Starting phenix.real_space_refine
on Wed Feb 14 13:34:27 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7w_7826/02_2024/6d7w_7826.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7w_7826/02_2024/6d7w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7w_7826/02_2024/6d7w_7826.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7w_7826/02_2024/6d7w_7826.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7w_7826/02_2024/6d7w_7826.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7w_7826/02_2024/6d7w_7826.pdb"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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
    Residue "A ARG  136": "NH1" <-> "NH2"
    Residue "A ARG  170": "NH1" <-> "NH2"
    Residue "C ARG  136": "NH1" <-> "NH2"
    Residue "C PHE  138": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  170": "NH1" <-> "NH2"
    Residue "C GLU  287": "OE1" <-> "OE2"
    Residue "C GLU  372": "OE1" <-> "OE2"
    Residue "B ARG  136": "NH1" <-> "NH2"
    Residue "B ARG  170": "NH1" <-> "NH2"
    Residue "B PHE  282": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  337": "NH1" <-> "NH2"
    Residue "B ARG  341": "NH1" <-> "NH2"
    Residue "D ARG  136": "NH1" <-> "NH2"
    Residue "D ARG  170": "NH1" <-> "NH2"
    Residue "D PHE  260": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  294": "OE1" <-> "OE2"
    Residue "D PHE  303": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  395": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 5.24, per 1000 atoms: 0.59
  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  - 3.50
        Amino acid           : False - 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: 3.18
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 0.80
  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: 2.36

  Time building geometry restraints manager: 3.45 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:
       97.72 -   105.13: 164
      105.13 -   112.53: 4506
      112.53 -   119.94: 3691
      119.94 -   127.35: 3891
      127.35 -   134.76: 114
  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 2.440
  nonbonded pdb=" O   PHE B 303 "
            pdb=" OG1 THR B 307 "
     model   vdw
     2.267 2.440
  nonbonded pdb=" OG1 THR B 133 "
            pdb=" O   LEU B 137 "
     model   vdw
     2.270 2.440
  nonbonded pdb=" O   VAL A 357 "
            pdb=" OG1 THR A 361 "
     model   vdw
     2.275 2.440
  nonbonded pdb=" O   LYS C 359 "
            pdb=" OG1 THR C 364 "
     model   vdw
     2.281 2.440
  ... (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
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:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.770
  Check model and map are aligned:         0.150
  Set scattering table:                    0.090
  Process input model:                     26.200
  Find NCS groups from input model:        0.620
  Set up NCS constraints:                  0.040
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.050
-------------------------------------------------------------------------------
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= 0.480
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (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
 TRP   0.027   0.003   TRP B 368 
 HIS   0.017   0.002   HIS A 336 
 PHE   0.036   0.004   PHE D 272 
 TYR   0.031   0.003   TYR C 308 
 ARG   0.014   0.001   ARG A 278 

*********************** 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 fitting.
    rotamer outliers: 26
    poor density    : 235
  time to evaluate  : 1.148 
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: 0.8847 (tt)
REVERT: A  198 LEU cc_start: 0.8256 (tp) cc_final: 0.7969 (tp)
REVERT: A  361 THR cc_start: 0.7709 (m) cc_final: 0.7492 (m)
REVERT: A  415 TYR cc_start: 0.7810 (p90) cc_final: 0.7435 (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: 0.6765 (tp30)
REVERT: B  453 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7925 (mmp-170)
REVERT: D  147 ILE cc_start: 0.8107 (mm) cc_final: 0.7897 (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: 0.6470 (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: 0.3109
  time to fit residues: 100.7053
Evaluate side-chains
  129 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
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 89 optimal weight:    0.4980
   chunk 80 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 GLN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 GLN
A 408 ASN
A 411 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN
B 162 GLN
** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9141  Z= 0.264
  Angle     :  0.766  12.951  12366  Z= 0.401
  Chirality :  0.048   0.258   1359
  Planarity :  0.006   0.055   1580
  Dihedral  :  7.317  68.676   1222
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.74 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 12.62 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.25), residues: 1063
  helix:  0.29 (0.22), residues: 543
  sheet: -2.74 (0.33), residues: 165
  loop : -2.45 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 354 
 HIS   0.010   0.001   HIS A 336 
 PHE   0.029   0.002   PHE A 282 
 TYR   0.040   0.003   TYR C 308 
 ARG   0.009   0.001   ARG A 278 

