Starting phenix.real_space_refine
on Wed Mar 12 04:31:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wny_37675/03_2025/8wny_37675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wny_37675/03_2025/8wny_37675.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wny_37675/03_2025/8wny_37675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wny_37675/03_2025/8wny_37675.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wny_37675/03_2025/8wny_37675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wny_37675/03_2025/8wny_37675.cif"
  }
  resolution = 3.5
  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=  -0.002 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4713      2.51       5
     N    1190      2.21       5
     O    1298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7233
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3645
          Classifications: {'peptide': 468}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445}
    Chain: "B"
      Number of atoms: 3525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3525
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 23, 'TRANS': 432}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
  Time building chain proxies: 4.64, per 1000 atoms: 0.64
  Number of scatterers: 7233
  At special positions: 0
  Unit cell: (105.12, 77.745, 122.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1298      8.00
     N    1190      7.00
     C    4713      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 154 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 366 "
      " NAG A 702 " - " ASN A 382 "
      " NAG A 703 " - " ASN A 425 "
      " NAG A 704 " - " ASN A 507 "
  Time building additional restraints: 1.94
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DSN B1001 "
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      63.4% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 167 through 175
    Processing helix  chain 'A' and resid 178 through 207
      removed outlier: 3.511A  pdb=" N   THR A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 236
      removed outlier: 3.693A  pdb=" N   PHE A 234 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.580A  pdb=" N   GLY A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 255
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 324 through 342
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 3.559A  pdb=" N   ASN A 353 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.780A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 394
      removed outlier: 4.219A  pdb=" N   ILE A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
    Processing helix  chain 'A' and resid 441 through 445
      removed outlier: 3.724A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 460
      removed outlier: 3.975A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 534
      removed outlier: 3.596A  pdb=" N   LEU A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 4.240A  pdb=" N   SER A 589 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 54
      removed outlier: 3.536A  pdb=" N   THR B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ILE B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE B  53 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 59
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.845A  pdb=" N   GLY B  64 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 100
      removed outlier: 3.765A  pdb=" N   VAL B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ALA B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 114
    Processing helix  chain 'B' and resid 115 through 129
    Processing helix  chain 'B' and resid 129 through 148
    Processing helix  chain 'B' and resid 157 through 179
      removed outlier: 3.547A  pdb=" N   SER B 179 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 211
    Processing helix  chain 'B' and resid 218 through 223
      removed outlier: 3.590A  pdb=" N   PHE B 223 " --> pdb=" O   PRO B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 242
    Processing helix  chain 'B' and resid 243 through 246
    Processing helix  chain 'B' and resid 247 through 258
      removed outlier: 3.518A  pdb=" N   PHE B 250 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LEU B 251 " --> pdb=" O   TRP B 248 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR B 255 " --> pdb=" O   ASN B 252 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   GLU B 256 " --> pdb=" O   TYR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 291
      removed outlier: 3.506A  pdb=" N   ASN B 264 " --> pdb=" O   ASP B 260 " (cutoff:3.500A)
      Proline residue:  B 266  - end of helix
      Proline residue:  B 274  - end of helix
    Processing helix  chain 'B' and resid 292 through 298
    Processing helix  chain 'B' and resid 301 through 311
    Processing helix  chain 'B' and resid 312 through 315
    Processing helix  chain 'B' and resid 316 through 347
      removed outlier: 3.933A  pdb=" N   VAL B 320 " --> pdb=" O   TRP B 316 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER B 325 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY B 332 " --> pdb=" O   GLY B 328 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER B 343 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 356
      removed outlier: 3.588A  pdb=" N   MET B 356 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 380
      removed outlier: 3.727A  pdb=" N   LEU B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 413
    Processing helix  chain 'B' and resid 424 through 445
    Processing helix  chain 'B' and resid 445 through 458
      removed outlier: 3.802A  pdb=" N   CYS B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 467
      removed outlier: 4.190A  pdb=" N   ILE B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 492
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403
      removed outlier: 3.548A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   VAL A 305 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 8.553A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   LEU A 260 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   LEU A 262 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 8.475A  pdb=" N   SER A 468 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 544
      removed outlier: 6.144A  pdb=" N   ARG A 626 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   LEU A 596 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 358

    425 hydrogen bonds defined for protein.
