Starting phenix.real_space_refine
on Sun May 11 04:14:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x0w_37983/05_2025/8x0w_37983.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x0w_37983/05_2025/8x0w_37983.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x0w_37983/05_2025/8x0w_37983.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x0w_37983/05_2025/8x0w_37983.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x0w_37983/05_2025/8x0w_37983.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x0w_37983/05_2025/8x0w_37983.cif"
  }
  resolution = 3.1
  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=  -0.001 sd=   0.033
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      27      5.16       5
     C    4813      2.51       5
     N    1189      2.21       5
     O    1339      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7368
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3661
          Classifications: {'peptide': 470}
          Link IDs: {'PTRANS': 22, 'TRANS': 447}
    Chain: "B"
      Number of atoms: 3586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3586
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 24, 'TRANS': 439}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 4.79, per 1000 atoms: 0.65
  Number of scatterers: 7368
  At special positions: 0
  Unit cell: (93.195, 78.66, 135.09, 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      27     16.00
     O    1339      8.00
     N    1189      7.00
     C    4813      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 164 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 2.25
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1722

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 4 sheets defined
      60.6% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
    Processing helix  chain 'A' and resid 176 through 207
      removed outlier: 3.655A  pdb=" N   VAL A 180 " --> pdb=" O   SER A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
    Processing helix  chain 'A' and resid 230 through 236
      removed outlier: 3.884A  pdb=" N   PHE A 234 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.605A  pdb=" N   GLY A 244 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 256
    Processing helix  chain 'A' and resid 287 through 302
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 3.718A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 354
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 4.250A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 3.610A  pdb=" N   THR A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
    Processing helix  chain 'A' and resid 450 through 459
    Processing helix  chain 'A' and resid 505 through 508
      removed outlier: 3.713A  pdb=" N   MET A 508 " --> pdb=" O   SER A 505 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 505 through 508'
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 519 through 534
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'A' and resid 585 through 589
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 80
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 81 through 110
    Processing helix  chain 'B' and resid 117 through 124
    Processing helix  chain 'B' and resid 126 through 137
      removed outlier: 3.878A  pdb=" N   ILE B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 157
      removed outlier: 3.782A  pdb=" N   SER B 144 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   TYR B 146 " --> pdb=" O   PRO B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.542A  pdb=" N   ALA B 171 " --> pdb=" O   PRO B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 221
    Processing helix  chain 'B' and resid 239 through 254
      removed outlier: 3.534A  pdb=" N   ILE B 243 " --> pdb=" O   ASP B 239 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 262
    Processing helix  chain 'B' and resid 269 through 298
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
      removed outlier: 3.599A  pdb=" N   PHE B 297 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR B 298 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 308
    Processing helix  chain 'B' and resid 310 through 321
    Processing helix  chain 'B' and resid 325 through 355
      removed outlier: 3.599A  pdb=" N   VAL B 329 " --> pdb=" O   TRP B 325 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE B 344 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR B 345 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
    Processing helix  chain 'B' and resid 387 through 389
      No H-bonds generated for 'chain 'B' and resid 387 through 389'
    Processing helix  chain 'B' and resid 393 through 398
      removed outlier: 4.167A  pdb=" N   ASN B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 422
      removed outlier: 3.748A  pdb=" N   VAL B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 453
      removed outlier: 3.811A  pdb=" N   VAL B 449 " --> pdb=" O   PHE B 445 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   SER B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 467
      removed outlier: 4.891A  pdb=" N   GLY B 461 " --> pdb=" O   GLU B 457 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ILE B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 4.651A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 3.838A  pdb=" N   LEU B 486 " --> pdb=" O   PRO B 482 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402
      removed outlier: 6.452A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 8.831A  pdb=" N   ARG A 349 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   TYR A 226 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   LEU A 225 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 8.670A  pdb=" N   SER A 468 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 543 through 544
      removed outlier: 3.569A  pdb=" N   HIS A 543 " --> pdb=" O   ILE A 555 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE A 627 " --> pdb=" O   ARG A 563 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A 567 " --> pdb=" O   LEU A 623 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 594

    393 hydrogen bonds defined for protein.