*********************** 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
  169 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 120
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 VAL cc_start: 0.8218 (t) cc_final: 0.7998 (p)
REVERT: A  415 TYR cc_start: 0.7936 (p90) cc_final: 0.7410 (p90)
REVERT: A  453 ARG cc_start: 0.8330 (mtt180) cc_final: 0.7963 (mmp-170)
REVERT: B  169 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7609 (tt0)
  outliers start: 49
  outliers final: 28
  residues processed: 163
  average time/residue: 0.2322
  time to fit residues: 50.4419
Evaluate side-chains
  114 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
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  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 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  169 GLU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  261 ILE
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  133 THR
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  336 HIS
Chi-restraints excluded: chain D residue  375 THR
Chi-restraints excluded: chain D residue  383 LEU
Chi-restraints excluded: chain D residue  388 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 80 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 96 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 95 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   overall best weight:    4.7990

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9141  Z= 0.333
  Angle     :  0.765  11.787  12366  Z= 0.399
  Chirality :  0.048   0.191   1359
  Planarity :  0.005   0.055   1580
  Dihedral  :  6.726  55.742   1213
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 13.88 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.25), residues: 1063
  helix:  0.73 (0.22), residues: 551
  sheet: -2.60 (0.35), residues: 159
  loop : -2.32 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 354 
 HIS   0.008   0.001   HIS A 336 
 PHE   0.032   0.002   PHE A 282 
 TYR   0.037   0.003   TYR C 308 
 ARG   0.009   0.001   ARG C 453 

*********************** 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
  150 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 98
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 VAL cc_start: 0.8258 (t) cc_final: 0.8030 (p)
REVERT: A  453 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7955 (mmp-170)
REVERT: A  454 LYS cc_start: 0.7597 (mttt) cc_final: 0.7013 (pttt)
REVERT: B  169 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7613 (tt0)
REVERT: B  194 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9114 (mt)
  outliers start: 52
  outliers final: 43
  residues processed: 139
  average time/residue: 0.2296
  time to fit residues: 43.3456
Evaluate side-chains
  127 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 82
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
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  261 ILE
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  375 THR
Chi-restraints excluded: chain A residue  377 LEU
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  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 C residue  344 LEU
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain C residue  415 TYR
Chi-restraints excluded: chain C residue  431 GLU
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  268 GLU
Chi-restraints excluded: chain B residue  342 VAL
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  133 THR
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:   20.0000
   chunk 72 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 102 optimal weight:    6.9990
   chunk 91 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 85 optimal weight:    9.9990
   overall best weight:    3.1386

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.4380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9141  Z= 0.239
  Angle     :  0.687  10.388  12366  Z= 0.356
  Chirality :  0.045   0.171   1359
  Planarity :  0.005   0.045   1580
  Dihedral  :  6.373  58.727   1211
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 15.25 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.26), residues: 1063
  helix:  1.01 (0.22), residues: 553
  sheet: -2.33 (0.38), residues: 150
  loop : -1.98 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 389 
 HIS   0.008   0.001   HIS A 336 
 PHE   0.025   0.002   PHE A 282 
 TYR   0.025   0.002   TYR C 308 
 ARG   0.008   0.001   ARG A 278 