    1218 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: 2.24

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1128
        1.31 -     1.44: 2067
        1.44 -     1.56: 4174
        1.56 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 7419
  Sorted by residual:
  bond pdb=" CA  DSN B1001 "
       pdb=" CB  DSN B1001 "
    ideal  model  delta    sigma   weight residual
    1.530  1.462  0.068 2.00e-02 2.50e+03 1.15e+01
  bond pdb=" N   ILE A 367 "
       pdb=" CA  ILE A 367 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.56e+00
  bond pdb=" N   ASN A 366 "
       pdb=" CA  ASN A 366 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.029 1.17e-02 7.31e+03 6.30e+00
  bond pdb=" N   SER A 505 "
       pdb=" CA  SER A 505 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.23e-02 6.61e+03 6.22e+00
  bond pdb=" N   THR A 276 "
       pdb=" CA  THR A 276 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.57e+00
  ... (remaining 7414 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 9944
        2.20 -     4.39: 122
        4.39 -     6.59: 23
        6.59 -     8.78: 5
        8.78 -    10.98: 5
  Bond angle restraints: 10099
  Sorted by residual:
  angle pdb=" C   ASN A 507 "
        pdb=" CA  ASN A 507 "
        pdb=" CB  ASN A 507 "
      ideal   model   delta    sigma   weight residual
     109.16  120.14  -10.98 1.29e+00 6.01e-01 7.25e+01
  angle pdb=" N   ASN A 507 "
        pdb=" CA  ASN A 507 "
        pdb=" C   ASN A 507 "
      ideal   model   delta    sigma   weight residual
     114.75  105.39    9.36 1.26e+00 6.30e-01 5.52e+01
  angle pdb=" CA  ASN A 507 "
        pdb=" CB  ASN A 507 "
        pdb=" CG  ASN A 507 "
      ideal   model   delta    sigma   weight residual
     112.60  118.46   -5.86 1.00e+00 1.00e+00 3.44e+01
  angle pdb=" O   ASN A 507 "
        pdb=" C   ASN A 507 "
        pdb=" N   MET A 508 "
      ideal   model   delta    sigma   weight residual
     121.64  128.12   -6.48 1.23e+00 6.61e-01 2.78e+01
  angle pdb=" CA  ASN A 507 "
        pdb=" C   ASN A 507 "
        pdb=" N   MET A 508 "
      ideal   model   delta    sigma   weight residual
     119.80  113.05    6.75 1.34e+00 5.57e-01 2.54e+01
  ... (remaining 10094 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 3830
       17.60 -    35.20: 397
       35.20 -    52.79: 120
       52.79 -    70.39: 17
       70.39 -    87.99: 8
  Dihedral angle restraints: 4372
    sinusoidal: 1736
      harmonic: 2636
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 154 "
           pdb=" CB  CYS B 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.09   53.09     1      1.00e+01 1.00e-02 3.83e+01
  dihedral pdb=" CA  ASN A 366 "
           pdb=" CB  ASN A 366 "
           pdb=" CG  ASN A 366 "
           pdb=" OD1 ASN A 366 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -166.23  -73.77     2      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CG  ARG B 360 "
           pdb=" CD  ARG B 360 "
           pdb=" NE  ARG B 360 "
           pdb=" CZ  ARG B 360 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.36   44.64     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 4369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.269: 1163
       0.269 -    0.538: 1
       0.538 -    0.808: 0
       0.808 -    1.077: 1
       1.077 -    1.346: 1
  Chirality restraints: 1166
  Sorted by residual:
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 425 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.05   -1.35 2.00e-01 2.50e+01 4.53e+01
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.44   -0.96 2.00e-01 2.50e+01 2.33e+01
  chirality pdb=" C1  NAG A 704 "
            pdb=" ND2 ASN A 507 "
            pdb=" C2  NAG A 704 "
            pdb=" O5  NAG A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.17e+00
  ... (remaining 1163 not shown)

  Planarity restraints: 1262
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 425 "    0.158 2.00e-02 2.50e+03   1.82e-01 4.15e+02
        pdb=" CG  ASN A 425 "   -0.063 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 425 "   -0.023 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 425 "   -0.295 2.00e-02 2.50e+03
        pdb=" C1  NAG A 703 "    0.222 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 382 "    0.106 2.00e-02 2.50e+03   1.69e-01 3.56e+02
        pdb=" CG  ASN A 382 "   -0.054 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 382 "    0.055 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 382 "   -0.298 2.00e-02 2.50e+03
        pdb=" C1  NAG A 702 "    0.191 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 366 "   -0.091 2.00e-02 2.50e+03   1.01e-01 1.27e+02
        pdb=" CG  ASN A 366 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 366 "    0.017 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 366 "    0.162 2.00e-02 2.50e+03