    1134 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: 2.05

  Time building geometry restraints manager: 2.45 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2279
        1.34 -     1.46: 1787
        1.46 -     1.58: 3442
        1.58 -     1.70: 0
        1.70 -     1.81: 40
  Bond restraints: 7548
  Sorted by residual:
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.481 -0.075 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.475 -0.069 2.00e-02 2.50e+03 1.18e+01
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.473 -0.067 2.00e-02 2.50e+03 1.12e+01
  bond pdb=" C   LEU A 584 "
       pdb=" N   PRO A 585 "
    ideal  model  delta    sigma   weight residual
    1.333  1.354 -0.021 1.01e-02 9.80e+03 4.16e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.54e+00
  ... (remaining 7543 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 10094
        1.95 -     3.90: 147
        3.90 -     5.85: 30
        5.85 -     7.80: 6
        7.80 -     9.75: 2
  Bond angle restraints: 10279
  Sorted by residual:
  angle pdb=" CA  ARG A 614 "
        pdb=" CB  ARG A 614 "
        pdb=" CG  ARG A 614 "
      ideal   model   delta    sigma   weight residual
     114.10  120.35   -6.25 2.00e+00 2.50e-01 9.75e+00
  angle pdb=" CA  LEU B 137 "
        pdb=" CB  LEU B 137 "
        pdb=" CG  LEU B 137 "
      ideal   model   delta    sigma   weight residual
     116.30  126.05   -9.75 3.50e+00 8.16e-02 7.76e+00
  angle pdb=" CA  LEU B 466 "
        pdb=" CB  LEU B 466 "
        pdb=" CG  LEU B 466 "
      ideal   model   delta    sigma   weight residual
     116.30  126.00   -9.70 3.50e+00 8.16e-02 7.69e+00
  angle pdb=" C   ILE B  59 "
        pdb=" CA  ILE B  59 "
        pdb=" CB  ILE B  59 "
      ideal   model   delta    sigma   weight residual
     111.97  108.47    3.50 1.28e+00 6.10e-01 7.47e+00
  angle pdb=" C   SER A 321 "
        pdb=" CA  SER A 321 "
        pdb=" CB  SER A 321 "
      ideal   model   delta    sigma   weight residual
     110.42  115.75   -5.33 1.99e+00 2.53e-01 7.18e+00
  ... (remaining 10274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.02: 4136
       25.02 -    50.04: 298
       50.04 -    75.06: 24
       75.06 -   100.08: 40
      100.08 -   125.11: 29
  Dihedral angle restraints: 4527
    sinusoidal: 1848
      harmonic: 2679
  Sorted by residual:
  dihedral pdb=" C2  NAG F   1 "
           pdb=" C1  NAG F   1 "
           pdb=" O5  NAG F   1 "
           pdb=" C5  NAG F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   62.15 -125.11     1      3.00e+01 1.11e-03 1.68e+01
  dihedral pdb=" C2  NAG D   2 "
           pdb=" C1  NAG D   2 "
           pdb=" O5  NAG D   2 "
           pdb=" C5  NAG D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   60.92 -123.88     1      3.00e+01 1.11e-03 1.66e+01
  dihedral pdb=" N2  NAG C   1 "
           pdb=" C1  NAG C   1 "
           pdb=" C2  NAG C   1 "
           pdb=" O5  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -60.85 -117.34     1      3.00e+01 1.11e-03 1.56e+01
  ... (remaining 4524 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1112
       0.068 -    0.136: 99
       0.136 -    0.204: 3
       0.204 -    0.272: 1
       0.272 -    0.340: 1
  Chirality restraints: 1216
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 425 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CG  LEU B 444 "
            pdb=" CB  LEU B 444 "
            pdb=" CD1 LEU B 444 "
            pdb=" CD2 LEU B 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.37e-01
  ... (remaining 1213 not shown)

  Planarity restraints: 1276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  71 "   -0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO B  72 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B  72 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  72 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 503 "   -0.023 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO B 504 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 504 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 504 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 481 "   -0.023 5.00e-02 4.00e+02   3.47e-02 1.93e+00
        pdb=" N   PRO B 482 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 482 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 482 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1273 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1345
        2.76 -     3.30: 7398
        3.30 -     3.83: 12726
        3.83 -     4.37: 13445
        4.37 -     4.90: 23495
  Nonbonded interactions: 58409
  Sorted by model distance:
  nonbonded pdb=" O   GLY B  67 "
            pdb=" OG1 THR B  71 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   ILE B 139 "
            pdb=" OG  SER B 143 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" OH  TYR A 469 "
            pdb=" O   PRO A 488 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   ASP A 272 "
            pdb=" OG1 THR A 276 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OD1 ASP A 271 "
            pdb=" ND2 ASN A 312 "
     model   vdw
     2.327 3.120
  ... (remaining 58404 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     20.670
  Find NCS groups from input model:        0.120
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
