Starting phenix.real_space_refine
on Fri Aug 22 17:35:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aqw_15592/08_2025/8aqw_15592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aqw_15592/08_2025/8aqw_15592.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8aqw_15592/08_2025/8aqw_15592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aqw_15592/08_2025/8aqw_15592.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aqw_15592/08_2025/8aqw_15592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aqw_15592/08_2025/8aqw_15592.cif"
  }
  resolution = 3.3
  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=   0.021
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      37      5.16       5
     C    4121      2.51       5
     N    1083      2.21       5
     O    1216      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  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: 6457
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1543
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 4872
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 596, 4857
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 596, 4857
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 4982
      Conformer: "C"
        Number of residues, atoms: 596, 4854
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
          Unresolved chain links: 2
          Unresolved chain link angles: 6
          Unresolved chain link dihedrals: 6
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 2
          bond proxies already assigned to first conformer: 4982
    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: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLN A  34 " occ=0.00
      ... (22 atoms not shown)
      pdb=" NE2CGLN A  34 " occ=0.31
  Time building chain proxies: 3.41, per 1000 atoms: 0.53
  Number of scatterers: 6457
  At special positions: 0
  Unit cell: (87.2384, 87.2384, 115.642, 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      37     16.00
     O    1216      8.00
     N    1083      7.00
     C    4121      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " 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-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG C   1 " - " ASN A  53 "
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 676.0 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      53.6% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 3.928A  pdb=" N   VAL B 367 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE B 371 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 3.771A  pdb=" N   VAL B 407 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
      removed outlier: 3.750A  pdb=" N   GLN B 506 " --> pdb=" O   VAL B 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 40
      removed outlier: 3.599A  pdb=" N   THR A  27 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A  28 " --> pdb=" O   ASN A  24 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N  AGLN A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLU A  35 " --> pdb=" O   ASN A  31 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   ASP A  38 " --> pdb=" O  AGLN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 53
    Processing helix  chain 'A' and resid 56 through 81
      removed outlier: 3.729A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.630A  pdb=" N   THR A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 155
      removed outlier: 4.016A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 172
      removed outlier: 3.609A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 175
      No H-bonds generated for 'chain 'A' and resid 173 through 175'
    Processing helix  chain 'A' and resid 176 through 194
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 218 through 220
      No H-bonds generated for 'chain 'A' and resid 218 through 220'
    Processing helix  chain 'A' and resid 221 through 231
      removed outlier: 3.525A  pdb=" N   ASP A 225 " --> pdb=" O   GLN A 221 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   GLU A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR A 229 " --> pdb=" O   ASP A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 248
      removed outlier: 3.702A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 3.678A  pdb=" N   GLY A 301 " --> pdb=" O   MET A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.569A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.934A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 3.591A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 4.212A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 466
      removed outlier: 3.655A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU A 450 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 472 through 485
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.409A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.671A  pdb=" N   LYS A 541 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   CYS A 542 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 538 through 542'
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.875A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 4.129A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
      removed outlier: 3.901A  pdb=" N   ASP A 593 " --> pdb=" O   GLN A 589 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 358
      removed outlier: 3.518A  pdb=" N   ASP B 398 " --> pdb=" O   VAL B 512 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.609A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.510A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)

    269 hydrogen bonds defined for protein.
