Starting phenix.real_space_refine
on Fri Aug 22 19:52:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x0w_37983/08_2025/8x0w_37983.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x0w_37983/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x0w_37983/08_2025/8x0w_37983.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x0w_37983/08_2025/8x0w_37983.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x0w_37983/08_2025/8x0w_37983.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x0w_37983/08_2025/8x0w_37983.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.54, per 1000 atoms: 0.21
  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: 0.40
  Conformation dependent library (CDL) restraints added in 352.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.17
  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: 0.78

  Time building geometry restraints manager: 0.56 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:             1.470
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.770
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.390
-------------------------------------------------------------------------------
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 : 8.89
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG A 227 
 TYR   0.005   0.001   TYR B 289 
 PHE   0.015   0.001   PHE B 233 
 TRP   0.009   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 

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

*********************** 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  : 0.179 
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: 0.0578
  time to fit residues: 5.0706
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  : 0.280 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.7922

-------------------------------------------------------------------------------
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 = 0.068485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.047359 restraints weight = 28496.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 4.76
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.0744

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= 0.109
  Angle     :  0.646  11.449  10305  Z= 0.292
  Chirality :  0.043   0.319   1216
  Planarity :  0.004   0.051   1272
  Dihedral  : 20.518 116.478   1162
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.69 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.29), residues: 930
  helix:  2.48 (0.24), residues: 499
  sheet: -0.47 (0.60), residues: 63
  loop : -0.79 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 452 
 TYR   0.015   0.001   TYR A 423 
 PHE   0.013   0.001   PHE A 627 
 TRP   0.007   0.001   TRP B 417 
 HIS   0.005   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7548)
  covalent geometry    : angle       0.61641 (10279)
  SS BOND              : bond        0.00787 (    1)
  SS BOND              : angle       3.94999 (    2)
  hydrogen bonds       : bond        0.03541 (  393)
  hydrogen bonds       : angle       4.18734 ( 1134)
  link_BETA1-4         : bond        0.00393 (    4)
  link_BETA1-4         : angle       3.68863 (   12)
  link_NAG-ASN         : bond        0.00959 (    4)
  link_NAG-ASN         : angle       4.09407 (   12)

*********************** 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
  68 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8902 (tt)
REVERT: A  423 TYR cc_start: 0.9603 (t80) cc_final: 0.9384 (t80)
REVERT: A  485 MET cc_start: 0.9071 (mmp) cc_final: 0.8481 (ppp)
REVERT: B  365 MET cc_start: 0.9144 (tpp) cc_final: 0.8260 (mmt)
REVERT: B  466 LEU cc_start: 0.9323 (tt) cc_final: 0.9116 (mm)
  outliers start: 14
  outliers final: 5
  residues processed: 66
  average time/residue: 0.0576
  time to fit residues: 5.9801
Evaluate side-chains
  52 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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  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 80 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 46 optimal weight:    9.9990
   chunk 82 optimal weight:    6.9990
   chunk 56 optimal weight:    0.6980
   chunk 8 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    3.5186

-------------------------------------------------------------------------------
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 = 0.064895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.043257 restraints weight = 28582.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.2702 rms_B_bonded: 4.71
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7557  Z= 0.235
  Angle     :  0.737  11.302  10305  Z= 0.340
  Chirality :  0.045   0.332   1216
  Planarity :  0.004   0.047   1272
  Dihedral  : 18.075 116.784   1160
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.96 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.29), residues: 930
  helix:  2.46 (0.24), residues: 494
  sheet: -0.74 (0.60), residues: 63
  loop : -0.87 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 614 
 TYR   0.013   0.002   TYR A 423 
 PHE   0.018   0.002   PHE A 524 
 TRP   0.013   0.001   TRP B 405 
 HIS   0.006   0.002   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 7548)
  covalent geometry    : angle       0.71076 (10279)
  SS BOND              : bond        0.00476 (    1)
  SS BOND              : angle       3.25573 (    2)
  hydrogen bonds       : bond        0.05012 (  393)
  hydrogen bonds       : angle       4.46358 ( 1134)
  link_BETA1-4         : bond        0.01045 (    4)
  link_BETA1-4         : angle       3.94237 (   12)
  link_NAG-ASN         : bond        0.00901 (    4)
  link_NAG-ASN         : angle       3.97757 (   12)