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   0.075   7557  Z= 0.155
  Angle     :  0.624  10.879  10305  Z= 0.297
  Chirality :  0.040   0.340   1216
  Planarity :  0.003   0.050   1272
  Dihedral  : 21.595 125.106   2802
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 13.69 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.29), residues: 930
  helix:  2.32 (0.24), residues: 495
  sheet: -0.35 (0.63), residues: 63
  loop : -0.81 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.015   0.001   PHE B 233 
 TYR   0.005   0.001   TYR B 289 
 ARG   0.001   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01042 (    4)
  link_NAG-ASN         : angle       4.15866 (   12)
  link_BETA1-4         : bond        0.00607 (    4)
  link_BETA1-4         : angle       1.73521 (   12)
  hydrogen bonds       : bond        0.13941 (  393)
  hydrogen bonds       : angle       5.18194 ( 1134)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       1.08288 (    2)
  covalent geometry    : bond        0.00304 ( 7548)
  covalent geometry    : angle       0.60492 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9126 (mmp) cc_final: 0.8164 (ppp)
  outliers start: 4
  outliers final: 2
  residues processed: 57
  average time/residue: 0.1628
  time to fit residues: 14.0346
Evaluate side-chains
  50 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain B residue  233 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    0.0060
   chunk 70 optimal weight:    0.0170
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 47 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 44 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.6436

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

Flipped N/Q/H residues before XYZ refinement:
A 221 HIS
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.068885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.047772 restraints weight = 28021.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 4.75
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.0730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7557  Z= 0.110
  Angle     :  0.645  11.461  10305  Z= 0.292
  Chirality :  0.043   0.318   1216
  Planarity :  0.004   0.052   1272
  Dihedral  : 20.620 116.664   1162
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.69 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.29), residues: 930
  helix:  2.47 (0.24), residues: 499
  sheet: -0.45 (0.60), residues: 63
  loop : -0.78 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 417 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.013   0.001   PHE A 627 
 TYR   0.017   0.001   TYR A 423 
 ARG   0.002   0.000   ARG A 452 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00926 (    4)
  link_NAG-ASN         : angle       4.06586 (   12)
  link_BETA1-4         : bond        0.00464 (    4)
  link_BETA1-4         : angle       3.59714 (   12)
  hydrogen bonds       : bond        0.03552 (  393)
  hydrogen bonds       : angle       4.18272 ( 1134)
  SS BOND              : bond        0.00690 (    1)
  SS BOND              : angle       3.89292 (    2)
  covalent geometry    : bond        0.00229 ( 7548)
  covalent geometry    : angle       0.61572 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8904 (tt)
REVERT: A  423 TYR cc_start: 0.9598 (t80) cc_final: 0.9374 (t80)
REVERT: A  485 MET cc_start: 0.9070 (mmp) cc_final: 0.8477 (ppp)
REVERT: B  365 MET cc_start: 0.9131 (tpp) cc_final: 0.8269 (mmt)
REVERT: B  466 LEU cc_start: 0.9322 (tt) cc_final: 0.9113 (mm)
  outliers start: 13
  outliers final: 4
  residues processed: 65
  average time/residue: 0.1512
  time to fit residues: 14.9495
Evaluate side-chains
  52 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  446 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 69 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** 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 = 0.3344 r_free = 0.3344 target = 0.064941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.043323 restraints weight = 28918.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.2729 rms_B_bonded: 4.73
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
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      :  0.006   0.043   7557  Z= 0.245
  Angle     :  0.730  11.265  10305  Z= 0.338
  Chirality :  0.045   0.334   1216
  Planarity :  0.004   0.047   1272
  Dihedral  : 18.152 116.731   1160
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.83 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.29), residues: 930
  helix:  2.47 (0.24), residues: 494
  sheet: -0.70 (0.60), residues: 63
  loop : -0.85 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  89 
 HIS   0.006   0.002   HIS B 367 
 PHE   0.017   0.002   PHE A 524 
 TYR   0.014   0.002   TYR A 423 
 ARG   0.005   0.001   ARG A 248 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00928 (    4)
  link_NAG-ASN         : angle       3.98099 (   12)
  link_BETA1-4         : bond        0.00983 (    4)
  link_BETA1-4         : angle       3.94401 (   12)
  hydrogen bonds       : bond        0.04884 (  393)
  hydrogen bonds       : angle       4.43211 ( 1134)
  SS BOND              : bond        0.00498 (    1)
  SS BOND              : angle       3.26993 (    2)
  covalent geometry    : bond        0.00559 ( 7548)
