Starting phenix.real_space_refine
on Wed Feb 12 04:49:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wny_37675/02_2025/8wny_37675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wny_37675/02_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_37675/02_2025/8wny_37675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wny_37675/02_2025/8wny_37675.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wny_37675/02_2025/8wny_37675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wny_37675/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.23, per 1000 atoms: 0.58
  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: 1.91
  Conformation dependent library (CDL) restraints added in 1.1 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: 2.37

  Time building geometry restraints manager: 2.16 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:             1.110
  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:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.750
  Find NCS groups from input model:        0.100
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.250
-------------------------------------------------------------------------------
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  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 96
  average time/residue: 0.1812
  time to fit residues: 24.1528
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  : 0.735 
-------------------------------------------------------------------------------
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 = 0.178538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.137896 restraints weight = 9245.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136715 restraints weight = 8861.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.138299 restraints weight = 9141.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
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  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8517 (m) cc_final: 0.8120 (t)
REVERT: A  452 ARG cc_start: 0.7822 (mtt-85) cc_final: 0.6488 (mtt90)
REVERT: B  170 MET cc_start: 0.7792 (mtt) cc_final: 0.7519 (mtp)
REVERT: B  227 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5828 (ttp)
  outliers start: 24
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1831
  time to fit residues: 29.5224
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  : 0.799 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.178683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.138443 restraints weight = 9348.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.137549 restraints weight = 9306.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.139402 restraints weight = 9081.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.1291

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= 0.204
  Angle     :  0.539   7.486  10099  Z= 0.270
  Chirality :  0.039   0.169   1166
  Planarity :  0.004   0.052   1258
  Dihedral  :  4.215  58.053   1075
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 20.39 %
    Favored  : 76.90 %
  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:  1.73 (0.28), residues: 920
  helix:  2.39 (0.23), residues: 516
  sheet:  0.77 (0.67), residues: 57
  loop : -0.74 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 316 
 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
  122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8489 (m) cc_final: 0.8118 (t)
REVERT: A  452 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.6484 (mtt90)
REVERT: B   60 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7787 (mt)
REVERT: B  170 MET cc_start: 0.7654 (mtt) cc_final: 0.7367 (mtp)
REVERT: B  227 MET cc_start: 0.6247 (OUTLIER) cc_final: 0.5830 (ttp)
REVERT: B  318 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6115 (ttp)
  outliers start: 21
  outliers final: 9
  residues processed: 116
  average time/residue: 0.1798
  time to fit residues: 28.6045
Evaluate side-chains
  108 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  227 MET
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:    0.0070
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.6400

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.179893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.138948 restraints weight = 9347.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.138111 restraints weight = 9091.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.139701 restraints weight = 9323.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7419  Z= 0.177
  Angle     :  0.532   9.775  10099  Z= 0.262
  Chirality :  0.038   0.160   1166
  Planarity :  0.004   0.045   1258
  Dihedral  :  4.034  54.399   1075
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 19.35 %
    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:  1.88 (0.28), residues: 920
  helix:  2.57 (0.23), residues: 510
  sheet:  0.87 (0.68), residues: 57
  loop : -0.73 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 316 
 HIS   0.002   0.001   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.012   0.001   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
  130 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 99
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8517 (m) cc_final: 0.8097 (t)
REVERT: A  452 ARG cc_start: 0.7880 (mtt-85) cc_final: 0.6445 (mtt90)
REVERT: B   60 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7806 (mt)
REVERT: B  208 GLN cc_start: 0.7609 (mm-40) cc_final: 0.6875 (tt0)
REVERT: B  227 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5830 (ttp)
  outliers start: 31
  outliers final: 19
  residues processed: 121
  average time/residue: 0.1845
  time to fit residues: 30.9433
Evaluate side-chains
  119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
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  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  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  625 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  106 ASP
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  297 LEU
Chi-restraints excluded: chain B residue  438 LEU
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:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0270
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0270
   chunk 83 optimal weight:    7.9990
   overall best weight:    0.4896

