Starting phenix.real_space_refine
on Thu Jul 24 17:58:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aqw_15592/07_2025/8aqw_15592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aqw_15592/07_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_15592/07_2025/8aqw_15592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aqw_15592/07_2025/8aqw_15592.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aqw_15592/07_2025/8aqw_15592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aqw_15592/07_2025/8aqw_15592.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.021
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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.21, per 1000 atoms: 1.43
  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: 1.49
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  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: 0.61
  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: 1.61

  Time building geometry restraints manager: 1.81 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:             3.250
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     24.720
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.450
-------------------------------------------------------------------------------
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 : 5.96
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.029   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.010   0.001   PHE A 400 
 TYR   0.016   0.001   TYR B 501 
 ARG   0.005   0.000   ARG A 518 

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

*********************** 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  : 0.648 
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: 0.2068
  time to fit residues: 31.4343
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  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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  24 ASN
A  34 GLN    C
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4249 r_free = 0.4249 target = 0.184454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.161572 restraints weight = 21173.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 3.14
r_work: 0.3831 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3859 r_free = 0.3859    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3859 r_free = 0.3859    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1199

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= 0.133
  Angle     :  0.645  10.323   9040  Z= 0.321
  Chirality :  0.042   0.185    942
  Planarity :  0.005   0.046   1171
  Dihedral  :  8.181  63.706    929
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.73 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  7.85 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.30), residues: 788
  helix:  1.14 (0.28), residues: 365
  sheet: -0.81 (0.69), residues: 53
  loop : -2.32 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 239 
 PHE   0.028   0.001   PHE A  72 
 TYR   0.015   0.001   TYR A 183 
 ARG   0.005   0.001   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    2)
  link_NAG-ASN         : angle       1.99851 (    6)
  link_BETA1-4         : bond        0.00824 (    1)
  link_BETA1-4         : angle       1.37509 (    3)
  hydrogen bonds       : bond        0.04619 (  269)
  hydrogen bonds       : angle       4.28007 (  759)
  SS BOND              : bond        0.00319 (    7)
  SS BOND              : angle       2.00814 (   14)
  covalent geometry    : bond        0.00295 ( 6638)
  covalent geometry    : angle       0.63884 ( 9017)

*********************** 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
  104 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7136 (mm-40)
REVERT: A  249 MET cc_start: 0.6102 (tpt) cc_final: 0.5495 (tpt)
  outliers start: 4
  outliers final: 2
  residues processed: 100
  average time/residue: 0.2017
  time to fit residues: 26.3734
Evaluate side-chains
  94 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
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 68 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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  34 GLN    C ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 HIS
A 508 ASN
** 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 = 0.4218 r_free = 0.4218 target = 0.181425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.158265 restraints weight = 26930.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 4.01
r_work: 0.3771 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3799
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3799 r_free = 0.3799    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3799 r_free = 0.3799    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3799
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6648  Z= 0.150
  Angle     :  0.639  10.352   9040  Z= 0.321
  Chirality :  0.042   0.153    942
  Planarity :  0.005   0.046   1171
  Dihedral  :  5.635  37.395    929
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.37 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.34 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.30), residues: 788
  helix:  1.03 (0.28), residues: 368
  sheet: -0.94 (0.70), residues: 53
  loop : -2.36 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 374 
 PHE   0.028   0.002   PHE A  72 
 TYR   0.019   0.001   TYR A 183 
 ARG   0.004   0.000   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    2)
  link_NAG-ASN         : angle       2.13233 (    6)
  link_BETA1-4         : bond        0.00961 (    1)
  link_BETA1-4         : angle       1.74139 (    3)
  hydrogen bonds       : bond        0.05062 (  269)
  hydrogen bonds       : angle       4.30520 (  759)
  SS BOND              : bond        0.00344 (    7)
  SS BOND              : angle       2.21010 (   14)
  covalent geometry    : bond        0.00340 ( 6638)
  covalent geometry    : angle       0.63085 ( 9017)

*********************** 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
  99 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  455 MET cc_start: 0.7057 (tpp) cc_final: 0.6499 (tpp)
  outliers start: 6
  outliers final: 4
  residues processed: 97
  average time/residue: 0.2075
  time to fit residues: 26.3245
Evaluate side-chains
  92 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
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   97 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0170
   overall best weight:    1.1422

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.179989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.156832 restraints weight = 29855.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 4.91
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1721

