Starting phenix.real_space_refine
on Thu Jul 24 21:36:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7li6_23361/07_2025/7li6_23361.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7li6_23361/07_2025/7li6_23361.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2025/7li6_23361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2025/7li6_23361.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2025/7li6_23361.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2025/7li6_23361.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.040
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: 5
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     Cl      1      4.86       5
     C    4178      2.51       5
     N     958      2.21       5
     O    1078      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6249
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4284
          Classifications: {'peptide': 539}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 23, 'TRANS': 515}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 912
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 196
          Unusual residues: {' CL': 1, 'D10': 6, 'D12': 3, 'HP6': 9, 'LNK': 4, 'R16': 1}
          Classifications: {'undetermined': 24}
          Link IDs: {None: 23}
  Time building chain proxies: 5.83, per 1000 atoms: 0.93
  Number of scatterers: 6249
  At special positions: 0
  Unit cell: (70.066, 79.981, 123.607, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      34     16.00
     O    1078      8.00
     N     958      7.00
     C    4178      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 112 " 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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 208 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.99
  Conformation dependent library (CDL) restraints added in 924.2 milliseconds
  

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      51.5% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 88 through 93
    Processing helix  chain 'A' and resid 103 through 112
      removed outlier: 3.597A  pdb=" N   TYR A 107 " --> pdb=" O   TRP A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 129 through 143
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.332A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 4.324A  pdb=" N   CYS A 258 " --> pdb=" O   GLN A 254 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 285 through 301
      removed outlier: 4.174A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 3.528A  pdb=" N   VAL A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 310 " --> pdb=" O   TRP A 306 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   PHE A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 322
      removed outlier: 3.763A  pdb=" N   LEU A 321 " --> pdb=" O   TRP A 317 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLU A 322 " --> pdb=" O   GLN A 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 317 through 322'
    Processing helix  chain 'A' and resid 325 through 338
      removed outlier: 3.909A  pdb=" N   GLY A 338 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 348
      removed outlier: 3.518A  pdb=" N   ALA A 346 " --> pdb=" O   GLY A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 391
    Processing helix  chain 'A' and resid 393 through 397
      removed outlier: 3.800A  pdb=" N   VAL A 397 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
      removed outlier: 4.248A  pdb=" N   ALA A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 443
      removed outlier: 4.000A  pdb=" N   ALA A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 454
      removed outlier: 3.813A  pdb=" N   ILE A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   ALA A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASP A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 4.454A  pdb=" N   ARG A 461 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A 462 " --> pdb=" O   TRP A 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 457 through 462'
    Processing helix  chain 'A' and resid 463 through 476
      removed outlier: 3.521A  pdb=" N   ALA A 468 " --> pdb=" O   ARG A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 490
      removed outlier: 3.659A  pdb=" N   LYS A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 495
      removed outlier: 4.402A  pdb=" N   GLU A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 515
    Processing helix  chain 'A' and resid 517 through 530
    Processing helix  chain 'A' and resid 534 through 544
      removed outlier: 4.105A  pdb=" N   TRP A 541 " --> pdb=" O   TRP A 537 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   VAL A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA A 543 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 559
    Processing helix  chain 'A' and resid 572 through 585
      removed outlier: 4.354A  pdb=" N   ILE A 576 " --> pdb=" O   TYR A 572 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 3.656A  pdb=" N   LEU A 597 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ILE A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ILE A 599 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR A 600 " --> pdb=" O   ARG A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 613
      removed outlier: 3.634A  pdb=" N   THR A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 3.987A  pdb=" N   TYR B  50 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER B  51 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 47 through 51'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 25
      removed outlier: 3.827A  pdb=" N   VAL B  37 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 79
      removed outlier: 7.174A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79
      removed outlier: 7.174A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TYR B 113 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 25 through 26
      removed outlier: 3.567A  pdb=" N   THR C  25 " --> pdb=" O   ARG C  44 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31
      removed outlier: 3.731A  pdb=" N   LEU C  31 " --> pdb=" O   LYS C 127 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR C 126 " --> pdb=" O   TYR C 110 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TYR C 110 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.538A  pdb=" N   TYR C  73 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   LEU C  70 " --> pdb=" O   GLN C  61 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   GLN C  61 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89

    265 hydrogen bonds defined for protein.