  covalent geometry    : angle       0.70433 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 43
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.9454 (pm20) cc_final: 0.9253 (pm20)
REVERT: A  485 MET cc_start: 0.9155 (mmt) cc_final: 0.8200 (ppp)
  outliers start: 20
  outliers final: 10
  residues processed: 61
  average time/residue: 0.1459
  time to fit residues: 13.7253
Evaluate side-chains
  51 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  386 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0370
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    1.6064

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** 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 = 0.3372 r_free = 0.3372 target = 0.066291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.044921 restraints weight = 28533.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 4.76
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7557  Z= 0.128
  Angle     :  0.672  11.233  10305  Z= 0.295
  Chirality :  0.042   0.319   1216
  Planarity :  0.003   0.050   1272
  Dihedral  : 16.215 117.383   1158
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.22 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.29), residues: 930
  helix:  2.60 (0.24), residues: 495
  sheet: -0.76 (0.60), residues: 63
  loop : -0.81 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 405 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.014   0.001   PHE B 233 
 TYR   0.018   0.001   TYR A 251 
 ARG   0.002   0.000   ARG B 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00976 (    4)
  link_NAG-ASN         : angle       4.02396 (   12)
  link_BETA1-4         : bond        0.00995 (    4)
  link_BETA1-4         : angle       4.49758 (   12)
  hydrogen bonds       : bond        0.03906 (  393)
  hydrogen bonds       : angle       4.16278 ( 1134)
  SS BOND              : bond        0.00486 (    1)
  SS BOND              : angle       3.13438 (    2)
  covalent geometry    : bond        0.00284 ( 7548)
  covalent geometry    : angle       0.63933 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9157 (mmt) cc_final: 0.8293 (ppp)
REVERT: B  136 GLU cc_start: 0.9324 (tp30) cc_final: 0.9111 (tp30)
  outliers start: 15
  outliers final: 11
  residues processed: 58
  average time/residue: 0.1448
  time to fit residues: 12.9995
Evaluate side-chains
  52 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  487 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0020
   chunk 70 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0040
   chunk 84 optimal weight:    1.9990
   chunk 35 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.3804

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.066409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.045044 restraints weight = 28292.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 4.70
r_work: 0.2632 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7557  Z= 0.123
  Angle     :  0.644  11.092  10305  Z= 0.287
  Chirality :  0.041   0.311   1216
  Planarity :  0.003   0.052   1272
  Dihedral  : 14.851 117.355   1158
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.73 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.29), residues: 930
  helix:  2.64 (0.24), residues: 493
  sheet: -0.74 (0.61), residues: 63
  loop : -0.86 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 405 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.024   0.001   PHE B 403 
 TYR   0.019   0.001   TYR A 251 
 ARG   0.002   0.000   ARG B 348 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00934 (    4)
  link_NAG-ASN         : angle       4.15998 (   12)
  link_BETA1-4         : bond        0.00815 (    4)
  link_BETA1-4         : angle       4.61711 (   12)
  hydrogen bonds       : bond        0.03698 (  393)
  hydrogen bonds       : angle       4.07409 ( 1134)
  SS BOND              : bond        0.00464 (    1)
  SS BOND              : angle       2.88186 (    2)
  covalent geometry    : bond        0.00275 ( 7548)
  covalent geometry    : angle       0.60758 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9166 (mmt) cc_final: 0.8546 (ppp)
REVERT: B  296 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8370 (t80)
REVERT: B  365 MET cc_start: 0.9559 (tpp) cc_final: 0.8685 (tpp)
  outliers start: 17
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1462
  time to fit residues: 12.8734
Evaluate side-chains
  51 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  296 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.067090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.045850 restraints weight = 28441.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 4.71
r_work: 0.2649 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7557  Z= 0.112
  Angle     :  0.641  11.084  10305  Z= 0.285
  Chirality :  0.041   0.315   1216
  Planarity :  0.003   0.052   1272
  Dihedral  : 14.083 117.026   1158
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.36 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.29), residues: 930
  helix:  2.62 (0.24), residues: 493
  sheet: -0.69 (0.61), residues: 63
  loop : -0.82 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 405 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.027   0.001   PHE B 403 
