 "
        pdb=" CA  PRO D 188 "
      ideal   model   delta    sigma   weight residual
     120.38  127.65   -7.27 1.03e+00 9.43e-01 4.98e+01
  ... (remaining 12361 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.82: 5091
       15.82 -    31.65: 304
       31.65 -    47.47: 77
       47.47 -    63.30: 12
       63.30 -    79.12: 6
  Dihedral angle restraints: 5490
    sinusoidal: 2319
      harmonic: 3171
  Sorted by residual:
  dihedral pdb=" N   GLU D 182 "
           pdb=" C   GLU D 182 "
           pdb=" CA  GLU D 182 "
           pdb=" CB  GLU D 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.46  -16.66     0      2.50e+00 1.60e-01 4.44e+01
  dihedral pdb=" C   GLU D 182 "
           pdb=" N   GLU D 182 "
           pdb=" CA  GLU D 182 "
           pdb=" CB  GLU D 182 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.85   16.25     0      2.50e+00 1.60e-01 4.23e+01
  dihedral pdb=" CA  TYR D 415 "
           pdb=" C   TYR D 415 "
           pdb=" N   GLN D 416 "
           pdb=" CA  GLN D 416 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.13   26.87     0      5.00e+00 4.00e-02 2.89e+01
  ... (remaining 5487 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.130: 1263
       0.130 -    0.260: 83
       0.260 -    0.390: 9
       0.390 -    0.520: 3
       0.520 -    0.650: 1
  Chirality restraints: 1359
  Sorted by residual:
  chirality pdb=" CA  GLU D 182 "
            pdb=" N   GLU D 182 "
            pdb=" C   GLU D 182 "
            pdb=" CB  GLU D 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.06e+01
  chirality pdb=" CA  GLU D 294 "
            pdb=" N   GLU D 294 "
            pdb=" C   GLU D 294 "
            pdb=" CB  GLU D 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.86e+00
  chirality pdb=" CA  LEU A 293 "
            pdb=" N   LEU A 293 "
            pdb=" C   LEU A 293 "
            pdb=" CB  LEU A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.04e+00
  ... (remaining 1356 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 147 "   -0.026 2.00e-02 2.50e+03   5.19e-02 2.70e+01
        pdb=" C   ILE B 147 "    0.090 2.00e-02 2.50e+03
        pdb=" O   ILE B 147 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   ASN B 148 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 394 "    0.020 2.00e-02 2.50e+03   4.01e-02 1.61e+01
        pdb=" C   ASN C 394 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   ASN C 394 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ARG C 395 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 381 "   -0.015 2.00e-02 2.50e+03   3.07e-02 9.41e+00
        pdb=" C   SER C 381 "    0.053 2.00e-02 2.50e+03
        pdb=" O   SER C 381 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   THR C 382 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1040
        2.75 -     3.29: 8399
        3.29 -     3.82: 13688
        3.82 -     4.36: 15192
        4.36 -     4.90: 25607
  Nonbonded interactions: 63926
  Sorted by model distance:
  nonbonded pdb=" O   PHE C 303 "
            pdb=" OG1 THR C 307 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PHE B 303 "
            pdb=" OG1 THR B 307 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG1 THR B 133 "
            pdb=" O   LEU B 137 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   VAL A 357 "
            pdb=" OG1 THR A 361 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   LYS C 359 "
            pdb=" OG1 THR C 364 "
     model   vdw
     2.281 3.040
  ... (remaining 63921 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 124 through 196 or resid 259 through 396 or resid 406 thro \ 
ugh 461))
  selection = (chain 'B' and (resid 124 through 196 or resid 259 through 396 or resid 406 thro \ 
ugh 461))
  selection = (chain 'C' and (resid 124 through 396 or resid 406 through 461))
  selection = (chain 'D' and (resid 124 through 396 or resid 406 through 461))
}

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:             0.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.450
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
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      :  0.007   0.075   9141  Z= 0.345
  Angle     :  1.205  13.366  12366  Z= 0.703
  Chirality :  0.074   0.650   1359
  Planarity :  0.009   0.120   1580
  Dihedral  : 11.663  79.123   3428
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  :  6.62 %
    Favored  : 90.64 %
  Cbeta Deviations :  0.39 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.65 (0.22), residues: 1063
  helix: -1.70 (0.19), residues: 554
  sheet: -3.18 (0.31), residues: 163
  loop : -2.91 (0.29), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 278 
 TYR   0.031   0.003   TYR C 308 
 PHE   0.036   0.004   PHE D 272 
 TRP   0.027   0.003   TRP B 368 
 HIS   0.017   0.002   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00746 ( 9141)
  covalent geometry    : angle       1.20516 (12366)
  hydrogen bonds       : bond        0.18062 (  477)
  hydrogen bonds       : angle       8.78638 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 235
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8846 (tt)
REVERT: A  198 LEU cc_start: 0.8256 (tp) cc_final: 0.7970 (tp)
REVERT: A  361 THR cc_start: 0.7709 (m) cc_final: 0.7491 (m)
REVERT: A  415 TYR cc_start: 0.7810 (p90) cc_final: 0.7434 (p90)
REVERT: A  453 ARG cc_start: 0.8310 (mtt180) cc_final: 0.7759 (mmp-170)
REVERT: C  352 PHE cc_start: 0.7591 (t80) cc_final: 0.7326 (t80)
REVERT: B  328 LYS cc_start: 0.8045 (tppt) cc_final: 0.7844 (tttt)
REVERT: B  361 THR cc_start: 0.7513 (m) cc_final: 0.6197 (m)