    765 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: 1.83

  Time building geometry restraints manager: 2.31 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: 1808
        1.34 -     1.46: 1610
        1.46 -     1.58: 2936
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 6403
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" C2  NAG D   1 "
       pdb=" N2  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.52e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.51e+00
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.30e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.25e+00
  ... (remaining 6398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 8224
        1.11 -     2.22: 194
        2.22 -     3.34: 91
        3.34 -     4.45: 111
        4.45 -     5.56: 12
  Bond angle restraints: 8632
  Sorted by residual:
  angle pdb=" N   TYR A 495 "
        pdb=" CA  TYR A 495 "
        pdb=" C   TYR A 495 "
      ideal   model   delta    sigma   weight residual
     114.04  110.66    3.38 1.24e+00 6.50e-01 7.43e+00
  angle pdb=" N   VAL A 102 "
        pdb=" CA  VAL A 102 "
        pdb=" C   VAL A 102 "
      ideal   model   delta    sigma   weight residual
     113.39  109.50    3.89 1.47e+00 4.63e-01 7.01e+00
  angle pdb=" C   ALA C  74 "
        pdb=" N   ALA C  75 "
        pdb=" CA  ALA C  75 "
      ideal   model   delta    sigma   weight residual
     121.54  126.36   -4.82 1.91e+00 2.74e-01 6.38e+00
  angle pdb=" CA  GLY C  90 "
        pdb=" C   GLY C  90 "
        pdb=" O   GLY C  90 "
      ideal   model   delta    sigma   weight residual
     122.22  120.64    1.58 6.50e-01 2.37e+00 5.92e+00
  angle pdb=" C   ARG A 461 "
        pdb=" N   ARG A 462 "
        pdb=" CA  ARG A 462 "
      ideal   model   delta    sigma   weight residual
     121.54  126.02   -4.48 1.91e+00 2.74e-01 5.51e+00
  ... (remaining 8627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 3426
       17.66 -    35.32: 225
       35.32 -    52.98: 48
       52.98 -    70.64: 6
       70.64 -    88.30: 6
  Dihedral angle restraints: 3711
    sinusoidal: 1505
      harmonic: 2206
  Sorted by residual:
  dihedral pdb=" CB  CYS A 200 "
           pdb=" SG  CYS A 200 "
           pdb=" SG  CYS A 209 "
           pdb=" CB  CYS A 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -150.26   64.26     1      1.00e+01 1.00e-02 5.43e+01
  dihedral pdb=" CB  GLU A 606 "
           pdb=" CG  GLU A 606 "
           pdb=" CD  GLU A 606 "
           pdb=" OE1 GLU A 606 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.30  -88.30     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU A 412 "
           pdb=" CG  GLU A 412 "
           pdb=" CD  GLU A 412 "
           pdb=" OE1 GLU A 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.56  -83.56     1      3.00e+01 1.11e-03 9.47e+00
  ... (remaining 3708 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.331: 941
       0.331 -    0.661: 0
       0.661 -    0.992: 0
       0.992 -    1.322: 0
       1.322 -    1.653: 1
  Chirality restraints: 942
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.75   -1.65 2.00e-02 2.50e+03 6.83e+03
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.17 2.00e-01 2.50e+01 7.43e-01
  chirality pdb=" CB  ILE C  99 "
            pdb=" CA  ILE C  99 "
            pdb=" CG1 ILE C  99 "
            pdb=" CG2 ILE C  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 5.00e-01
  ... (remaining 939 not shown)

  Planarity restraints: 1045
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 338 "   -0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO A 339 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 339 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 339 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 287 "   -0.023 5.00e-02 4.00e+02   3.51e-02 1.97e+00
        pdb=" N   PRO A 288 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  88 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.30e+00
        pdb=" C   PHE A  88 "    0.020 2.00e-02 2.50e+03
        pdb=" O   PHE A  88 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   LEU A  89 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1042 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1963
        2.83 -     3.35: 5435
        3.35 -     3.86: 9805
        3.86 -     4.38: 10688
        4.38 -     4.90: 19047
  Nonbonded interactions: 46938