    759 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: 0.98

  Time building geometry restraints manager: 0.65 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: 2081
        1.34 -     1.46: 1685
        1.46 -     1.58: 2814
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6638
  Sorted by residual:
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.99e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C5  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  bond pdb=" C5  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.22e+00
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.06e+00
  ... (remaining 6633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 8888
        2.10 -     4.20: 110
        4.20 -     6.29: 14
        6.29 -     8.39: 3
        8.39 -    10.49: 2
  Bond angle restraints: 9017
  Sorted by residual:
  angle pdb=" N   VAL B 341 "
        pdb=" CA  VAL B 341 "
        pdb=" C   VAL B 341 "
      ideal   model   delta    sigma   weight residual
     113.53  108.46    5.07 9.80e-01 1.04e+00 2.67e+01
  angle pdb=" N   GLU A  35 "
        pdb=" CA  GLU A  35 "
        pdb=" C   GLU A  35 "
      ideal   model   delta    sigma   weight residual
     113.43  107.81    5.62 1.26e+00 6.30e-01 1.99e+01
  angle pdb=" C   PHE B 371 "
        pdb=" N   ALA B 372 "
        pdb=" CA  ALA B 372 "
      ideal   model   delta    sigma   weight residual
     121.80  132.29  -10.49 2.44e+00 1.68e-01 1.85e+01
  angle pdb=" N   ARG A 228 "
        pdb=" CA  ARG A 228 "
        pdb=" C   ARG A 228 "
      ideal   model   delta    sigma   weight residual
     113.01  109.52    3.49 1.20e+00 6.94e-01 8.47e+00
  angle pdb=" N   ASP B 420 "
        pdb=" CA  ASP B 420 "
        pdb=" C   ASP B 420 "
      ideal   model   delta    sigma   weight residual
     114.04  110.58    3.46 1.24e+00 6.50e-01 7.79e+00
  ... (remaining 9012 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.46: 3644
       21.46 -    42.91: 272
       42.91 -    64.37: 36
       64.37 -    85.82: 7
       85.82 -   107.28: 9
  Dihedral angle restraints: 3968
    sinusoidal: 1643
      harmonic: 2325
  Sorted by residual:
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -22.20  -63.80     1      1.00e+01 1.00e-02 5.36e+01
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.11   58.11     1      1.00e+01 1.00e-02 4.53e+01
  dihedral pdb=" CA  CYS B 432 "
           pdb=" C   CYS B 432 "
           pdb=" N   VAL B 433 "
           pdb=" CA  VAL B 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.06  -19.94     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 3965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 580
       0.032 -    0.064: 253
       0.064 -    0.096: 81
       0.096 -    0.128: 26
       0.128 -    0.160: 2
  Chirality restraints: 942
  Sorted by residual:
  chirality pdb=" CA  ILE A  88 "
            pdb=" N   ILE A  88 "
            pdb=" C   ILE A  88 "
            pdb=" CB  ILE A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  chirality pdb=" CA  PRO B 491 "
            pdb=" N   PRO B 491 "
            pdb=" C   PRO B 491 "
            pdb=" CB  PRO B 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 939 not shown)

  Planarity restraints: 1173
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 478 "    0.039 5.00e-02 4.00e+02   5.87e-02 5.51e+00
        pdb=" N   PRO B 479 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 479 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 479 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 288 "   -0.030 5.00e-02 4.00e+02   4.54e-02 3.30e+00
        pdb=" N   PRO A 289 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 594 "   -0.011 2.00e-02 2.50e+03   1.09e-02 2.96e+00
        pdb=" CG  TRP A 594 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 594 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 594 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 594 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 594 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 594 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 594 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 594 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 594 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1170 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 237
        2.72 -     3.27: 6347
        3.27 -     3.81: 9986
        3.81 -     4.36: 11959
        4.36 -     4.90: 21173
  Nonbonded interactions: 49702
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 439 "
            pdb=" OG  SER B 443 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" OE1CGLN A  34 "
            pdb=" N   GLU A  35 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O   ILE A 151 "
            pdb=" OG  SER A 155 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG1 THR A 229 "
            pdb=" OH  TYR A 516 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   PHE A 327 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.257 3.040
  ... (remaining 49697 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             3.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.090
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
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      :  0.002   0.028   6648  Z= 0.125
  Angle     :  0.600  10.488   9040  Z= 0.324
  Chirality :  0.040   0.160    942
  Planarity :  0.005   0.059   1171
  Dihedral  : 15.582 107.280   2455
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.11 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.29 %
    Favored  : 99.56 %
  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: -0.74 (0.30), residues: 788