        pdb=" C1  NAG A 701 "   -0.122 2.00e-02 2.50e+03
  ... (remaining 1259 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1203
        2.76 -     3.29: 6852
        3.29 -     3.83: 12011
        3.83 -     4.36: 13013
        4.36 -     4.90: 23510
  Nonbonded interactions: 56589
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 456 "
            pdb=" OG1 THR A 460 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   SER A 582 "
            pdb=" OG  SER A 582 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OD1 ASP A 493 "
            pdb=" OG  SER A 495 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   HIS A 266 "
            pdb=" OH  TYR A 313 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OH  TYR A 251 "
            pdb=" OE2 GLU A 472 "
     model   vdw
     2.263 3.040
  ... (remaining 56584 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.880
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   7419  Z= 0.232
  Angle     :  0.665  10.980  10099  Z= 0.365
  Chirality :  0.064   1.346   1166
  Planarity :  0.004   0.072   1258
  Dihedral  : 15.851  87.990   2681
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 21.29 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.28), residues: 920
  helix:  2.03 (0.23), residues: 508
  sheet:  0.93 (0.70), residues: 57
  loop : -0.94 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.014   0.001   PHE A 360 
 TYR   0.011   0.001   TYR B 385 
 ARG   0.002   0.000   ARG A 210 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 96
  average time/residue: 0.1762
  time to fit residues: 23.8456
Evaluate side-chains
  92 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 ASN
Chi-restraints excluded: chain A residue  507 ASN
Chi-restraints excluded: chain A residue  508 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 280 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.178543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.137843 restraints weight = 9245.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.136566 restraints weight = 8858.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.138035 restraints weight = 9110.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.0885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7419  Z= 0.233
  Angle     :  0.573   7.262  10099  Z= 0.289
  Chirality :  0.040   0.141   1166
  Planarity :  0.004   0.060   1258
  Dihedral  :  4.866  59.754   1079
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.97 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.28), residues: 920
  helix:  2.26 (0.23), residues: 515
  sheet:  0.78 (0.68), residues: 57
  loop : -0.82 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.014   0.001   PHE B 327 
 TYR   0.015   0.002   TYR B 385 
 ARG   0.004   0.000   ARG A 227 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8514 (m) cc_final: 0.8116 (t)
REVERT: A  452 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.6489 (mtt90)
REVERT: B  170 MET cc_start: 0.7796 (mtt) cc_final: 0.7524 (mtp)
REVERT: B  227 MET cc_start: 0.6236 (OUTLIER) cc_final: 0.5828 (ttp)
  outliers start: 24
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1682
  time to fit residues: 27.2158
Evaluate side-chains
  112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0980
   chunk 77 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    0.3980
   chunk 80 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.178162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137760 restraints weight = 9355.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136872 restraints weight = 9345.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.138653 restraints weight = 9107.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7419  Z= 0.214
  Angle     :  0.546   7.776  10099  Z= 0.273
  Chirality :  0.039   0.167   1166
  Planarity :  0.004   0.051   1258
  Dihedral  :  4.240  58.149   1075
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.13 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.28), residues: 920
  helix:  2.33 (0.23), residues: 521
  sheet:  0.75 (0.67), residues: 57
  loop : -0.74 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 434 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.014   0.001   TYR B 385 
 ARG   0.002   0.000   ARG A 227 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8524 (m) cc_final: 0.8141 (t)
REVERT: A  452 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.6464 (mtt90)
REVERT: B   60 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7799 (mt)
REVERT: B  170 MET cc_start: 0.7652 (mtt) cc_final: 0.7356 (mtp)
REVERT: B  227 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5850 (ttp)
REVERT: B  318 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6224 (ttp)