  Sorted by model distance:
  nonbonded pdb=" O   SER A 190 "
            pdb=" OG  SER A 190 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   GLU A 229 "
            pdb=" OG1 THR A 233 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" NE2 GLN C 114 "
            pdb=" O   SER C 119 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" O   VAL A 297 "
            pdb=" OG1 THR A 301 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OG  SER C  87 "
            pdb=" OD1 ASN C  98 "
     model   vdw
     2.354 3.040
  ... (remaining 46933 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.960
  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:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.610
  Find NCS groups from input model:        0.070
  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:5.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
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   0.065   6409  Z= 0.111
  Angle     :  0.744  28.058   8644  Z= 0.324
  Chirality :  0.066   1.653    942
  Planarity :  0.003   0.039   1044
  Dihedral  : 12.312  88.297   2302
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.53 %
    Favored  : 88.75 %
  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: -3.07 (0.27), residues: 761
  helix: -0.87 (0.25), residues: 343
  sheet: -2.44 (0.62), residues: 76
  loop : -3.22 (0.28), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 282 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.003   0.000   PHE A  88 
 TYR   0.011   0.001   TYR A 175 
 ARG   0.001   0.000   ARG A 234 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00286 (    1)
  link_NAG-ASN         : angle       1.79528 (    3)
  link_BETA1-4         : bond        0.06474 (    1)
  link_BETA1-4         : angle      17.65278 (    3)
  hydrogen bonds       : bond        0.19283 (  260)
  hydrogen bonds       : angle       5.83562 (  765)
  SS BOND              : bond        0.00070 (    3)
  SS BOND              : angle       0.21395 (    6)
  covalent geometry    : bond        0.00192 ( 6403)
  covalent geometry    : angle       0.66671 ( 8632)
  Misc. bond           : bond        0.00064 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 2.239 
Fit side-chains
REVERT: A  306 TRP cc_start: 0.7018 (t-100) cc_final: 0.6154 (p-90)
REVERT: A  514 TRP cc_start: 0.7063 (m-10) cc_final: 0.6686 (m100)
REVERT: A  535 TRP cc_start: 0.6493 (t60) cc_final: 0.6135 (p-90)
REVERT: A  607 ARG cc_start: 0.7332 (mtt180) cc_final: 0.7032 (mtt180)
REVERT: B   99 TYR cc_start: 0.8296 (m-80) cc_final: 0.8051 (m-80)
REVERT: C   69 LYS cc_start: 0.7459 (tttp) cc_final: 0.7254 (tttm)
REVERT: C   71 LEU cc_start: 0.7884 (tp) cc_final: 0.7629 (tp)
REVERT: C  116 LYS cc_start: 0.6969 (tttt) cc_final: 0.6637 (mttp)
  outliers start: 11
  outliers final: 7
  residues processed: 110
  average time/residue: 0.3819
  time to fit residues: 52.4453
Evaluate side-chains
  73 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0970
   chunk 22 optimal weight:    0.0470
   chunk 35 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
A 145 ASN
A 254 GLN
A 416 ASN
A 520 GLN
B  24 GLN
C  98 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.185224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.163780 restraints weight = 6857.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.165458 restraints weight = 5033.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.166610 restraints weight = 4259.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6409  Z= 0.104
  Angle     :  0.518  10.116   8644  Z= 0.261
  Chirality :  0.040   0.246    942
  Planarity :  0.004   0.035   1044
  Dihedral  :  5.160  56.724   1009
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.22 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.30), residues: 761
  helix:  0.29 (0.28), residues: 350
  sheet: -1.79 (0.61), residues: 86
  loop : -2.83 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  59 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.008   0.001   PHE A 380 
 TYR   0.022   0.001   TYR A 358 
 ARG   0.007   0.001   ARG A 564 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00160 (    1)
  link_NAG-ASN         : angle       1.53730 (    3)
  link_BETA1-4         : bond        0.00031 (    1)
  link_BETA1-4         : angle       0.77692 (    3)
  hydrogen bonds       : bond        0.03184 (  260)