*********************** 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
  65 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 43
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9164 (mmt) cc_final: 0.8201 (ppp)
  outliers start: 22
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0619
  time to fit residues: 6.0041
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  : 0.321 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain B residue  446 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 91 optimal weight:    8.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3324 r_free = 0.3324 target = 0.064336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.042855 restraints weight = 29314.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.2713 rms_B_bonded: 4.67
r_work: 0.2567 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7557  Z= 0.221
  Angle     :  0.718  11.365  10305  Z= 0.326
  Chirality :  0.044   0.315   1216
  Planarity :  0.004   0.048   1272
  Dihedral  : 16.080 118.250   1158
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.22 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.29), residues: 930
  helix:  2.41 (0.23), residues: 498
  sheet: -0.96 (0.60), residues: 63
  loop : -0.84 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 248 
 TYR   0.017   0.001   TYR A 251 
 PHE   0.016   0.002   PHE B 233 
 TRP   0.011   0.001   TRP B 405 
 HIS   0.006   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 7548)
  covalent geometry    : angle       0.68635 (10279)
  SS BOND              : bond        0.00460 (    1)
  SS BOND              : angle       3.22032 (    2)
  hydrogen bonds       : bond        0.04672 (  393)
  hydrogen bonds       : angle       4.41590 ( 1134)
  link_BETA1-4         : bond        0.00941 (    4)
  link_BETA1-4         : angle       4.51273 (   12)
  link_NAG-ASN         : bond        0.00922 (    4)
  link_NAG-ASN         : angle       4.06807 (   12)

*********************** 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: 17
    poor density    : 44
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.9687 (t80) cc_final: 0.9484 (t80)
REVERT: A  485 MET cc_start: 0.9141 (mmt) cc_final: 0.8254 (ppp)
  outliers start: 17
  outliers final: 10
  residues processed: 58
  average time/residue: 0.0547
  time to fit residues: 5.0069
Evaluate side-chains
  49 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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  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  446 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3362 r_free = 0.3362 target = 0.066006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.044797 restraints weight = 28775.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 4.68
r_work: 0.2605 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.1566

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= 0.125
  Angle     :  0.668  11.153  10305  Z= 0.298
  Chirality :  0.042   0.313   1216
  Planarity :  0.004   0.052   1272
  Dihedral  : 15.000 117.746   1158
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.87 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.29), residues: 930
  helix:  2.52 (0.24), residues: 495
  sheet: -0.84 (0.60), residues: 63
  loop : -0.88 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 348 
 TYR   0.009   0.001   TYR B 387 
 PHE   0.016   0.001   PHE B 233 
 TRP   0.010   0.001   TRP B 405 
 HIS   0.005   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7548)
  covalent geometry    : angle       0.63329 (10279)
  SS BOND              : bond        0.00489 (    1)
  SS BOND              : angle       2.99625 (    2)
  hydrogen bonds       : bond        0.04001 (  393)
  hydrogen bonds       : angle       4.19103 ( 1134)
  link_BETA1-4         : bond        0.00831 (    4)
  link_BETA1-4         : angle       4.61321 (   12)
  link_NAG-ASN         : bond        0.00927 (    4)
  link_NAG-ASN         : angle       4.14304 (   12)

*********************** 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
  65 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.9689 (t80) cc_final: 0.9455 (t80)
REVERT: A  485 MET cc_start: 0.9141 (mmt) cc_final: 0.8221 (ppp)
REVERT: B  296 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8410 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 61
  average time/residue: 0.0653
  time to fit residues: 6.2351
Evaluate side-chains
  53 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3369 r_free = 0.3369 target = 0.066601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.045299 restraints weight = 28682.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 4.65
r_work: 0.2632 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7557  Z= 0.113
  Angle     :  0.644  11.156  10305  Z= 0.286
  Chirality :  0.042   0.312   1216
  Planarity :  0.003   0.052   1272
  Dihedral  : 13.931 117.121   1158
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.74 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.29), residues: 930
  helix:  2.64 (0.24), residues: 493
  sheet: -0.77 (0.61), residues: 63
  loop : -0.87 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 141 
 TYR   0.022   0.001   TYR A 251 
 PHE   0.016   0.001   PHE B 233 
 TRP   0.009   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7548)
  covalent geometry    : angle       0.60710 (10279)
  SS BOND              : bond        0.00449 (    1)
  SS BOND              : angle       2.79408 (    2)
  hydrogen bonds       : bond        0.03544 (  393)
  hydrogen bonds       : angle       4.04822 ( 1134)
  link_BETA1-4         : bond        0.00757 (    4)
  link_BETA1-4         : angle       4.63267 (   12)
  link_NAG-ASN         : bond        0.00937 (    4)
  link_NAG-ASN         : angle       4.18305 (   12)