REVERT: B  335 PHE cc_start: 0.7078 (m-80) cc_final: 0.6836 (m-80)
  outliers start: 25
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1771
  time to fit residues: 29.6379
Evaluate side-chains
  110 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 264 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.176187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.137541 restraints weight = 9409.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.135488 restraints weight = 9639.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.137688 restraints weight = 9695.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7419  Z= 0.271
  Angle     :  0.584   8.884  10099  Z= 0.291
  Chirality :  0.040   0.162   1166
  Planarity :  0.004   0.048   1258
  Dihedral  :  4.241  53.122   1075
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 19.23 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.28), residues: 920
  helix:  2.22 (0.23), residues: 519
  sheet:  0.70 (0.68), residues: 57
  loop : -0.73 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 434 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.016   0.002   TYR B 385 
 ARG   0.007   0.000   ARG A 314 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 99
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8569 (m) cc_final: 0.8218 (t)
REVERT: A  340 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7363 (mm-40)
REVERT: A  452 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.6455 (mtt90)
REVERT: B   60 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7827 (mt)
REVERT: B  170 MET cc_start: 0.7732 (mtt) cc_final: 0.7431 (mtp)
REVERT: B  208 GLN cc_start: 0.7591 (mm-40) cc_final: 0.6848 (tt0)
REVERT: B  227 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5935 (ttp)
REVERT: B  318 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6648 (ttp)
  outliers start: 37
  outliers final: 26
  residues processed: 124
  average time/residue: 0.1812
  time to fit residues: 30.7509
Evaluate side-chains
  126 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 83 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.178762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.137930 restraints weight = 9151.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.137057 restraints weight = 8984.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.138306 restraints weight = 9504.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7419  Z= 0.175
  Angle     :  0.535   7.816  10099  Z= 0.264
  Chirality :  0.038   0.160   1166
  Planarity :  0.004   0.043   1258
  Dihedral  :  4.047  49.627   1075
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.55 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.28), residues: 920
  helix:  2.48 (0.23), residues: 513
  sheet:  0.87 (0.68), residues: 57
  loop : -0.72 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.012   0.001   TYR B 385 
 ARG   0.006   0.000   ARG A 314 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8540 (m) cc_final: 0.8117 (t)
REVERT: A  340 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7177 (mm-40)
REVERT: A  452 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.6425 (mtt90)
REVERT: B   60 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7826 (mt)
REVERT: B  208 GLN cc_start: 0.7641 (mm-40) cc_final: 0.6913 (tt0)
REVERT: B  227 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5848 (ttp)
REVERT: B  318 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6057 (ttp)
REVERT: B  481 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7709 (mt-10)
  outliers start: 23
  outliers final: 13
  residues processed: 116
  average time/residue: 0.1865
  time to fit residues: 29.6623
Evaluate side-chains
  112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.177411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.137987 restraints weight = 9200.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.135912 restraints weight = 9121.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137733 restraints weight = 9952.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7419  Z= 0.208
  Angle     :  0.541   7.502  10099  Z= 0.269
  Chirality :  0.039   0.164   1166
  Planarity :  0.004   0.041   1258
  Dihedral  :  3.992  44.301   1075
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.45 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.28), residues: 920
  helix:  2.44 (0.23), residues: 514
  sheet:  0.60 (0.63), residues: 65
  loop : -0.67 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.013   0.001   TYR B 385 
 ARG   0.002   0.000   ARG A 314 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A  290 ASP cc_start: 0.7823 (m-30) cc_final: 0.7455 (t0)
REVERT: A  310 THR cc_start: 0.8500 (m) cc_final: 0.8070 (t)
REVERT: A  340 GLN cc_start: 0.7866 (mm110) cc_final: 0.7454 (mm-40)