REVERT: B  372 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6767 (tp30)
REVERT: B  453 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7928 (mmp-170)
REVERT: D  147 ILE cc_start: 0.8107 (mm) cc_final: 0.7898 (mt)
REVERT: D  307 THR cc_start: 0.6756 (m) cc_final: 0.6463 (p)
REVERT: D  311 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6469 (mpp-170)
REVERT: D  352 PHE cc_start: 0.7459 (t80) cc_final: 0.7242 (t80)
  outliers start: 26
  outliers final: 9
  residues processed: 261
  average time/residue: 0.1394
  time to fit residues: 45.3987
Evaluate side-chains
  129 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  308 TYR
Chi-restraints excluded: chain D residue  311 ARG
Chi-restraints excluded: chain D residue  383 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:   30.0000
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
A 295 GLN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 GLN
A 408 ASN
A 411 GLN
A 433 ASN
B 148 ASN
B 167 HIS
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 GLN
D 167 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.137813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.113298 restraints weight = 20818.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.114912 restraints weight = 13493.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.115685 restraints weight = 10232.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.115960 restraints weight = 9031.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.116087 restraints weight = 8991.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9141  Z= 0.189
  Angle     :  0.769   9.968  12366  Z= 0.409
  Chirality :  0.047   0.225   1359
  Planarity :  0.006   0.054   1580
  Dihedral  :  7.332  61.841   1222
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.36 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 12.51 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.25), residues: 1063
  helix:  0.21 (0.22), residues: 543
  sheet: -2.69 (0.33), residues: 165
  loop : -2.39 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 278 
 TYR   0.043   0.003   TYR C 308 
 PHE   0.026   0.002   PHE A 282 
 TRP   0.010   0.001   TRP B 354 
 HIS   0.010   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 9141)
  covalent geometry    : angle       0.76913 (12366)
  hydrogen bonds       : bond        0.07502 (  477)
  hydrogen bonds       : angle       5.77606 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 121
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 VAL cc_start: 0.8195 (t) cc_final: 0.7981 (p)
REVERT: A  415 TYR cc_start: 0.7816 (p90) cc_final: 0.7368 (p90)
REVERT: A  453 ARG cc_start: 0.8264 (mtt180) cc_final: 0.7991 (mmp-170)
REVERT: A  454 LYS cc_start: 0.7462 (mttt) cc_final: 0.7030 (pttt)
REVERT: C  142 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8125 (tt)
REVERT: C  169 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: B  328 LYS cc_start: 0.8068 (tppt) cc_final: 0.7681 (tttt)
REVERT: D  147 ILE cc_start: 0.7994 (mm) cc_final: 0.7792 (mt)
  outliers start: 47
  outliers final: 28
  residues processed: 160
  average time/residue: 0.1116
  time to fit residues: 23.5077
Evaluate side-chains
  117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  433 ASN
Chi-restraints excluded: chain C residue  142 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  304 ASP
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  382 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  260 PHE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  308 TYR
Chi-restraints excluded: chain D residue  321 ILE
Chi-restraints excluded: chain D residue  375 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Chi-restraints excluded: chain D residue  451 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 42 optimal weight:   20.0000
   chunk 22 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 12 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0170
   chunk 99 optimal weight:    8.9990
   overall best weight:    2.3222

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.136731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.113353 restraints weight = 21107.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.113807 restraints weight = 13738.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.114992 restraints weight = 11324.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.115712 restraints weight = 9568.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.115749 restraints weight = 9031.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9141  Z= 0.166
  Angle     :  0.716  12.825  12366  Z= 0.372
  Chirality :  0.045   0.178   1359
  Planarity :  0.005   0.049   1580
  Dihedral  :  6.280  54.160   1210
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 13.04 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.25), residues: 1063
  helix:  0.85 (0.22), residues: 543
  sheet: -2.44 (0.36), residues: 159
  loop : -2.10 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 278 
 TYR   0.031   0.002   TYR C 308 
 PHE   0.022   0.002   PHE A 282 
 TRP   0.011   0.001   TRP B 354 
 HIS   0.008   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9141)
  covalent geometry    : angle       0.71575 (12366)
  hydrogen bonds       : bond        0.06833 (  477)
  hydrogen bonds       : angle       5.26998 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 101
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8110 (tt)
REVERT: C  271 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7252 (t70)
REVERT: B  328 LYS cc_start: 0.8037 (tppt) cc_final: 0.7612 (tttt)