  hydrogen bonds       : angle       4.08150 (  765)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       0.73150 (    6)
  covalent geometry    : bond        0.00229 ( 6403)
  covalent geometry    : angle       0.51731 ( 8632)
  Misc. bond           : bond        0.00017 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
REVERT: A  301 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7474 (p)
REVERT: A  370 MET cc_start: 0.7106 (mmp) cc_final: 0.6717 (mmt)
REVERT: C   69 LYS cc_start: 0.7987 (tttp) cc_final: 0.7771 (tttm)
  outliers start: 19
  outliers final: 11
  residues processed: 93
  average time/residue: 0.2459
  time to fit residues: 29.6458
Evaluate side-chains
  75 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.162694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.128684 restraints weight = 7623.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.133813 restraints weight = 4564.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.137181 restraints weight = 3278.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6409  Z= 0.154
  Angle     :  0.560   9.394   8644  Z= 0.287
  Chirality :  0.042   0.268    942
  Planarity :  0.004   0.030   1044
  Dihedral  :  5.181  57.282   1003
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 15.31 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.31), residues: 761
  helix:  0.46 (0.28), residues: 355
  sheet: -1.81 (0.56), residues: 98
  loop : -2.68 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 204 
 HIS   0.002   0.001   HIS A 223 
 PHE   0.017   0.001   PHE A 334 
 TYR   0.023   0.002   TYR A 176 
 ARG   0.005   0.001   ARG A 462 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00099 (    1)
  link_NAG-ASN         : angle       2.10073 (    3)
  link_BETA1-4         : bond        0.00518 (    1)
  link_BETA1-4         : angle       1.35597 (    3)
  hydrogen bonds       : bond        0.04065 (  260)
  hydrogen bonds       : angle       4.18476 (  765)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       1.48757 (    6)
  covalent geometry    : bond        0.00367 ( 6403)
  covalent geometry    : angle       0.55697 ( 8632)
  Misc. bond           : bond        0.00036 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
REVERT: A  306 TRP cc_start: 0.7177 (t-100) cc_final: 0.6288 (p-90)
REVERT: A  370 MET cc_start: 0.7239 (mmp) cc_final: 0.6839 (mmt)
REVERT: A  386 MET cc_start: 0.7359 (ttp) cc_final: 0.7079 (mtm)
REVERT: A  458 TRP cc_start: 0.8275 (m100) cc_final: 0.7863 (m100)
REVERT: B   53 MET cc_start: 0.8271 (tpt) cc_final: 0.8009 (mmt)
  outliers start: 28
  outliers final: 19
  residues processed: 89
  average time/residue: 0.1860
  time to fit residues: 22.3882
Evaluate side-chains
  83 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 14 optimal weight:    0.1980
   chunk 61 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0670
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.162480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.126753 restraints weight = 7503.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.132493 restraints weight = 4332.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.136362 restraints weight = 3033.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6409  Z= 0.112
  Angle     :  0.533   9.471   8644  Z= 0.268
  Chirality :  0.041   0.257    942
  Planarity :  0.004   0.030   1044
  Dihedral  :  4.976  56.930   1003
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 17.03 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.31), residues: 761
  helix:  0.66 (0.28), residues: 354
  sheet: -1.22 (0.60), residues: 92
  loop : -2.56 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.010   0.001   PHE A 133 
 TYR   0.023   0.001   TYR A 176 
 ARG   0.004   0.000   ARG A 462 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00157 (    1)
  link_NAG-ASN         : angle       2.06052 (    3)
  link_BETA1-4         : bond        0.00415 (    1)
  link_BETA1-4         : angle       0.85588 (    3)
  hydrogen bonds       : bond        0.03351 (  260)
  hydrogen bonds       : angle       4.07124 (  765)
  SS BOND              : bond        0.00208 (    3)
  SS BOND              : angle       1.39937 (    6)
  covalent geometry    : bond        0.00262 ( 6403)
  covalent geometry    : angle       0.52999 ( 8632)
  Misc. bond           : bond        0.00022 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 64