REVERT: A  452 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.6508 (mtt90)
REVERT: B   60 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7805 (mt)
REVERT: B  170 MET cc_start: 0.7621 (mtt) cc_final: 0.7315 (mtp)
REVERT: B  208 GLN cc_start: 0.7671 (mm-40) cc_final: 0.6968 (tt0)
REVERT: B  318 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6145 (ttp)
  outliers start: 28
  outliers final: 18
  residues processed: 117
  average time/residue: 0.1771
  time to fit residues: 28.9189
Evaluate side-chains
  113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    0.2980
   chunk 74 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0670
   chunk 20 optimal weight:    0.0570
   chunk 86 optimal weight:    0.0670
   chunk 76 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.2574

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.181575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.141686 restraints weight = 9122.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.140546 restraints weight = 8779.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.141850 restraints weight = 9054.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7419  Z= 0.144
  Angle     :  0.542  13.439  10099  Z= 0.263
  Chirality :  0.038   0.191   1166
  Planarity :  0.004   0.038   1258
  Dihedral  :  3.843  38.107   1075
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 22.97 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.28), residues: 920
  helix:  2.55 (0.23), residues: 514
  sheet:  0.93 (0.67), residues: 57
  loop : -0.68 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 316 
 HIS   0.001   0.000   HIS B 358 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.013   0.001   TYR B 390 
 ARG   0.001   0.000   ARG A 563 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A  267 LYS cc_start: 0.7612 (tppt) cc_final: 0.7391 (tttp)
REVERT: A  290 ASP cc_start: 0.7659 (m-30) cc_final: 0.7358 (t0)
REVERT: A  340 GLN cc_start: 0.7724 (mm110) cc_final: 0.7281 (mm-40)
REVERT: A  452 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.6463 (mtt90)
REVERT: A  534 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7592 (tp30)
REVERT: B   60 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7799 (mt)
REVERT: B  208 GLN cc_start: 0.7634 (mm-40) cc_final: 0.6907 (tt0)
REVERT: B  227 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5806 (ttp)
REVERT: B  318 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6184 (ttp)
  outliers start: 22
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1860
  time to fit residues: 29.0192
Evaluate side-chains
  109 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Chi-restraints excluded: chain B residue  488 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 33 optimal weight:    0.0770
   chunk 71 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 67 optimal weight:    0.3980
   chunk 87 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0770
   chunk 29 optimal weight:    0.0270
   overall best weight:    0.2554

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.182442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.142537 restraints weight = 9202.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.141355 restraints weight = 9357.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.143141 restraints weight = 8927.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7419  Z= 0.145
  Angle     :  0.536  11.155  10099  Z= 0.259
  Chirality :  0.038   0.161   1166
  Planarity :  0.003   0.037   1258
  Dihedral  :  3.529  17.700   1072
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.61 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.28), residues: 920
  helix:  2.61 (0.23), residues: 514
  sheet:  0.95 (0.68), residues: 57
  loop : -0.72 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 316 
 HIS   0.001   0.000   HIS A 539 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.013   0.001   TYR B 390 
 ARG   0.001   0.000   ARG A 314 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7703 (m-30) cc_final: 0.7397 (t0)
REVERT: A  340 GLN cc_start: 0.7809 (mm110) cc_final: 0.7347 (mm-40)
REVERT: A  452 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.6480 (mtt90)
REVERT: B   60 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7680 (mt)
REVERT: B  208 GLN cc_start: 0.7568 (mm-40) cc_final: 0.6842 (tt0)
REVERT: B  227 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5827 (ttp)
REVERT: B  318 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5783 (ttp)
  outliers start: 23
  outliers final: 14
  residues processed: 109
  average time/residue: 0.2038
  time to fit residues: 30.6912
Evaluate side-chains
  106 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  488 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0070