*********************** 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
  144 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 94
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 VAL cc_start: 0.8188 (t) cc_final: 0.7982 (p)
REVERT: C  152 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7265 (tt)
REVERT: C  162 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8339 (mm-40)
REVERT: C  387 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.6010 (t80)
REVERT: B  169 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7663 (tt0)
REVERT: D  169 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7888 (tt0)
REVERT: D  260 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6802 (p90)
  outliers start: 50
  outliers final: 35
  residues processed: 138
  average time/residue: 0.2504
  time to fit residues: 46.7642
Evaluate side-chains
  118 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 79
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
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  307 THR
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  140 LEU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  152 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 C residue  344 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  342 VAL
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  133 THR
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
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
Chi-restraints excluded: chain D residue  407 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 87 optimal weight:    0.6980
   chunk 70 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 91 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   overall best weight:    5.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 GLN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.4630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   9141  Z= 0.352
  Angle     :  0.752  11.127  12366  Z= 0.393
  Chirality :  0.048   0.208   1359
  Planarity :  0.005   0.052   1580
  Dihedral  :  6.482  58.127   1211
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 14.93 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.25), residues: 1063
  helix:  1.03 (0.22), residues: 552
  sheet: -2.54 (0.36), residues: 150
  loop : -1.95 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 389 
 HIS   0.007   0.001   HIS A 336 
 PHE   0.031   0.003   PHE A 282 
 TYR   0.034   0.003   TYR C 308 
 ARG   0.008   0.001   ARG A 278 

*********************** 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
  143 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 80
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ARG cc_start: 0.3664 (tpt90) cc_final: 0.3295 (mmm-85)
REVERT: A  342 VAL cc_start: 0.8200 (t) cc_final: 0.7983 (p)
REVERT: A  454 LYS cc_start: 0.7605 (mttt) cc_final: 0.6984 (pttt)
REVERT: C  152 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7311 (tt)
REVERT: B  169 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7697 (tt0)
  outliers start: 63
  outliers final: 48
  residues processed: 135
  average time/residue: 0.2229
  time to fit residues: 41.3442
Evaluate side-chains
  128 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 78
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
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  261 ILE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  307 THR
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  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  152 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain C residue  415 TYR
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  342 VAL
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  133 THR
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  159 ILE
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  260 PHE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  307 THR
Chi-restraints excluded: chain D residue  310 LEU
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
Chi-restraints excluded: chain D residue  407 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   chunk 60 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 102 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 98 optimal weight:    4.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.4852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9141  Z= 0.341
  Angle     :  0.753  13.019  12366  Z= 0.391
  Chirality :  0.048   0.204   1359
  Planarity :  0.005   0.048   1580
  Dihedral  :  6.522  59.867   1211
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 15.25 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.25), residues: 1063
  helix:  1.07 (0.21), residues: 550
  sheet: -2.57 (0.36), residues: 150
  loop : -1.92 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 389 
 HIS   0.007   0.001   HIS A 336 
 PHE   0.031   0.002   PHE A 282 
 TYR   0.032   0.003   TYR C 308 
 ARG   0.008   0.001   ARG A 278 

*********************** 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
  152 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 83
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.7935 (t0)
REVERT: A  342 VAL cc_start: 0.8167 (t) cc_final: 0.7953 (p)
REVERT: A  454 LYS cc_start: 0.7624 (mttt) cc_final: 0.7022 (pttt)
REVERT: C  152 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7219 (tt)
REVERT: B  153 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7423 (tm-30)
REVERT: B  169 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7848 (tt0)
  outliers start: 69
  outliers final: 53
  residues processed: 144
  average time/residue: 0.1983
  time to fit residues: 40.0346
Evaluate side-chains
  134 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 78
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
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  261 ILE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  307 THR
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  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  140 LEU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  378 VAL
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain C residue  415 TYR
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  342 VAL
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  133 THR
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  159 ILE
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  260 PHE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  307 THR
Chi-restraints excluded: chain D residue  310 LEU
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
Chi-restraints excluded: chain D residue  407 ILE
Chi-restraints excluded: chain D residue  421 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 58 optimal weight:   20.0000
   chunk 74 optimal weight:   30.0000
   chunk 86 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 102 optimal weight:   20.0000
   chunk 63 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    2.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9141  Z= 0.227
  Angle     :  0.688  12.172  12366  Z= 0.353
  Chirality :  0.045   0.198   1359
  Planarity :  0.004   0.045   1580
  Dihedral  :  6.251  56.169   1211
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 15.56 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.26), residues: 1063
  helix:  1.35 (0.22), residues: 554
  sheet: -2.43 (0.37), residues: 150
  loop : -1.78 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 368 
 HIS   0.008   0.001   HIS A 336 
 PHE   0.022   0.002   PHE A 282 
 TYR   0.022   0.002   TYR C 446 
 ARG   0.003   0.000   ARG D 313 