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  152 ARG cc_start: 0.8424 (tpp80) cc_final: 0.7999 (tpp80)
REVERT: A  347 PHE cc_start: 0.6898 (m-80) cc_final: 0.6662 (m-80)
REVERT: A  370 MET cc_start: 0.6664 (mmp) cc_final: 0.6305 (mmt)
REVERT: A  386 MET cc_start: 0.6802 (ttp) cc_final: 0.6577 (mtm)
REVERT: A  564 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7478 (ttt-90)
  outliers start: 27
  outliers final: 21
  residues processed: 84
  average time/residue: 0.1893
  time to fit residues: 21.4888
Evaluate side-chains
  84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 59 optimal weight:    0.0270
   chunk 4 optimal weight:    0.3980
   chunk 34 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6638

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.158429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.122922 restraints weight = 7388.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.128404 restraints weight = 4354.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.132122 restraints weight = 3076.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6409  Z= 0.127
  Angle     :  0.544   9.440   8644  Z= 0.274
  Chirality :  0.042   0.264    942
  Planarity :  0.004   0.032   1044
  Dihedral  :  5.160  57.151   1003
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 17.19 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.32), residues: 761
  helix:  0.72 (0.28), residues: 354
  sheet: -1.32 (0.59), residues: 97
  loop : -2.41 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 514 
 HIS   0.002   0.001   HIS C 100 
 PHE   0.012   0.001   PHE A 213 
 TYR   0.024   0.001   TYR A 176 
 ARG   0.002   0.000   ARG A 462 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00161 (    1)
  link_NAG-ASN         : angle       2.43358 (    3)
  link_BETA1-4         : bond        0.00477 (    1)
  link_BETA1-4         : angle       0.73284 (    3)
  hydrogen bonds       : bond        0.03540 (  260)
  hydrogen bonds       : angle       4.10538 (  765)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       1.87771 (    6)
  covalent geometry    : bond        0.00305 ( 6403)
  covalent geometry    : angle       0.54051 ( 8632)
  Misc. bond           : bond        0.00038 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 70
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A  107 TYR cc_start: 0.5759 (OUTLIER) cc_final: 0.5089 (t80)
REVERT: A  306 TRP cc_start: 0.6935 (t-100) cc_final: 0.5734 (p-90)
REVERT: A  370 MET cc_start: 0.6662 (mmp) cc_final: 0.6319 (mmt)
REVERT: A  493 GLU cc_start: 0.7877 (tt0) cc_final: 0.7650 (tt0)
REVERT: A  564 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7374 (ttt-90)
REVERT: B   53 MET cc_start: 0.8251 (tpt) cc_final: 0.7616 (mmt)
  outliers start: 30
  outliers final: 21
  residues processed: 94
  average time/residue: 0.1844
  time to fit residues: 23.4389
Evaluate side-chains
  83 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.160797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.126154 restraints weight = 7776.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131344 restraints weight = 4581.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.134801 restraints weight = 3272.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6409  Z= 0.134
  Angle     :  0.558   9.403   8644  Z= 0.282
  Chirality :  0.042   0.262    942
  Planarity :  0.004   0.033   1044
  Dihedral  :  5.287  57.068   1003
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.75 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.32), residues: 761
  helix:  0.77 (0.28), residues: 353
  sheet: -1.24 (0.59), residues: 97
  loop : -2.38 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 514 
 HIS   0.001   0.001   HIS A 235 
 PHE   0.017   0.001   PHE A 423 
 TYR   0.023   0.001   TYR A 176 
 ARG   0.008   0.001   ARG A 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00110 (    1)
  link_NAG-ASN         : angle       2.52558 (    3)
  link_BETA1-4         : bond        0.00399 (    1)
  link_BETA1-4         : angle       0.63051 (    3)
  hydrogen bonds       : bond        0.03608 (  260)
  hydrogen bonds       : angle       4.15672 (  765)
  SS BOND              : bond        0.00255 (    3)
  SS BOND              : angle       1.91368 (    6)
  covalent geometry    : bond        0.00319 ( 6403)
  covalent geometry    : angle       0.55421 ( 8632)