  outliers start: 46
  outliers final: 31
  residues processed: 139
  average time/residue: 0.1129
  time to fit residues: 20.8600
Evaluate side-chains
  117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 84
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  336 HIS
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  408 ASN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain C residue  142 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  271 ASP
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  304 ASP
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain C residue  431 GLU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  308 TYR
Chi-restraints excluded: chain D residue  336 HIS
Chi-restraints excluded: chain D residue  382 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Chi-restraints excluded: chain D residue  451 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 100 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN
A 336 HIS
B 148 ASN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.136346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.111891 restraints weight = 21495.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.113171 restraints weight = 14118.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.114228 restraints weight = 11156.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.114534 restraints weight = 9748.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114658 restraints weight = 9385.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.4340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9141  Z= 0.154
  Angle     :  0.676  11.608  12366  Z= 0.346
  Chirality :  0.045   0.164   1359
  Planarity :  0.004   0.044   1580
  Dihedral  :  5.986  56.557   1210
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 13.67 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.26), residues: 1063
  helix:  1.04 (0.22), residues: 555
  sheet: -2.14 (0.40), residues: 150
  loop : -1.92 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 453 
 TYR   0.024   0.002   TYR C 308 
 PHE   0.020   0.001   PHE A 282 
 TRP   0.010   0.001   TRP A 354 
 HIS   0.008   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9141)
  covalent geometry    : angle       0.67636 (12366)
  hydrogen bonds       : bond        0.06397 (  477)
  hydrogen bonds       : angle       4.94766 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 99
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  453 ARG cc_start: 0.8044 (mmp-170) cc_final: 0.7483 (mtt90)
REVERT: C  271 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7245 (t70)
REVERT: C  387 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.6174 (t80)
  outliers start: 49
  outliers final: 38
  residues processed: 143
  average time/residue: 0.1134
  time to fit residues: 21.5790
Evaluate side-chains
  120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 80
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  336 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  408 ASN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  271 ASP
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  304 ASP
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  382 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  260 PHE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  317 ILE
Chi-restraints excluded: chain D residue  336 HIS
Chi-restraints excluded: chain D residue  375 THR
Chi-restraints excluded: chain D residue  382 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 68 optimal weight:   20.0000
   chunk 38 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   chunk 12 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
B 148 ASN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 297 HIS
D 167 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.138332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.113202 restraints weight = 21533.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.115514 restraints weight = 13740.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.117002 restraints weight = 10375.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.117924 restraints weight = 8722.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.118347 restraints weight = 7849.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.4642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9141  Z= 0.137
  Angle     :  0.652  11.589  12366  Z= 0.332
  Chirality :  0.044   0.174   1359
  Planarity :  0.004   0.045   1580
  Dihedral  :  5.718  58.485   1208
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 15.46 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.26), residues: 1063
  helix:  1.31 (0.22), residues: 552
  sheet: -2.00 (0.41), residues: 150
  loop : -1.69 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 278 
 TYR   0.020   0.002   TYR C 376 
 PHE   0.023   0.001   PHE B 352 
 TRP   0.008   0.001   TRP B 425 
 HIS   0.016   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9141)
  covalent geometry    : angle       0.65201 (12366)
  hydrogen bonds       : bond        0.05978 (  477)
  hydrogen bonds       : angle       4.73406 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 92
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  453 ARG cc_start: 0.7918 (mmp-170) cc_final: 0.7402 (mtt90)
REVERT: C  271 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7277 (t70)
REVERT: C  387 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.6279 (t80)
  outliers start: 50
  outliers final: 31
  residues processed: 137
  average time/residue: 0.1022