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= 0.153
  Angle     :  0.640  10.400   9040  Z= 0.323
  Chirality :  0.042   0.150    942
  Planarity :  0.005   0.046   1171
  Dihedral  :  5.109  36.397    929
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.24 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.92 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.30), residues: 788
  helix:  1.00 (0.28), residues: 367
  sheet: -0.90 (0.71), residues: 53
  loop : -2.43 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.023   0.001   PHE A  72 
 TYR   0.020   0.001   TYR A 183 
 ARG   0.006   0.001   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00203 (    2)
  link_NAG-ASN         : angle       2.15024 (    6)
  link_BETA1-4         : bond        0.00788 (    1)
  link_BETA1-4         : angle       1.68638 (    3)
  hydrogen bonds       : bond        0.05084 (  269)
  hydrogen bonds       : angle       4.33000 (  759)
  SS BOND              : bond        0.00300 (    7)
  SS BOND              : angle       2.23759 (   14)
  covalent geometry    : bond        0.00347 ( 6638)
  covalent geometry    : angle       0.63125 ( 9017)

*********************** 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
  105 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  455 MET cc_start: 0.6883 (tpp) cc_final: 0.6211 (tpp)
  outliers start: 9
  outliers final: 4
  residues processed: 101
  average time/residue: 0.2064
  time to fit residues: 26.9232
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  : 0.638 
-------------------------------------------------------------------------------
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  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 5 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0970
   chunk 45 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4213 r_free = 0.4213 target = 0.180790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.157314 restraints weight = 23652.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 3.58
r_work: 0.3752 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3780 r_free = 0.3780    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 = 0.3780 r_free = 0.3780    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1790

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= 0.138
  Angle     :  0.620  10.465   9040  Z= 0.313
  Chirality :  0.042   0.150    942
  Planarity :  0.005   0.047   1171
  Dihedral  :  4.798  33.814    929
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.50 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.48 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.30), residues: 788
  helix:  1.08 (0.28), residues: 364
  sheet: -0.82 (0.72), residues: 53
  loop : -2.45 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 322 
 PHE   0.020   0.001   PHE A  72 
 TYR   0.019   0.001   TYR A 183 
 ARG   0.004   0.000   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00143 (    2)
  link_NAG-ASN         : angle       2.13641 (    6)
  link_BETA1-4         : bond        0.00731 (    1)
  link_BETA1-4         : angle       1.22661 (    3)
  hydrogen bonds       : bond        0.04831 (  269)
  hydrogen bonds       : angle       4.30443 (  759)
  SS BOND              : bond        0.00366 (    7)
  SS BOND              : angle       2.15852 (   14)
  covalent geometry    : bond        0.00312 ( 6638)
  covalent geometry    : angle       0.61197 ( 9017)

*********************** 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
  108 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  249 MET cc_start: 0.6041 (tpt) cc_final: 0.5243 (tpt)
  outliers start: 11
  outliers final: 6
  residues processed: 103
  average time/residue: 0.2221
  time to fit residues: 30.0865
Evaluate side-chains
  100 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0470
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7878

-------------------------------------------------------------------------------
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 = 0.4222 r_free = 0.4222 target = 0.181719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.158971 restraints weight = 26027.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3969 rms_B_bonded: 3.90
r_work: 0.3776 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3811 r_free = 0.3811    target_work(ls_wunit_k1) = 0.143         |
| 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) = 0.143         |
| 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: 0.7694
moved from start:          0.1871

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= 0.126
  Angle     :  0.611  10.525   9040  Z= 0.307
  Chirality :  0.041   0.151    942
  Planarity :  0.004   0.046   1171
  Dihedral  :  4.637  30.881    929
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.24 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.35 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.30), residues: 788
  helix:  1.07 (0.28), residues: 370
  sheet: -0.81 (0.72), residues: 53
  loop : -2.47 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 322 
 PHE   0.019   0.001   PHE A  72 
 TYR   0.019   0.001   TYR A 183 
 ARG   0.005   0.000   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00134 (    2)
  link_NAG-ASN         : angle       2.05479 (    6)
  link_BETA1-4         : bond        0.00582 (    1)
  link_BETA1-4         : angle       0.93417 (    3)
  hydrogen bonds       : bond        0.04521 (  269)
  hydrogen bonds       : angle       4.26666 (  759)
  SS BOND              : bond        0.00269 (    7)
  SS BOND              : angle       2.02886 (   14)
  covalent geometry    : bond        0.00283 ( 6638)
  covalent geometry    : angle       0.60386 ( 9017)