  helix:  1.10 (0.28), residues: 364
  sheet: -0.24 (0.69), residues: 52
  loop : -2.27 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 518 
 TYR   0.016   0.001   TYR B 501 
 PHE   0.010   0.001   PHE A 400 
 TRP   0.029   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6638)
  covalent geometry    : angle       0.59274 ( 9017)
  SS BOND              : bond        0.00345 (    7)
  SS BOND              : angle       2.02377 (   14)
  hydrogen bonds       : bond        0.14639 (  269)
  hydrogen bonds       : angle       5.15799 (  759)
  link_BETA1-4         : bond        0.00970 (    1)
  link_BETA1-4         : angle       1.21135 (    3)
  link_NAG-ASN         : bond        0.00078 (    2)
  link_NAG-ASN         : angle       2.14970 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  277 ASN cc_start: 0.7426 (m-40) cc_final: 0.7092 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0966
  time to fit residues: 14.7928
Evaluate side-chains
  94 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0030
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.2980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN
** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  24 ASN
A  34 GLN    C
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 ASN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.186435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.162513 restraints weight = 31274.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 4.94
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4002 r_free = 0.4002    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4002 r_free = 0.4002    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.4002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6648  Z= 0.119
  Angle     :  0.627  10.378   9040  Z= 0.312
  Chirality :  0.042   0.181    942
  Planarity :  0.005   0.046   1171
  Dihedral  :  8.212  65.281    929
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.22 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  7.12 %
    Favored  : 92.30 %
  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: -0.69 (0.30), residues: 788
  helix:  1.24 (0.28), residues: 363
  sheet: -0.71 (0.68), residues: 52
  loop : -2.26 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 518 
 TYR   0.019   0.001   TYR A 183 
 PHE   0.027   0.001   PHE A  72 
 TRP   0.015   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6638)
  covalent geometry    : angle       0.62162 ( 9017)
  SS BOND              : bond        0.00318 (    7)
  SS BOND              : angle       1.83742 (   14)
  hydrogen bonds       : bond        0.04270 (  269)
  hydrogen bonds       : angle       4.23521 (  759)
  link_BETA1-4         : bond        0.00889 (    1)
  link_BETA1-4         : angle       1.21595 (    3)
  link_NAG-ASN         : bond        0.00143 (    2)
  link_NAG-ASN         : angle       1.84023 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6964 (mm-40)
REVERT: A  249 MET cc_start: 0.5583 (tpt) cc_final: 0.2343 (ptm)
  outliers start: 4
  outliers final: 2
  residues processed: 103
  average time/residue: 0.0791
  time to fit residues: 10.7511
Evaluate side-chains
  96 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain A residue  183 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 34 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN
** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.179781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.156696 restraints weight = 26774.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 3.96
r_work: 0.3751 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6648  Z= 0.169
  Angle     :  0.662  10.323   9040  Z= 0.334
  Chirality :  0.043   0.155    942
  Planarity :  0.005   0.046   1171
  Dihedral  :  5.669  37.637    929
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.75 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.05 %
    Favored  : 87.94 %
  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: -0.85 (0.30), residues: 788
  helix:  1.06 (0.28), residues: 364
  sheet: -0.92 (0.70), residues: 53
  loop : -2.30 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 460 
 TYR   0.019   0.002   TYR B 501 
 PHE   0.030   0.002   PHE A  72 
 TRP   0.017   0.002   TRP A 477 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6638)
  covalent geometry    : angle       0.65279 ( 9017)
  SS BOND              : bond        0.00365 (    7)
  SS BOND              : angle       2.37054 (   14)
  hydrogen bonds       : bond        0.05481 (  269)
  hydrogen bonds       : angle       4.35671 (  759)
  link_BETA1-4         : bond        0.00714 (    1)
  link_BETA1-4         : angle       1.85332 (    3)
  link_NAG-ASN         : bond        0.00250 (    2)
  link_NAG-ASN         : angle       2.24490 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  455 MET cc_start: 0.7098 (tpp) cc_final: 0.6570 (tpp)
  outliers start: 7
  outliers final: 4
  residues processed: 98
  average time/residue: 0.1024
  time to fit residues: 13.0262
Evaluate side-chains
  91 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  285 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN
A  34 GLN    C
A 378 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.183655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.159868 restraints weight = 29155.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 4.32
r_work: 0.3782 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6648  Z= 0.114
  Angle     :  0.592  10.523   9040  Z= 0.297
  Chirality :  0.041   0.154    942
  Planarity :  0.004   0.044   1171
  Dihedral  :  4.853  36.332    929