*********************** 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
  66 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.9695 (t80) cc_final: 0.9438 (t80)
REVERT: A  485 MET cc_start: 0.9133 (mmt) cc_final: 0.8248 (ppp)
REVERT: B  365 MET cc_start: 0.9524 (tpp) cc_final: 0.8915 (tpp)
  outliers start: 20
  outliers final: 11
  residues processed: 61
  average time/residue: 0.0637
  time to fit residues: 6.0406
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  : 0.292 
-------------------------------------------------------------------------------
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 92 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 11 optimal weight:   20.0000
   chunk 10 optimal weight:    0.0770
   chunk 75 optimal weight:    0.0670
   chunk 24 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    1.1278

-------------------------------------------------------------------------------
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 = 0.3377 r_free = 0.3377 target = 0.066621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.045279 restraints weight = 28715.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 4.71
r_work: 0.2631 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7557  Z= 0.114
  Angle     :  0.665  15.528  10305  Z= 0.292
  Chirality :  0.041   0.315   1216
  Planarity :  0.003   0.052   1272
  Dihedral  : 13.522 117.213   1158
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.65 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.29), residues: 930
  helix:  2.62 (0.24), residues: 493
  sheet: -0.76 (0.61), residues: 63
  loop : -0.87 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 614 
 TYR   0.021   0.001   TYR A 251 
 PHE   0.017   0.001   PHE B 233 
 TRP   0.008   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7548)
  covalent geometry    : angle       0.63024 (10279)
  SS BOND              : bond        0.00450 (    1)
  SS BOND              : angle       2.65832 (    2)
  hydrogen bonds       : bond        0.03462 (  393)
  hydrogen bonds       : angle       4.03930 ( 1134)
  link_BETA1-4         : bond        0.00821 (    4)
  link_BETA1-4         : angle       4.62459 (   12)
  link_NAG-ASN         : bond        0.00941 (    4)
  link_NAG-ASN         : angle       4.16841 (   12)

*********************** 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
  60 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.9695 (t80) cc_final: 0.9437 (t80)
REVERT: A  485 MET cc_start: 0.9154 (mmt) cc_final: 0.8234 (ppp)
REVERT: B  365 MET cc_start: 0.9629 (tpp) cc_final: 0.8964 (tpp)
  outliers start: 16
  outliers final: 10
  residues processed: 58
  average time/residue: 0.0621
  time to fit residues: 5.7252
Evaluate side-chains
  50 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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  309 LEU
Chi-restraints excluded: chain A residue  326 THR
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 75 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0870
   chunk 60 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 = 0.3390 r_free = 0.3390 target = 0.067353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.046133 restraints weight = 28715.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.2794 rms_B_bonded: 4.71
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.1668

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= 0.107
  Angle     :  0.667  12.914  10305  Z= 0.294
  Chirality :  0.041   0.314   1216
  Planarity :  0.003   0.053   1272
  Dihedral  : 13.070 117.011   1158
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 19.90 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.29), residues: 930
  helix:  2.61 (0.24), residues: 493
  sheet: -0.69 (0.61), residues: 63
  loop : -0.84 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 348 
 TYR   0.018   0.001   TYR A 251 
 PHE   0.016   0.001   PHE B 233 
 TRP   0.009   0.001   TRP B 484 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7548)
  covalent geometry    : angle       0.63196 (10279)
  SS BOND              : bond        0.00455 (    1)
  SS BOND              : angle       2.58064 (    2)
  hydrogen bonds       : bond        0.03272 (  393)
  hydrogen bonds       : angle       4.03033 ( 1134)
  link_BETA1-4         : bond        0.00804 (    4)
  link_BETA1-4         : angle       4.65090 (   12)
  link_NAG-ASN         : bond        0.00940 (    4)
  link_NAG-ASN         : angle       4.20108 (   12)

*********************** 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
  60 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.9673 (t80) cc_final: 0.9391 (t80)
REVERT: A  485 MET cc_start: 0.9156 (mmt) cc_final: 0.8312 (ppp)
REVERT: B  365 MET cc_start: 0.9529 (tpp) cc_final: 0.9182 (tpp)
  outliers start: 12
  outliers final: 9
  residues processed: 59
  average time/residue: 0.0583
  time to fit residues: 5.4458
Evaluate side-chains
  53 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  326 THR
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  296 TYR
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  446 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 56 optimal weight:    0.0370
   chunk 92 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    1.3864