-------------------------------------------------------------------------------
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**
A 365 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.180712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.140408 restraints weight = 9119.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.139307 restraints weight = 8953.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.141015 restraints weight = 9015.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7419  Z= 0.161
  Angle     :  0.531  10.248  10099  Z= 0.259
  Chirality :  0.038   0.248   1166
  Planarity :  0.004   0.042   1258
  Dihedral  :  3.924  52.029   1075
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 20.26 %
    Favored  : 76.39 %
  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:  1.90 (0.28), residues: 920
  helix:  2.55 (0.23), residues: 516
  sheet:  0.95 (0.68), residues: 57
  loop : -0.73 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 316 
 HIS   0.002   0.000   HIS B 358 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.011   0.001   TYR B 390 
 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
  128 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7759 (m-30) cc_final: 0.7396 (t0)
REVERT: A  310 THR cc_start: 0.8464 (m) cc_final: 0.8047 (t)
REVERT: A  452 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.6422 (mtt90)
REVERT: B   60 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7791 (mt)
REVERT: B  208 GLN cc_start: 0.7534 (mm-40) cc_final: 0.6800 (tt0)
REVERT: B  227 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5748 (ttp)
  outliers start: 26
  outliers final: 19
  residues processed: 120
  average time/residue: 0.2046
  time to fit residues: 33.9612
Evaluate side-chains
  119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
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  424 LEU
Chi-restraints excluded: chain A residue  508 MET
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   43 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  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  297 LEU
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:    0.8980
   chunk 63 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 86 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0370
   overall best weight:    0.6860

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.179239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.140524 restraints weight = 9188.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.138606 restraints weight = 8845.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.140637 restraints weight = 8762.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7419  Z= 0.183
  Angle     :  0.527   8.134  10099  Z= 0.259
  Chirality :  0.038   0.163   1166
  Planarity :  0.004   0.040   1258
  Dihedral  :  3.855  46.477   1075
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.90 %
    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:  1.95 (0.28), residues: 920
  helix:  2.55 (0.23), residues: 515
  sheet:  0.95 (0.68), residues: 57
  loop : -0.63 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 316 
 HIS   0.002   0.001   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.012   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
  124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7773 (m-30) cc_final: 0.7433 (t0)
REVERT: A  340 GLN cc_start: 0.7004 (mm-40) cc_final: 0.6769 (mm-40)
REVERT: A  452 ARG cc_start: 0.7816 (mtt-85) cc_final: 0.6432 (mtt90)
REVERT: B   60 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7815 (mt)
REVERT: B  208 GLN cc_start: 0.7643 (mm-40) cc_final: 0.6906 (tt0)
REVERT: B  316 TRP cc_start: 0.8192 (p-90) cc_final: 0.7961 (p-90)
  outliers start: 28
  outliers final: 22
  residues processed: 119
  average time/residue: 0.1779
  time to fit residues: 29.4014
Evaluate side-chains
  118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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  424 LEU
Chi-restraints excluded: chain A residue  508 MET
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 A residue  625 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  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  438 LEU
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:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 69 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0670
   chunk 20 optimal weight:    6.9990
   chunk 86 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 16 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.3518

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.181548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.141761 restraints weight = 9137.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.140843 restraints weight = 8863.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.142345 restraints weight = 8955.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7419  Z= 0.150
  Angle     :  0.532  12.237  10099  Z= 0.258
  Chirality :  0.037   0.164   1166
  Planarity :  0.003   0.037   1258
  Dihedral  :  3.761  40.610   1075
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.19 %
    Favored  : 74.84 %
  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:  1.98 (0.28), residues: 920
  helix:  2.56 (0.23), residues: 520
  sheet:  1.06 (0.68), residues: 57
  loop : -0.67 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A 539 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.012   0.001   TYR B 390 
 ARG   0.002   0.000   ARG B 418 

*********************** 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
  118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A  267 LYS cc_start: 0.7670 (tppt) cc_final: 0.7448 (tttp)
REVERT: A  290 ASP cc_start: 0.7714 (m-30) cc_final: 0.7395 (t0)
REVERT: A  452 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.6455 (mtt90)
REVERT: B   60 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7634 (mt)
REVERT: B  208 GLN cc_start: 0.7558 (mm-40) cc_final: 0.6732 (tt0)
REVERT: B  227 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5835 (ttp)
  outliers start: 23
  outliers final: 18
  residues processed: 112
  average time/residue: 0.1881
  time to fit residues: 29.2982
Evaluate side-chains
  110 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
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  424 LEU
Chi-restraints excluded: chain A residue  508 MET
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 A residue  625 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  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 67 optimal weight:    0.4980
   chunk 87 optimal weight:    0.5980
   chunk 42 optimal weight:    5.9990
   chunk 72 optimal weight:    0.6980
   chunk 77 optimal weight:    0.2980
   chunk 66 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.180284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.139795 restraints weight = 9227.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.138802 restraints weight = 9263.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.140233 restraints weight = 9172.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7419  Z= 0.175
  Angle     :  0.552  11.320  10099  Z= 0.267
  Chirality :  0.038   0.164   1166
  Planarity :  0.003   0.036   1258
  Dihedral  :  3.688  35.497   1075
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.58 %
    Favored  : 74.32 %
  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:  2.05 (0.28), residues: 920
  helix:  2.57 (0.23), residues: 520
  sheet:  1.77 (0.70), residues: 51
  loop : -0.62 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.011   0.001   TYR B 385 
 ARG   0.002   0.000   ARG B 418 