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.22 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.63 %
    Favored  : 86.92 %
  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: -0.79 (0.30), residues: 788
  helix:  1.24 (0.28), residues: 361
  sheet: -0.85 (0.71), residues: 52
  loop : -2.39 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 518 
 TYR   0.020   0.001   TYR A 183 
 PHE   0.024   0.001   PHE A 504 
 TRP   0.018   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6638)
  covalent geometry    : angle       0.58501 ( 9017)
  SS BOND              : bond        0.00313 (    7)
  SS BOND              : angle       1.88074 (   14)
  hydrogen bonds       : bond        0.04113 (  269)
  hydrogen bonds       : angle       4.20065 (  759)
  link_BETA1-4         : bond        0.00757 (    1)
  link_BETA1-4         : angle       1.48497 (    3)
  link_NAG-ASN         : bond        0.00105 (    2)
  link_NAG-ASN         : angle       1.99706 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  249 MET cc_start: 0.5971 (tpt) cc_final: 0.5291 (tpt)
REVERT: A  455 MET cc_start: 0.7085 (tpp) cc_final: 0.6533 (tpp)
REVERT: A  480 MET cc_start: 0.5574 (mtt) cc_final: 0.5214 (ptp)
  outliers start: 10
  outliers final: 6
  residues processed: 100
  average time/residue: 0.0997
  time to fit residues: 13.0259
Evaluate side-chains
  96 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  285 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0570
   chunk 35 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0030
   chunk 39 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.5108

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN
B 487 ASN
A  34 GLN    C
A 378 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.173019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.148647 restraints weight = 26155.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 4.30
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3832 r_free = 0.3832    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3832 r_free = 0.3832    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6648  Z= 0.108
  Angle     :  0.577  10.497   9040  Z= 0.288
  Chirality :  0.040   0.158    942
  Planarity :  0.004   0.045   1171
  Dihedral  :  4.451  32.812    929
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.99 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 12.35 %
    Favored  : 86.77 %
  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: -0.72 (0.30), residues: 788
  helix:  1.32 (0.28), residues: 361
  sheet: -0.78 (0.71), residues: 52
  loop : -2.38 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 518 
 TYR   0.019   0.001   TYR A 183 
 PHE   0.022   0.001   PHE A 504 
 TRP   0.018   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6638)
  covalent geometry    : angle       0.57114 ( 9017)
  SS BOND              : bond        0.00398 (    7)
  SS BOND              : angle       1.78801 (   14)
  hydrogen bonds       : bond        0.03965 (  269)
  hydrogen bonds       : angle       4.12654 (  759)
  link_BETA1-4         : bond        0.00637 (    1)
  link_BETA1-4         : angle       1.13062 (    3)
  link_NAG-ASN         : bond        0.00129 (    2)
  link_NAG-ASN         : angle       1.96883 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  249 MET cc_start: 0.5752 (tpt) cc_final: 0.4807 (tpt)
REVERT: A  455 MET cc_start: 0.6726 (tpp) cc_final: 0.6160 (tpp)
REVERT: A  480 MET cc_start: 0.4819 (mtt) cc_final: 0.4542 (ptp)
  outliers start: 6
  outliers final: 4
  residues processed: 99
  average time/residue: 0.0961
  time to fit residues: 12.5005
Evaluate side-chains
  95 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain A residue  285 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN
A  34 GLN    C
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.181673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.158736 restraints weight = 23325.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 3.40
r_work: 0.3779 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3811 r_free = 0.3811    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3811 r_free = 0.3811    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6648  Z= 0.135
  Angle     :  0.603  10.489   9040  Z= 0.303
  Chirality :  0.041   0.149    942
  Planarity :  0.005   0.045   1171
  Dihedral  :  4.596  30.410    929
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.37 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.94 %
    Favored  : 85.47 %
  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: -0.76 (0.30), residues: 788
  helix:  1.23 (0.28), residues: 362
  sheet: -0.83 (0.71), residues: 53
  loop : -2.34 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 518 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.023   0.001   PHE A 504 
 TRP   0.017   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6638)
  covalent geometry    : angle       0.59531 ( 9017)
  SS BOND              : bond        0.00280 (    7)
  SS BOND              : angle       2.05905 (   14)
  hydrogen bonds       : bond        0.04629 (  269)
  hydrogen bonds       : angle       4.20863 (  759)
  link_BETA1-4         : bond        0.00767 (    1)
  link_BETA1-4         : angle       1.07305 (    3)
  link_NAG-ASN         : bond        0.00154 (    2)
  link_NAG-ASN         : angle       2.13348 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  455 MET cc_start: 0.6991 (tpp) cc_final: 0.6562 (tpp)
REVERT: A  480 MET cc_start: 0.5432 (mtt) cc_final: 0.5102 (ptp)
  outliers start: 11
  outliers final: 6
  residues processed: 101
  average time/residue: 0.1071