  time to fit residues: 19.2341
Evaluate side-chains
  113 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  336 HIS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  408 ASN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  271 ASP
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  304 ASP
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  317 ILE
Chi-restraints excluded: chain D residue  336 HIS
Chi-restraints excluded: chain D residue  382 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 30 optimal weight:    0.1980
   chunk 6 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.4388

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 HIS
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 GLN
B 411 GLN
D 167 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.136971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.112665 restraints weight = 21718.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.113742 restraints weight = 14529.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.114430 restraints weight = 11537.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.114734 restraints weight = 10235.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.114917 restraints weight = 9966.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.4836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9141  Z= 0.153
  Angle     :  0.666  11.583  12366  Z= 0.337
  Chirality :  0.045   0.196   1359
  Planarity :  0.004   0.042   1580
  Dihedral  :  5.646  58.639   1208
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 15.88 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.27), residues: 1063
  helix:  1.41 (0.22), residues: 553
  sheet: -1.99 (0.40), residues: 150
  loop : -1.58 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 278 
 TYR   0.022   0.002   TYR C 376 
 PHE   0.020   0.001   PHE B 282 
 TRP   0.010   0.001   TRP D 389 
 HIS   0.007   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9141)
  covalent geometry    : angle       0.66628 (12366)
  hydrogen bonds       : bond        0.06043 (  477)
  hydrogen bonds       : angle       4.66930 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 83
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  453 ARG cc_start: 0.8021 (mmp-170) cc_final: 0.7475 (mtt90)
REVERT: C  271 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7255 (t70)
REVERT: C  387 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.6219 (t80)
REVERT: B  411 GLN cc_start: 0.7142 (mp10) cc_final: 0.6659 (mp10)
  outliers start: 50
  outliers final: 39
  residues processed: 127
  average time/residue: 0.1089
  time to fit residues: 18.7104
Evaluate side-chains
  119 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 78
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  336 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  408 ASN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  271 ASP
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain D residue  133 THR
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  260 PHE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  317 ILE
Chi-restraints excluded: chain D residue  336 HIS
Chi-restraints excluded: chain D residue  375 THR
Chi-restraints excluded: chain D residue  382 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 2 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0970
   chunk 57 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    4.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 GLN
D 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.134916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.112160 restraints weight = 21693.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.112361 restraints weight = 16160.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.112915 restraints weight = 13179.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.113390 restraints weight = 12240.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.113516 restraints weight = 11279.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.4909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9141  Z= 0.192
  Angle     :  0.686  10.202  12366  Z= 0.352
  Chirality :  0.046   0.196   1359
  Planarity :  0.005   0.044   1580
  Dihedral  :  5.706  58.324   1208
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.19 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.26), residues: 1063
  helix:  1.37 (0.22), residues: 560
  sheet: -2.08 (0.39), residues: 150
  loop : -1.65 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 337 
 TYR   0.027   0.002   TYR C 308 
 PHE   0.025   0.002   PHE A 282 
 TRP   0.011   0.002   TRP D 389 
 HIS   0.012   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 9141)
  covalent geometry    : angle       0.68618 (12366)
  hydrogen bonds       : bond        0.06327 (  477)
  hydrogen bonds       : angle       4.74319 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 83
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  453 ARG cc_start: 0.8004 (mmp-170) cc_final: 0.7510 (mtt90)
REVERT: C  271 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7084 (t70)
REVERT: B  411 GLN cc_start: 0.7118 (mp10) cc_final: 0.6590 (mp10)
REVERT: D  350 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7488 (tt)
  outliers start: 43
  outliers final: 39
  residues processed: 120
  average time/residue: 0.1023
  time to fit residues: 16.6383
Evaluate side-chains
  117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 76
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  336 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  408 ASN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  271 ASP