*********************** 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
  109 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  249 MET cc_start: 0.6045 (tpt) cc_final: 0.5231 (tpt)
  outliers start: 11
  outliers final: 5
  residues processed: 104
  average time/residue: 0.3362
  time to fit residues: 47.2285
Evaluate side-chains
  96 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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  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 34 optimal weight:    0.0030
   chunk 56 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 73 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.182568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.160520 restraints weight = 24841.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 3.81
r_work: 0.3800 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3833 r_free = 0.3833    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 = 0.3833 r_free = 0.3833    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1896

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= 0.117
  Angle     :  0.597  10.573   9040  Z= 0.300
  Chirality :  0.041   0.147    942
  Planarity :  0.004   0.046   1171
  Dihedral  :  4.500  28.231    929
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.24 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 13.23 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.30), residues: 788
  helix:  1.18 (0.28), residues: 364
  sheet: -0.75 (0.72), residues: 52
  loop : -2.45 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 265 
 PHE   0.018   0.001   PHE A  72 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00136 (    2)
  link_NAG-ASN         : angle       1.96886 (    6)
  link_BETA1-4         : bond        0.00717 (    1)
  link_BETA1-4         : angle       0.85619 (    3)
  hydrogen bonds       : bond        0.04249 (  269)
  hydrogen bonds       : angle       4.22163 (  759)
  SS BOND              : bond        0.00300 (    7)
  SS BOND              : angle       1.98954 (   14)
  covalent geometry    : bond        0.00260 ( 6638)
  covalent geometry    : angle       0.58995 ( 9017)

*********************** 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
  103 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.919 
Fit side-chains
REVERT: A  249 MET cc_start: 0.6010 (tpt) cc_final: 0.5089 (tpt)
REVERT: A  480 MET cc_start: 0.5297 (mtt) cc_final: 0.5076 (ptp)
  outliers start: 10
  outliers final: 7
  residues processed: 99
  average time/residue: 0.3165
  time to fit residues: 41.9058
Evaluate side-chains
  98 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 1.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  353 TRP
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  598 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.0980
   chunk 18 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0370
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.183336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.160347 restraints weight = 22369.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3982 rms_B_bonded: 3.29
r_work: 0.3805 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3838 r_free = 0.3838    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 = 0.3838 r_free = 0.3838    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6648  Z= 0.114
  Angle     :  0.588  10.606   9040  Z= 0.294
  Chirality :  0.041   0.149    942
  Planarity :  0.004   0.045   1171
  Dihedral  :  4.360  25.564    929
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.99 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.23 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.30), residues: 788
  helix:  1.21 (0.28), residues: 366
  sheet: -0.86 (0.71), residues: 53
  loop : -2.38 (0.29), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 265 
 PHE   0.017   0.001   PHE A  72 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.003   0.000   ARG A 387 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00153 (    2)
  link_NAG-ASN         : angle       1.95572 (    6)
  link_BETA1-4         : bond        0.00686 (    1)
  link_BETA1-4         : angle       0.76881 (    3)
  hydrogen bonds       : bond        0.04079 (  269)
  hydrogen bonds       : angle       4.17119 (  759)
  SS BOND              : bond        0.00257 (    7)
  SS BOND              : angle       1.89086 (   14)
  covalent geometry    : bond        0.00253 ( 6638)
  covalent geometry    : angle       0.58206 ( 9017)

*********************** 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
  105 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.636 
Fit side-chains
REVERT: A  249 MET cc_start: 0.6068 (tpt) cc_final: 0.5156 (tpt)
  outliers start: 13
  outliers final: 10
  residues processed: 101
  average time/residue: 0.3755
  time to fit residues: 51.0806
Evaluate side-chains
  100 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  468 ILE
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
Chi-restraints excluded: chain A residue  473 TRP
Chi-restraints excluded: chain A residue  598 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0870
   chunk 54 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 65 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    0.9162

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  34 GLN    C ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 HIS
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 = 0.4220 r_free = 0.4220 target = 0.181729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.158148 restraints weight = 35288.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3969 rms_B_bonded: 5.65
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3969
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3969 r_free = 0.3969    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2039