*********************** 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
  149 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 87
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 ASP cc_start: 0.8587 (p0) cc_final: 0.7879 (t0)
REVERT: A  342 VAL cc_start: 0.8168 (t) cc_final: 0.7958 (p)
REVERT: C  152 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7356 (tt)
REVERT: C  175 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7586 (pp20)
REVERT: C  387 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.5886 (t80)
REVERT: B  153 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7433 (tm-30)
REVERT: B  169 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7822 (tt0)
REVERT: D  260 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6912 (p90)
  outliers start: 62
  outliers final: 49
  residues processed: 142
  average time/residue: 0.1886
  time to fit residues: 38.3242
Evaluate side-chains
  132 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 79
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
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  307 THR
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  152 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain C residue  421 ASP
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  169 GLU
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  269 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  342 VAL
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  133 THR
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  260 PHE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  307 THR
Chi-restraints excluded: chain D residue  336 HIS
Chi-restraints excluded: chain D residue  361 THR
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
Chi-restraints excluded: chain D residue  407 ILE
Chi-restraints excluded: chain D residue  421 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 20 optimal weight:   20.0000
   chunk 19 optimal weight:    6.9990
   chunk 64 optimal weight:    0.6980
   chunk 69 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   chunk 9 optimal weight:    9.9990
   chunk 80 optimal weight:    9.9990
   chunk 92 optimal weight:    0.5980
   chunk 97 optimal weight:   10.0000
   chunk 89 optimal weight:    5.9990
   overall best weight:    2.6584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.5198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9141  Z= 0.220
  Angle     :  0.682  10.785  12366  Z= 0.349
  Chirality :  0.045   0.194   1359
  Planarity :  0.004   0.045   1580
  Dihedral  :  6.131  53.936   1211
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 16.19 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.26), residues: 1063
  helix:  1.49 (0.22), residues: 554
  sheet: -2.32 (0.37), residues: 151
  loop : -1.73 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 425 
 HIS   0.008   0.001   HIS A 336 
 PHE   0.026   0.002   PHE B 352 
 TYR   0.027   0.002   TYR C 376 
 ARG   0.003   0.000   ARG D 313 

*********************** 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
  143 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 87
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.7873 (t0)
REVERT: C  152 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7203 (tt)
REVERT: C  175 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7597 (pp20)
REVERT: C  387 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.5820 (t80)
REVERT: B  153 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7410 (tm-30)
REVERT: B  169 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7804 (tt0)
REVERT: B  384 MET cc_start: 0.4017 (mtt) cc_final: 0.3423 (mtm)
REVERT: D  136 ARG cc_start: 0.8348 (ptt-90) cc_final: 0.8114 (mtm-85)
REVERT: D  260 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6904 (p90)
  outliers start: 56
  outliers final: 45
  residues processed: 135
  average time/residue: 0.1933
  time to fit residues: 37.2652
Evaluate side-chains
  130 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 80
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
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  304 ASP
Chi-restraints excluded: chain A residue  307 THR
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  152 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain C residue  421 ASP
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  169 GLU
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  269 ILE
Chi-restraints excluded: chain B residue  342 VAL
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  133 THR
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  260 PHE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  307 THR
Chi-restraints excluded: chain D residue  361 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
Chi-restraints excluded: chain D residue  407 ILE
Chi-restraints excluded: chain D residue  421 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 74 optimal weight:   20.0000
   chunk 29 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 94 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 167 HIS
C 336 HIS
B 148 ASN
B 162 GLN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9141  Z= 0.331
  Angle     :  0.748  12.270  12366  Z= 0.385
  Chirality :  0.047   0.196   1359
  Planarity :  0.005   0.048   1580
  Dihedral  :  6.299  55.134   1211
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 16.40 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.26), residues: 1063
  helix:  1.35 (0.22), residues: 553
  sheet: -2.35 (0.38), residues: 150
  loop : -1.77 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 389 
 HIS   0.013   0.002   HIS A 336 
 PHE   0.028   0.002   PHE A 282 
 TYR   0.030   0.003   TYR C 308 
 ARG   0.004   0.000   ARG A 337 