 TYR   0.021   0.001   TYR A 251 
 ARG   0.002   0.000   ARG B 348 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00944 (    4)
  link_NAG-ASN         : angle       4.14191 (   12)
  link_BETA1-4         : bond        0.00791 (    4)
  link_BETA1-4         : angle       4.67048 (   12)
  hydrogen bonds       : bond        0.03461 (  393)
  hydrogen bonds       : angle       4.03260 ( 1134)
  SS BOND              : bond        0.00472 (    1)
  SS BOND              : angle       2.73996 (    2)
  covalent geometry    : bond        0.00246 ( 7548)
  covalent geometry    : angle       0.60367 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9173 (mmt) cc_final: 0.8278 (ppp)
REVERT: B  296 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8406 (t80)
REVERT: B  365 MET cc_start: 0.9564 (tpp) cc_final: 0.9116 (tpp)
  outliers start: 17
  outliers final: 11
  residues processed: 59
  average time/residue: 0.1520
  time to fit residues: 13.8057
Evaluate side-chains
  54 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  444 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0370
   chunk 10 optimal weight:    0.0570
   chunk 87 optimal weight:    0.5980
   chunk 84 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   overall best weight:    0.3976

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.046857 restraints weight = 28116.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 4.72
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7557  Z= 0.103
  Angle     :  0.653  16.226  10305  Z= 0.285
  Chirality :  0.041   0.313   1216
  Planarity :  0.003   0.054   1272
  Dihedral  : 13.473 116.771   1158
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.25 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.29), residues: 930
  helix:  2.56 (0.24), residues: 493
  sheet: -0.65 (0.61), residues: 63
  loop : -0.82 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.025   0.001   PHE B 403 
 TYR   0.014   0.001   TYR A 251 
 ARG   0.002   0.000   ARG B 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00971 (    4)
  link_NAG-ASN         : angle       4.14844 (   12)
  link_BETA1-4         : bond        0.00783 (    4)
  link_BETA1-4         : angle       4.67743 (   12)
  hydrogen bonds       : bond        0.03077 (  393)
  hydrogen bonds       : angle       3.97292 ( 1134)
  SS BOND              : bond        0.00469 (    1)
  SS BOND              : angle       2.60891 (    2)
  covalent geometry    : bond        0.00212 ( 7548)
  covalent geometry    : angle       0.61677 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9152 (mmt) cc_final: 0.8284 (ppp)
REVERT: B  296 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8502 (t80)
REVERT: B  365 MET cc_start: 0.9434 (tpp) cc_final: 0.9219 (tpp)
  outliers start: 16
  outliers final: 8
  residues processed: 67
  average time/residue: 0.1412
  time to fit residues: 14.5175
Evaluate side-chains
  55 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  446 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 12 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   chunk 46 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.067717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.046470 restraints weight = 28239.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 4.78
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7557  Z= 0.108
  Angle     :  0.648  13.373  10305  Z= 0.285
  Chirality :  0.041   0.316   1216
  Planarity :  0.003   0.053   1272
  Dihedral  : 13.078 116.774   1158
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 19.52 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.29), residues: 930
  helix:  2.59 (0.24), residues: 493
  sheet: -0.64 (0.61), residues: 63
  loop : -0.83 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 220 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.022   0.001   PHE B 403 
 TYR   0.023   0.001   TYR A 251 
 ARG   0.001   0.000   ARG B 348 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00956 (    4)
  link_NAG-ASN         : angle       4.14808 (   12)
  link_BETA1-4         : bond        0.00784 (    4)
  link_BETA1-4         : angle       4.66933 (   12)
  hydrogen bonds       : bond        0.03120 (  393)
  hydrogen bonds       : angle       3.94739 ( 1134)
  SS BOND              : bond        0.00445 (    1)
  SS BOND              : angle       2.53844 (    2)
  covalent geometry    : bond        0.00239 ( 7548)
  covalent geometry    : angle       0.61209 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9165 (mmt) cc_final: 0.8593 (ppp)
REVERT: B  296 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8522 (t80)
REVERT: B  365 MET cc_start: 0.9580 (tpp) cc_final: 0.9188 (mtp)
  outliers start: 13
  outliers final: 10
  residues processed: 55
  average time/residue: 0.1486
  time to fit residues: 12.7207
Evaluate side-chains
  54 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  466 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 25 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 79 optimal weight:    0.2980
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.068118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.046954 restraints weight = 28381.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 4.78
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7557  Z= 0.105