   chunk 30 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.179990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.140937 restraints weight = 9246.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.139942 restraints weight = 9791.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.141495 restraints weight = 9803.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7419  Z= 0.182
  Angle     :  0.547  10.285  10099  Z= 0.265
  Chirality :  0.039   0.164   1166
  Planarity :  0.004   0.037   1258
  Dihedral  :  3.538  16.599   1072
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 24.13 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.29), residues: 920
  helix:  2.60 (0.23), residues: 514
  sheet:  1.61 (0.70), residues: 51
  loop : -0.64 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.046   0.002   TYR A 251 
 ARG   0.002   0.000   ARG B 418 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7601 (m-30) cc_final: 0.7392 (t0)
REVERT: A  340 GLN cc_start: 0.7760 (mm110) cc_final: 0.7322 (mm-40)
REVERT: A  452 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.6454 (mtt90)
REVERT: B   60 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7792 (mt)
REVERT: B  208 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7043 (tt0)
REVERT: B  227 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5888 (ttp)
REVERT: B  318 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.5839 (ttp)
  outliers start: 21
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1795
  time to fit residues: 26.5727
Evaluate side-chains
  114 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Chi-restraints excluded: chain B residue  488 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0050
   chunk 47 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.179221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.138944 restraints weight = 9368.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.137501 restraints weight = 8754.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139150 restraints weight = 9662.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7419  Z= 0.195
  Angle     :  0.560   9.944  10099  Z= 0.273
  Chirality :  0.039   0.166   1166
  Planarity :  0.004   0.038   1258
  Dihedral  :  3.552  15.968   1072
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 24.26 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.28), residues: 920
  helix:  2.55 (0.23), residues: 514
  sheet:  1.62 (0.70), residues: 51
  loop : -0.64 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B 316 
 HIS   0.001   0.000   HIS B 361 
 PHE   0.013   0.001   PHE A 542 
 TYR   0.043   0.002   TYR A 251 
 ARG   0.002   0.000   ARG B 418 

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7726 (m-30) cc_final: 0.7475 (t0)
REVERT: A  340 GLN cc_start: 0.7810 (mm110) cc_final: 0.7363 (mm-40)
REVERT: A  452 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.6512 (mtt90)
REVERT: B   60 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7830 (mt)
REVERT: B  208 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7083 (tt0)
REVERT: B  227 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5903 (ttp)
REVERT: B  318 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.6222 (ttp)
  outliers start: 22
  outliers final: 18
  residues processed: 109
  average time/residue: 0.1825
  time to fit residues: 27.4837
Evaluate side-chains
  112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Chi-restraints excluded: chain B residue  488 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 28 optimal weight:    0.2980
   chunk 84 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 56 optimal weight:    0.5980
   chunk 62 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 488 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.176283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.136868 restraints weight = 9229.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.135115 restraints weight = 9299.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.136662 restraints weight = 10325.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7419  Z= 0.268
  Angle     :  0.601   9.131  10099  Z= 0.297
  Chirality :  0.041   0.171   1166
  Planarity :  0.004   0.038   1258
  Dihedral  :  3.746  15.150   1072
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.87 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.28), residues: 920
  helix:  2.37 (0.23), residues: 514
  sheet:  1.53 (0.69), residues: 51
  loop : -0.66 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B 316 
 HIS   0.002   0.001   HIS A 557 
 PHE   0.014   0.001   PHE A 545 
 TYR   0.038   0.002   TYR A 251 
 ARG   0.002   0.000   ARG A 212 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2858.13 seconds
wall clock time: 51 minutes 6.48 seconds (3066.48 seconds total)