  time to fit residues: 13.9136
Evaluate side-chains
  97 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  501 TYR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain A residue  285 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 16 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 47 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN
B 493 GLN
A  34 GLN    C
A 378 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.183164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.159571 restraints weight = 36047.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 5.98
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3977
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3977 r_free = 0.3977    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3977 r_free = 0.3977    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3977
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6648  Z= 0.116
  Angle     :  0.593  10.565   9040  Z= 0.297
  Chirality :  0.041   0.146    942
  Planarity :  0.005   0.048   1171
  Dihedral  :  4.434  28.430    929
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.99 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.52 %
    Favored  : 85.17 %
  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: -0.71 (0.30), residues: 788
  helix:  1.25 (0.28), residues: 364
  sheet: -0.84 (0.71), residues: 53
  loop : -2.29 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 457 
 TYR   0.019   0.001   TYR A 183 
 PHE   0.025   0.001   PHE A 504 
 TRP   0.021   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6638)
  covalent geometry    : angle       0.58638 ( 9017)
  SS BOND              : bond        0.00207 (    7)
  SS BOND              : angle       1.99011 (   14)
  hydrogen bonds       : bond        0.04196 (  269)
  hydrogen bonds       : angle       4.16063 (  759)
  link_BETA1-4         : bond        0.00715 (    1)
  link_BETA1-4         : angle       0.84793 (    3)
  link_NAG-ASN         : bond        0.00148 (    2)
  link_NAG-ASN         : angle       1.97183 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  249 MET cc_start: 0.5850 (tpt) cc_final: 0.4835 (tpt)
REVERT: A  455 MET cc_start: 0.6704 (tpp) cc_final: 0.6199 (tpp)
REVERT: A  480 MET cc_start: 0.5000 (mtt) cc_final: 0.4757 (ptp)
  outliers start: 9
  outliers final: 6
  residues processed: 98
  average time/residue: 0.0914
  time to fit residues: 11.5802
Evaluate side-chains
  95 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  501 TYR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain A residue  285 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0670
   chunk 58 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN
B 493 GLN
A  34 GLN    C
A 378 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.182771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.160053 restraints weight = 24640.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 3.47
r_work: 0.3798 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6648  Z= 0.122
  Angle     :  0.607  10.543   9040  Z= 0.302
  Chirality :  0.041   0.147    942
  Planarity :  0.005   0.051   1171
  Dihedral  :  4.466  26.960    929
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.50 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.95 %
    Favored  : 84.74 %
  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: -0.71 (0.30), residues: 788
  helix:  1.24 (0.28), residues: 365
  sheet: -0.87 (0.71), residues: 53
  loop : -2.30 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 518 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.026   0.001   PHE A 504 
 TRP   0.021   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6638)
  covalent geometry    : angle       0.59986 ( 9017)
  SS BOND              : bond        0.00294 (    7)
  SS BOND              : angle       1.98577 (   14)
  hydrogen bonds       : bond        0.04283 (  269)
  hydrogen bonds       : angle       4.15625 (  759)
  link_BETA1-4         : bond        0.00775 (    1)
  link_BETA1-4         : angle       0.86305 (    3)
  link_NAG-ASN         : bond        0.00178 (    2)
  link_NAG-ASN         : angle       2.02962 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  249 MET cc_start: 0.6137 (tpt) cc_final: 0.5004 (tpt)
REVERT: A  455 MET cc_start: 0.6951 (tpp) cc_final: 0.6575 (tpp)
REVERT: A  480 MET cc_start: 0.5309 (mtt) cc_final: 0.5025 (ptp)
REVERT: A  594 TRP cc_start: 0.5843 (t-100) cc_final: 0.5616 (t-100)
  outliers start: 9
  outliers final: 6
  residues processed: 94
  average time/residue: 0.0910
  time to fit residues: 11.0402
Evaluate side-chains
  95 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  501 TYR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain A residue  285 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0970
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 0 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN
B 493 GLN
A  34 GLN    C
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.183925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.161163 restraints weight = 22532.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 3.26
r_work: 0.3808 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3836 r_free = 0.3836    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3836 r_free = 0.3836    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6648  Z= 0.114
  Angle     :  0.595  10.760   9040  Z= 0.296
  Chirality :  0.041   0.148    942
  Planarity :  0.004   0.044   1171
  Dihedral  :  4.332  25.327    929
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.11 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 14.10 %