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  382 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  260 PHE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  317 ILE
Chi-restraints excluded: chain D residue  336 HIS
Chi-restraints excluded: chain D residue  350 LEU
Chi-restraints excluded: chain D residue  375 THR
Chi-restraints excluded: chain D residue  382 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 48 optimal weight:   20.0000
   chunk 1 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0060
   chunk 89 optimal weight:    0.9990
   chunk 80 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.5802

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
A 265 GLN
A 336 HIS
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.136987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.113574 restraints weight = 21470.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.114231 restraints weight = 15566.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.114685 restraints weight = 13273.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.115626 restraints weight = 11785.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.115614 restraints weight = 11233.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.5120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9141  Z= 0.136
  Angle     :  0.639  11.169  12366  Z= 0.323
  Chirality :  0.044   0.189   1359
  Planarity :  0.004   0.045   1580
  Dihedral  :  5.536  58.394   1208
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 15.88 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.27), residues: 1063
  helix:  1.59 (0.22), residues: 553
  sheet: -1.89 (0.40), residues: 150
  loop : -1.41 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 278 
 TYR   0.023   0.002   TYR C 376 
 PHE   0.017   0.001   PHE B 352 
 TRP   0.009   0.001   TRP A 263 
 HIS   0.008   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9141)
  covalent geometry    : angle       0.63911 (12366)
  hydrogen bonds       : bond        0.05876 (  477)
  hydrogen bonds       : angle       4.53849 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 93
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  453 ARG cc_start: 0.7956 (mmp-170) cc_final: 0.7513 (mtt90)
REVERT: C  271 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7051 (t70)
REVERT: C  387 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.6048 (t80)
REVERT: B  411 GLN cc_start: 0.7084 (mp10) cc_final: 0.6535 (mp10)
REVERT: D  152 ILE cc_start: 0.7796 (pp) cc_final: 0.7575 (pp)
REVERT: D  350 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7434 (tt)
  outliers start: 47
  outliers final: 39
  residues processed: 134
  average time/residue: 0.1034
  time to fit residues: 18.9134
Evaluate side-chains
  123 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 81
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  336 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  408 ASN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  271 ASP
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain D residue  133 THR
Chi-restraints excluded: chain D residue  136 ARG
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  317 ILE
Chi-restraints excluded: chain D residue  336 HIS
Chi-restraints excluded: chain D residue  350 LEU
Chi-restraints excluded: chain D residue  382 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Chi-restraints excluded: chain D residue  407 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0970
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 HIS
C 183 ASN
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.137330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.114130 restraints weight = 21363.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.114914 restraints weight = 15362.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.115379 restraints weight = 12746.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.115779 restraints weight = 11662.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.115922 restraints weight = 11155.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9141  Z= 0.142
  Angle     :  0.661  10.481  12366  Z= 0.336
  Chirality :  0.045   0.259   1359
  Planarity :  0.004   0.037   1580
  Dihedral  :  5.503  58.368   1208
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 16.19 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.27), residues: 1063
  helix:  1.60 (0.22), residues: 555
  sheet: -1.83 (0.41), residues: 150
  loop : -1.36 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 278 
 TYR   0.024   0.002   TYR C 376 
 PHE   0.016   0.001   PHE A 282 
 TRP   0.033   0.001   TRP A 425 
 HIS   0.007   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9141)
  covalent geometry    : angle       0.66123 (12366)
  hydrogen bonds       : bond        0.05822 (  477)
  hydrogen bonds       : angle       4.52244 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 83
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  453 ARG cc_start: 0.7934 (mmp-170) cc_final: 0.7561 (mtt90)
REVERT: C  271 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7053 (t70)
REVERT: C  387 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.6191 (t80)
REVERT: B  384 MET cc_start: 0.3360 (mtt) cc_final: 0.2882 (mtm)
REVERT: D  152 ILE cc_start: 0.7767 (pp) cc_final: 0.7538 (pp)
  outliers start: 47
  outliers final: 39
  residues processed: 123
  average time/residue: 0.1026
  time to fit residues: 17.1426
Evaluate side-chains