*********************** 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: 24
    poor density    : 91
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7691 (m-30) cc_final: 0.7424 (t0)
REVERT: A  452 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.6473 (mtt90)
REVERT: B   60 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7713 (mt)
REVERT: B  208 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7024 (tt0)
REVERT: B  227 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5948 (ttp)
  outliers start: 24
  outliers final: 20
  residues processed: 108
  average time/residue: 0.1798
  time to fit residues: 27.0689
Evaluate side-chains
  111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
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  424 LEU
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 A residue  625 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  227 MET
Chi-restraints excluded: chain B residue  297 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0020
   chunk 30 optimal weight:    0.0040
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.4600

-------------------------------------------------------------------------------
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 = 0.4035 r_free = 0.4035 target = 0.180663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.140438 restraints weight = 9223.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.139590 restraints weight = 9333.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.141301 restraints weight = 8900.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7419  Z= 0.161
  Angle     :  0.555  10.666  10099  Z= 0.266
  Chirality :  0.038   0.172   1166
  Planarity :  0.004   0.036   1258
  Dihedral  :  3.495  16.007   1072
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.45 %
    Favored  : 74.58 %
  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:  2.00 (0.28), residues: 920
  helix:  2.52 (0.23), residues: 520
  sheet:  1.78 (0.70), residues: 51
  loop : -0.65 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.015   0.001   PHE B 440 
 TYR   0.015   0.001   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
  113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7655 (m-30) cc_final: 0.7409 (t0)
REVERT: A  452 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.6472 (mtt90)
REVERT: B   60 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7679 (mt)
REVERT: B  208 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7042 (tt0)
REVERT: B  227 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5922 (ttp)
  outliers start: 23
  outliers final: 19
  residues processed: 107
  average time/residue: 0.1816
  time to fit residues: 27.0182
Evaluate side-chains
  111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
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  424 LEU
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 A residue  625 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  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
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:    0.9980
   chunk 47 optimal weight:    0.0870
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 62 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.179504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.139036 restraints weight = 9349.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137333 restraints weight = 8880.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.139065 restraints weight = 9917.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7419  Z= 0.189
  Angle     :  0.566   9.448  10099  Z= 0.274
  Chirality :  0.039   0.186   1166
  Planarity :  0.004   0.035   1258
  Dihedral  :  3.530  15.053   1072
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.84 %
    Favored  : 74.06 %
  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:  2.01 (0.29), residues: 920
  helix:  2.56 (0.23), residues: 514
  sheet:  1.78 (0.70), residues: 51
  loop : -0.63 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.013   0.001   PHE A 542 
 TYR   0.012   0.001   TYR B 385 
 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
  116 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7733 (m-30) cc_final: 0.7490 (t0)
REVERT: A  452 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.6508 (mtt90)
REVERT: B   60 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7816 (mt)
REVERT: B  208 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7024 (tt0)
REVERT: B  227 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.6040 (ttp)
  outliers start: 24
  outliers final: 20
  residues processed: 110
  average time/residue: 0.1833
  time to fit residues: 27.9222
Evaluate side-chains
  112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
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  424 LEU
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 A residue  625 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  227 MET
Chi-restraints excluded: chain B residue  297 LEU
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:    0.0470
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 ** 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 = 0.4023 r_free = 0.4023 target = 0.179499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.140339 restraints weight = 9178.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.139716 restraints weight = 9465.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.140829 restraints weight = 10043.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7419  Z= 0.178
  Angle     :  0.565   9.429  10099  Z= 0.271
  Chirality :  0.039   0.171   1166
  Planarity :  0.004   0.035   1258
  Dihedral  :  3.521  14.987   1072
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.71 %
    Favored  : 74.32 %
  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:  2.02 (0.28), residues: 920
  helix:  2.56 (0.23), residues: 514
  sheet:  1.81 (0.70), residues: 51
  loop : -0.63 (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   0.013   0.001   PHE A 542 
 TYR   0.049   0.002   TYR A 251 
 ARG   0.002   0.000   ARG B 418 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2219.62 seconds
wall clock time: 40 minutes 40.39 seconds (2440.39 seconds total)