*********************** 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
  141 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 78
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.7953 (t70)
REVERT: A  342 VAL cc_start: 0.8128 (t) cc_final: 0.7906 (p)
REVERT: C  152 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7231 (tt)
REVERT: C  175 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7596 (pp20)
REVERT: B  153 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7434 (tm-30)
REVERT: B  165 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8911 (mp)
REVERT: B  169 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7828 (tt0)
REVERT: B  384 MET cc_start: 0.4014 (mtt) cc_final: 0.3379 (mtm)
REVERT: D  350 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6958 (tt)
  outliers start: 63
  outliers final: 55
  residues processed: 132
  average time/residue: 0.1848
  time to fit residues: 35.0938
Evaluate side-chains
  136 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 76
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
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  304 ASP
Chi-restraints excluded: chain A residue  307 THR
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  152 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  378 VAL
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  387 TYR
Chi-restraints excluded: chain C residue  421 ASP
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  169 GLU
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  269 ILE
Chi-restraints excluded: chain B residue  304 ASP
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  342 VAL
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  133 THR
Chi-restraints excluded: chain D residue  146 THR
Chi-restraints excluded: chain D residue  159 ILE
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  260 PHE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  307 THR
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  361 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
Chi-restraints excluded: chain D residue  407 ILE
Chi-restraints excluded: chain D residue  421 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 47 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 105 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 51 optimal weight:    9.9990
   chunk 66 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0470
   overall best weight:    1.9882

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.5391

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= 0.198
  Angle     :  0.681  12.097  12366  Z= 0.345
  Chirality :  0.045   0.192   1359
  Planarity :  0.004   0.044   1580
  Dihedral  :  6.023  54.921   1211
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 17.88 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.27), residues: 1063
  helix:  1.58 (0.22), residues: 554
  sheet: -2.13 (0.39), residues: 151
  loop : -1.69 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 425 
 HIS   0.008   0.001   HIS A 336 
 PHE   0.026   0.001   PHE B 352 
 TYR   0.029   0.002   TYR C 446 
 ARG   0.004   0.000   ARG D 395 

********************** 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
  134 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 85
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8002 (t70)
REVERT: C  152 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7136 (tt)
REVERT: C  387 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.5867 (t80)
REVERT: B  169 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7783 (tt0)
REVERT: B  384 MET cc_start: 0.3825 (mtt) cc_final: 0.3227 (mtm)
REVERT: D  136 ARG cc_start: 0.8324 (ptt-90) cc_final: 0.8107 (mtm-85)
REVERT: D  169 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7709 (tt0)
REVERT: D  350 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6882 (tt)
  outliers start: 49
  outliers final: 41
  residues processed: 128
  average time/residue: 0.2036
  time to fit residues: 36.7154
Evaluate side-chains
  122 residues out of total 951 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 76
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
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  283 ILE
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  336 HIS
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  152 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  191 VAL
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 C residue  421 ASP
Chi-restraints excluded: chain B residue  169 GLU
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  269 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  383 LEU
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  298 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  307 THR
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  361 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
Chi-restraints excluded: chain D residue  407 ILE
Chi-restraints excluded: chain D residue  421 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 84 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   overall best weight:    4.5788

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.129819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.106393 restraints weight = 20038.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.108280 restraints weight = 13181.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.109484 restraints weight = 10128.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.5433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.118   9141  Z= 0.328
  Angle     :  0.732  11.354  12366  Z= 0.377
  Chirality :  0.047   0.198   1359
  Planarity :  0.005   0.050   1580
  Dihedral  :  6.130  54.086   1211
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 17.35 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.29 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.26), residues: 1063
  helix:  1.45 (0.22), residues: 554
  sheet: -2.19 (0.40), residues: 150
  loop : -1.72 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 425 
 HIS   0.010   0.001   HIS A 336 
 PHE   0.027   0.002   PHE A 282 
 TYR   0.028   0.003   TYR C 376 
 ARG   0.005   0.000   ARG B 453 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1820.83 seconds
wall clock time: 33 minutes 54.16 seconds (2034.16 seconds total)