-------------------------------------------------------------------------------
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 = 0.3370 r_free = 0.3370 target = 0.066590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.045207 restraints weight = 28619.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2772 rms_B_bonded: 4.71
r_work: 0.2628 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7557  Z= 0.123
  Angle     :  0.660  12.556  10305  Z= 0.294
  Chirality :  0.041   0.312   1216
  Planarity :  0.003   0.052   1272
  Dihedral  : 12.639 117.289   1158
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 20.15 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.29), residues: 930
  helix:  2.61 (0.24), residues: 495
  sheet: -0.68 (0.62), residues: 63
  loop : -0.83 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 348 
 TYR   0.025   0.001   TYR A 251 
 PHE   0.016   0.001   PHE B 233 
 TRP   0.007   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7548)
  covalent geometry    : angle       0.62405 (10279)
  SS BOND              : bond        0.00396 (    1)
  SS BOND              : angle       2.52921 (    2)
  hydrogen bonds       : bond        0.03485 (  393)
  hydrogen bonds       : angle       4.05987 ( 1134)
  link_BETA1-4         : bond        0.00810 (    4)
  link_BETA1-4         : angle       4.65764 (   12)
  link_NAG-ASN         : bond        0.00930 (    4)
  link_NAG-ASN         : angle       4.18911 (   12)

*********************** 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
  55 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9159 (mmt) cc_final: 0.8270 (ppp)
REVERT: B  365 MET cc_start: 0.9634 (tpp) cc_final: 0.9256 (mtp)
  outliers start: 12
  outliers final: 9
  residues processed: 53
  average time/residue: 0.0579
  time to fit residues: 4.6154
Evaluate side-chains
  52 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  326 THR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0870
   chunk 18 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 69 optimal weight:    0.2980
   chunk 32 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.067686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.046468 restraints weight = 28240.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 4.63
r_work: 0.2656 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7557  Z= 0.106
  Angle     :  0.667  12.597  10305  Z= 0.296
  Chirality :  0.041   0.306   1216
  Planarity :  0.003   0.053   1272
  Dihedral  : 12.359 117.505   1158
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 20.66 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.29), residues: 930
  helix:  2.62 (0.24), residues: 493
  sheet: -0.68 (0.62), residues: 63
  loop : -0.83 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 614 
 TYR   0.018   0.001   TYR A 423 
 PHE   0.023   0.001   PHE B 403 
 TRP   0.008   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7548)
  covalent geometry    : angle       0.63127 (10279)
  SS BOND              : bond        0.00442 (    1)
  SS BOND              : angle       2.50667 (    2)
  hydrogen bonds       : bond        0.03194 (  393)
  hydrogen bonds       : angle       3.98909 ( 1134)
  link_BETA1-4         : bond        0.00840 (    4)
  link_BETA1-4         : angle       4.69577 (   12)
  link_NAG-ASN         : bond        0.00959 (    4)
  link_NAG-ASN         : angle       4.19817 (   12)

********************** 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
  56 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.9163 (mmt) cc_final: 0.8284 (ppp)
  outliers start: 10
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0721
  time to fit residues: 6.1487
Evaluate side-chains
  53 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  326 THR
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  296 TYR
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  444 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 82 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3389 r_free = 0.3389 target = 0.067308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.046129 restraints weight = 28364.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 4.67
r_work: 0.2655 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.1773

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= 0.112
  Angle     :  0.663  12.400  10305  Z= 0.298
  Chirality :  0.041   0.305   1216
  Planarity :  0.003   0.053   1272
  Dihedral  : 12.144 117.648   1158
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 20.53 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.29), residues: 930
  helix:  2.53 (0.24), residues: 493
  sheet: -0.66 (0.62), residues: 63
  loop : -0.83 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 195 
 TYR   0.027   0.001   TYR A 251 
 PHE   0.025   0.001   PHE B 403 
 TRP   0.007   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7548)
  covalent geometry    : angle       0.62757 (10279)
  SS BOND              : bond        0.00423 (    1)
  SS BOND              : angle       2.47251 (    2)
  hydrogen bonds       : bond        0.03300 (  393)
  hydrogen bonds       : angle       4.01552 ( 1134)
  link_BETA1-4         : bond        0.00874 (    4)
  link_BETA1-4         : angle       4.68774 (   12)
  link_NAG-ASN         : bond        0.00935 (    4)
  link_NAG-ASN         : angle       4.20095 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1687.27 seconds
wall clock time: 29 minutes 43.22 seconds (1783.22 seconds total)