  123 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 82
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  336 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  408 ASN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  271 ASP
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain D residue  133 THR
Chi-restraints excluded: chain D residue  136 ARG
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  317 ILE
Chi-restraints excluded: chain D residue  336 HIS
Chi-restraints excluded: chain D residue  382 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Chi-restraints excluded: chain D residue  407 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 85 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 88 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 4 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 74 optimal weight:   20.0000
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 183 ASN
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.136205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.112056 restraints weight = 21509.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.113868 restraints weight = 14975.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.115096 restraints weight = 11916.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.115847 restraints weight = 10301.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.116153 restraints weight = 9416.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.5276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9141  Z= 0.154
  Angle     :  0.667  10.136  12366  Z= 0.340
  Chirality :  0.045   0.231   1359
  Planarity :  0.004   0.058   1580
  Dihedral  :  5.506  58.604   1208
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.51 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.27), residues: 1063
  helix:  1.64 (0.22), residues: 555
  sheet: -1.82 (0.41), residues: 150
  loop : -1.34 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 453 
 TYR   0.025   0.002   TYR C 376 
 PHE   0.019   0.001   PHE A 282 
 TRP   0.027   0.001   TRP A 425 
 HIS   0.013   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9141)
  covalent geometry    : angle       0.66742 (12366)
  hydrogen bonds       : bond        0.05925 (  477)
  hydrogen bonds       : angle       4.53488 ( 1380)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 82
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 ASP cc_start: 0.7502 (p0) cc_final: 0.6977 (t0)
REVERT: A  453 ARG cc_start: 0.7822 (mmp-170) cc_final: 0.7543 (mtt90)
REVERT: C  271 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6989 (t70)
REVERT: C  387 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.6191 (t80)
REVERT: B  384 MET cc_start: 0.3465 (mtt) cc_final: 0.2971 (mtm)
REVERT: D  152 ILE cc_start: 0.7755 (pp) cc_final: 0.7522 (pp)
REVERT: D  350 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7426 (tt)
  outliers start: 43
  outliers final: 40
  residues processed: 119
  average time/residue: 0.1040
  time to fit residues: 16.9699
Evaluate side-chains
  123 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 80
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  336 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  408 ASN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  271 ASP
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain D residue  133 THR
Chi-restraints excluded: chain D residue  136 ARG
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  317 ILE
Chi-restraints excluded: chain D residue  336 HIS
Chi-restraints excluded: chain D residue  350 LEU
Chi-restraints excluded: chain D residue  382 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Chi-restraints excluded: chain D residue  407 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 2 optimal weight:    0.0970
   chunk 57 optimal weight:    0.6980
   chunk 3 optimal weight:   10.0000
   chunk 33 optimal weight:    0.3980
   chunk 59 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 100 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 183 ASN
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.134593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.110917 restraints weight = 19615.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.113118 restraints weight = 12282.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.114514 restraints weight = 9163.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.115298 restraints weight = 7629.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.115892 restraints weight = 6849.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.5409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9141  Z= 0.141
  Angle     :  0.661  10.241  12366  Z= 0.336
  Chirality :  0.045   0.219   1359
  Planarity :  0.004   0.054   1580
  Dihedral  :  5.438  57.157   1208
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 16.19 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.27), residues: 1063
  helix:  1.71 (0.22), residues: 555
  sheet: -1.81 (0.41), residues: 153
  loop : -1.38 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 453 
 TYR   0.024   0.002   TYR C 376 
 PHE   0.016   0.001   PHE A 282 
 TRP   0.021   0.001   TRP A 425 
 HIS   0.008   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9141)
  covalent geometry    : angle       0.66125 (12366)
  hydrogen bonds       : bond        0.05775 (  477)
  hydrogen bonds       : angle       4.46216 ( 1380)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1487.54 seconds
wall clock time: 26 minutes 23.12 seconds (1583.12 seconds total)