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     :  0.624  10.548   9040  Z= 0.313
  Chirality :  0.042   0.146    942
  Planarity :  0.004   0.045   1171
  Dihedral  :  4.473  25.137    929
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.24 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.23 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.30), residues: 788
  helix:  1.10 (0.28), residues: 369
  sheet: -0.81 (0.73), residues: 53
  loop : -2.38 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 374 
 PHE   0.016   0.001   PHE A  72 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.004   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00210 (    2)
  link_NAG-ASN         : angle       2.08497 (    6)
  link_BETA1-4         : bond        0.00800 (    1)
  link_BETA1-4         : angle       0.85262 (    3)
  hydrogen bonds       : bond        0.04573 (  269)
  hydrogen bonds       : angle       4.22577 (  759)
  SS BOND              : bond        0.00277 (    7)
  SS BOND              : angle       2.05257 (   14)
  covalent geometry    : bond        0.00305 ( 6638)
  covalent geometry    : angle       0.61651 ( 9017)

*********************** 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
  104 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  249 MET cc_start: 0.5916 (tpt) cc_final: 0.4853 (tpt)
  outliers start: 12
  outliers final: 9
  residues processed: 101
  average time/residue: 0.4482
  time to fit residues: 59.9162
Evaluate side-chains
  100 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  353 TRP
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
Chi-restraints excluded: chain A residue  473 TRP
Chi-restraints excluded: chain A residue  598 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0270
   chunk 4 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0970
   chunk 30 optimal weight:    6.9990
   overall best weight:    0.4636

-------------------------------------------------------------------------------
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 508 ASN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.184352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.161978 restraints weight = 26764.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 4.18
r_work: 0.3798 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    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 = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6648  Z= 0.112
  Angle     :  0.615  10.675   9040  Z= 0.308
  Chirality :  0.041   0.214    942
  Planarity :  0.004   0.046   1171
  Dihedral  :  4.294  24.509    929
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.10 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.37 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.30), residues: 788
  helix:  1.09 (0.28), residues: 373
  sheet: -0.65 (0.72), residues: 52
  loop : -2.34 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 265 
 PHE   0.017   0.001   PHE A  72 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.004   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00119 (    2)
  link_NAG-ASN         : angle       1.91058 (    6)
  link_BETA1-4         : bond        0.00633 (    1)
  link_BETA1-4         : angle       0.66430 (    3)
  hydrogen bonds       : bond        0.03948 (  269)
  hydrogen bonds       : angle       4.21556 (  759)
  SS BOND              : bond        0.00328 (    7)
  SS BOND              : angle       1.86093 (   14)
  covalent geometry    : bond        0.00248 ( 6638)
  covalent geometry    : angle       0.60927 ( 9017)

********************** 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
  99 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A  249 MET cc_start: 0.6014 (tpt) cc_final: 0.5001 (tpt)
  outliers start: 9
  outliers final: 8
  residues processed: 96
  average time/residue: 0.2370
  time to fit residues: 30.0777
Evaluate side-chains
  94 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  353 TRP
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
Chi-restraints excluded: chain A residue  473 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 31 optimal weight:    9.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4229 r_free = 0.4229 target = 0.182584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.160102 restraints weight = 27397.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 4.36
r_work: 0.3767 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3799
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3799 r_free = 0.3799    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3799 r_free = 0.3799    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3799
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6648  Z= 0.129
  Angle     :  0.627  10.557   9040  Z= 0.314
  Chirality :  0.042   0.208    942
  Planarity :  0.004   0.044   1171
  Dihedral  :  4.367  23.660    929
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.24 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.66 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.30), residues: 788
  helix:  1.16 (0.28), residues: 368
  sheet: -0.79 (0.72), residues: 53
  loop : -2.37 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.016   0.001   PHE A  72 
 TYR   0.017   0.001   TYR A 183 
 ARG   0.004   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00201 (    2)
  link_NAG-ASN         : angle       2.04207 (    6)
  link_BETA1-4         : bond        0.00757 (    1)
  link_BETA1-4         : angle       0.78227 (    3)
  hydrogen bonds       : bond        0.04355 (  269)
  hydrogen bonds       : angle       4.22534 (  759)
  SS BOND              : bond        0.00261 (    7)
  SS BOND              : angle       2.01337 (   14)
  covalent geometry    : bond        0.00292 ( 6638)
  covalent geometry    : angle       0.62017 ( 9017)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4725.69 seconds
wall clock time: 87 minutes 21.49 seconds (5241.49 seconds total)