  Angle     :  0.651  13.073  10305  Z= 0.286
  Chirality :  0.041   0.317   1216
  Planarity :  0.003   0.053   1272
  Dihedral  : 12.635 116.755   1158
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 19.90 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.29), residues: 930
  helix:  2.62 (0.24), residues: 493
  sheet: -0.59 (0.61), residues: 63
  loop : -0.85 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 220 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.024   0.001   PHE B 403 
 TYR   0.020   0.001   TYR A 251 
 ARG   0.003   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00974 (    4)
  link_NAG-ASN         : angle       4.15573 (   12)
  link_BETA1-4         : bond        0.00821 (    4)
  link_BETA1-4         : angle       4.68953 (   12)
  hydrogen bonds       : bond        0.03012 (  393)
  hydrogen bonds       : angle       3.91396 ( 1134)
  SS BOND              : bond        0.00424 (    1)
  SS BOND              : angle       2.49327 (    2)
  covalent geometry    : bond        0.00229 ( 7548)
  covalent geometry    : angle       0.61460 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9175 (mmt) cc_final: 0.8255 (ppp)
REVERT: B  296 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8582 (t80)
REVERT: B  365 MET cc_start: 0.9585 (tpp) cc_final: 0.9210 (mtp)
  outliers start: 11
  outliers final: 9
  residues processed: 53
  average time/residue: 0.1530
  time to fit residues: 12.4346
Evaluate side-chains
  56 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  466 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 36 optimal weight:    0.1980
   chunk 18 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0170
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.8220

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.068141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.046926 restraints weight = 28679.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 4.74
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
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      :  0.002   0.032   7557  Z= 0.107
  Angle     :  0.668  12.994  10305  Z= 0.295
  Chirality :  0.041   0.316   1216
  Planarity :  0.004   0.053   1272
  Dihedral  : 12.333 116.870   1158
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 19.90 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.29), residues: 930
  helix:  2.63 (0.24), residues: 493
  sheet: -0.60 (0.61), residues: 63
  loop : -0.85 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 220 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.024   0.001   PHE B 403 
 TYR   0.027   0.001   TYR A 251 
 ARG   0.001   0.000   ARG B 348 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00971 (    4)
  link_NAG-ASN         : angle       4.15970 (   12)
  link_BETA1-4         : bond        0.00842 (    4)
  link_BETA1-4         : angle       4.71038 (   12)
  hydrogen bonds       : bond        0.03001 (  393)
  hydrogen bonds       : angle       3.90592 ( 1134)
  SS BOND              : bond        0.00442 (    1)
  SS BOND              : angle       2.45382 (    2)
  covalent geometry    : bond        0.00235 ( 7548)
  covalent geometry    : angle       0.63281 (10279)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9182 (mmt) cc_final: 0.8300 (ppp)
REVERT: B  296 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8580 (t80)
REVERT: B  365 MET cc_start: 0.9587 (tpp) cc_final: 0.9213 (mtp)
  outliers start: 11
  outliers final: 8
  residues processed: 54
  average time/residue: 0.1529
  time to fit residues: 12.7151
Evaluate side-chains
  55 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  466 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 58 optimal weight:    0.4980
   chunk 46 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.066972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.045517 restraints weight = 28402.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.2780 rms_B_bonded: 4.71
r_work: 0.2637 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7557  Z= 0.137
  Angle     :  0.679  13.242  10305  Z= 0.305
  Chirality :  0.041   0.316   1216
  Planarity :  0.003   0.051   1272
  Dihedral  : 12.041 117.275   1158
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.77 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.29), residues: 930
  helix:  2.63 (0.24), residues: 495
  sheet: -0.64 (0.62), residues: 63
  loop : -0.83 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  89 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.025   0.001   PHE B 403 
 TYR   0.009   0.001   TYR A 251 
 ARG   0.019   0.001   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00934 (    4)
  link_NAG-ASN         : angle       4.16289 (   12)
  link_BETA1-4         : bond        0.00900 (    4)
  link_BETA1-4         : angle       4.67627 (   12)
  hydrogen bonds       : bond        0.03448 (  393)
  hydrogen bonds       : angle       3.98893 ( 1134)
  SS BOND              : bond        0.00421 (    1)
  SS BOND              : angle       2.43244 (    2)
  covalent geometry    : bond        0.00312 ( 7548)
  covalent geometry    : angle       0.64439 (10279)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3270.15 seconds
wall clock time: 57 minutes 43.94 seconds (3463.94 seconds total)