    Favored  : 84.74 %
  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: -0.69 (0.30), residues: 788
  helix:  1.18 (0.28), residues: 371
  sheet: -0.85 (0.71), residues: 53
  loop : -2.26 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 457 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.028   0.001   PHE A 504 
 TRP   0.019   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6638)
  covalent geometry    : angle       0.58891 ( 9017)
  SS BOND              : bond        0.00265 (    7)
  SS BOND              : angle       1.88762 (   14)
  hydrogen bonds       : bond        0.04011 (  269)
  hydrogen bonds       : angle       4.12691 (  759)
  link_BETA1-4         : bond        0.00632 (    1)
  link_BETA1-4         : angle       0.70567 (    3)
  link_NAG-ASN         : bond        0.00155 (    2)
  link_NAG-ASN         : angle       1.96050 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  249 MET cc_start: 0.6117 (tpt) cc_final: 0.5026 (tpt)
REVERT: A  455 MET cc_start: 0.6932 (tpp) cc_final: 0.6587 (tpp)
REVERT: A  480 MET cc_start: 0.5320 (mtt) cc_final: 0.5080 (ptp)
REVERT: A  594 TRP cc_start: 0.5769 (t-100) cc_final: 0.5542 (t-100)
  outliers start: 8
  outliers final: 6
  residues processed: 96
  average time/residue: 0.0755
  time to fit residues: 9.4976
Evaluate side-chains
  95 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  501 TYR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain A residue  285 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0040
   chunk 68 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 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 = 0.4238 r_free = 0.4238 target = 0.183418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.159527 restraints weight = 34637.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 5.53
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3980 r_free = 0.3980    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3980 r_free = 0.3980    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6648  Z= 0.120
  Angle     :  0.603  10.872   9040  Z= 0.300
  Chirality :  0.041   0.147    942
  Planarity :  0.004   0.043   1171
  Dihedral  :  4.343  24.710    929
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.37 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 14.53 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.68 (0.30), residues: 788
  helix:  1.28 (0.28), residues: 365
  sheet: -0.88 (0.71), residues: 53
  loop : -2.28 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 457 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.030   0.001   PHE A 504 
 TRP   0.018   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6638)
  covalent geometry    : angle       0.59672 ( 9017)
  SS BOND              : bond        0.00277 (    7)
  SS BOND              : angle       1.91498 (   14)
  hydrogen bonds       : bond        0.04137 (  269)
  hydrogen bonds       : angle       4.14253 (  759)
  link_BETA1-4         : bond        0.00720 (    1)
  link_BETA1-4         : angle       0.76467 (    3)
  link_NAG-ASN         : bond        0.00181 (    2)
  link_NAG-ASN         : angle       2.01269 (    6)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  249 MET cc_start: 0.5929 (tpt) cc_final: 0.4723 (tpt)
REVERT: A  455 MET cc_start: 0.6710 (tpp) cc_final: 0.6271 (tpp)
REVERT: A  594 TRP cc_start: 0.5457 (t-100) cc_final: 0.5239 (t-100)
  outliers start: 7
  outliers final: 6
  residues processed: 94
  average time/residue: 0.0773
  time to fit residues: 9.5831
Evaluate side-chains
  95 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  501 TYR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain A residue  285 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0010
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 51 optimal weight:    0.1980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN
A  34 GLN    C
A 378 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.184304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.162083 restraints weight = 23540.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 3.67
r_work: 0.3816 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3847 r_free = 0.3847    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3847 r_free = 0.3847    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6648  Z= 0.113
  Angle     :  0.601  10.770   9040  Z= 0.300
  Chirality :  0.041   0.152    942
  Planarity :  0.004   0.044   1171
  Dihedral  :  4.273  24.174    929
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.99 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.95 %
    Favored  : 84.74 %
  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: -0.68 (0.30), residues: 788
  helix:  1.19 (0.28), residues: 371
  sheet: -0.88 (0.70), residues: 53
  loop : -2.24 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 457 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.029   0.001   PHE A 504 
 TRP   0.017   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6638)
  covalent geometry    : angle       0.59524 ( 9017)
  SS BOND              : bond        0.00280 (    7)
  SS BOND              : angle       1.84549 (   14)
  hydrogen bonds       : bond        0.03944 (  269)
  hydrogen bonds       : angle       4.13617 (  759)
  link_BETA1-4         : bond        0.00691 (    1)
  link_BETA1-4         : angle       0.70223 (    3)
  link_NAG-ASN         : bond        0.00153 (    2)
  link_NAG-ASN         : angle       1.97130 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1494.78 seconds
wall clock time: 26 minutes 20.47 seconds (1580.47 seconds total)