  Misc. bond           : bond        0.00038 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.593 
Fit side-chains
REVERT: A  102 VAL cc_start: 0.8895 (p) cc_final: 0.8665 (t)
REVERT: A  107 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.5722 (t80)
REVERT: A  185 TYR cc_start: 0.8379 (t80) cc_final: 0.8134 (t80)
REVERT: A  306 TRP cc_start: 0.7234 (t-100) cc_final: 0.6291 (p-90)
REVERT: A  370 MET cc_start: 0.7237 (mmp) cc_final: 0.6933 (mmt)
REVERT: A  388 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7523 (tm-30)
  outliers start: 25
  outliers final: 21
  residues processed: 87
  average time/residue: 0.1846
  time to fit residues: 21.8328
Evaluate side-chains
  89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 19 optimal weight:    0.0070
   chunk 18 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.162791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.127692 restraints weight = 7715.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.132969 restraints weight = 4563.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.136514 restraints weight = 3266.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6409  Z= 0.105
  Angle     :  0.528   9.392   8644  Z= 0.266
  Chirality :  0.041   0.260    942
  Planarity :  0.003   0.033   1044
  Dihedral  :  4.869  57.286   1001
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.84 %
    Favored  : 76.88 %
  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: -0.98 (0.32), residues: 761
  helix:  0.79 (0.28), residues: 360
  sheet: -0.78 (0.61), residues: 92
  loop : -2.41 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.010   0.001   PHE A 423 
 TYR   0.024   0.001   TYR A 176 
 ARG   0.006   0.000   ARG A 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00238 (    1)
  link_NAG-ASN         : angle       2.54434 (    3)
  link_BETA1-4         : bond        0.00453 (    1)
  link_BETA1-4         : angle       0.60541 (    3)
  hydrogen bonds       : bond        0.03156 (  260)
  hydrogen bonds       : angle       4.11706 (  765)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       1.75701 (    6)
  covalent geometry    : bond        0.00240 ( 6403)
  covalent geometry    : angle       0.52430 ( 8632)
  Misc. bond           : bond        0.00018 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 VAL cc_start: 0.8882 (p) cc_final: 0.8644 (t)
REVERT: A  185 TYR cc_start: 0.8343 (t80) cc_final: 0.8066 (t80)
REVERT: A  306 TRP cc_start: 0.7238 (t-100) cc_final: 0.6275 (p-90)
REVERT: A  370 MET cc_start: 0.7188 (mmp) cc_final: 0.6870 (mmt)
REVERT: A  385 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6448 (t80)
REVERT: B   38 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7294 (ttm-80)
REVERT: B   53 MET cc_start: 0.8320 (tpt) cc_final: 0.7929 (mmt)
  outliers start: 21
  outliers final: 19
  residues processed: 86
  average time/residue: 0.1812
  time to fit residues: 21.4458
Evaluate side-chains
  88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    0.2980
   chunk 24 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.166313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.144396 restraints weight = 7087.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.145237 restraints weight = 5624.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.146763 restraints weight = 4980.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6409  Z= 0.119
  Angle     :  0.540   9.388   8644  Z= 0.274
  Chirality :  0.041   0.262    942
  Planarity :  0.003   0.033   1044
  Dihedral  :  4.934  57.293   1001
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.53 %
    Favored  : 77.19 %
  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 (0.32), residues: 761
  helix:  0.82 (0.28), residues: 360
  sheet: -0.65 (0.62), residues: 92
  loop : -2.38 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.013   0.001   PHE A 423 
 TYR   0.024   0.001   TYR A 176 
 ARG   0.005   0.000   ARG A 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00202 (    1)
  link_NAG-ASN         : angle       2.63795 (    3)
  link_BETA1-4         : bond        0.00397 (    1)
  link_BETA1-4         : angle       0.55900 (    3)
  hydrogen bonds       : bond        0.03264 (  260)
  hydrogen bonds       : angle       4.14522 (  765)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       1.78683 (    6)
  covalent geometry    : bond        0.00281 ( 6403)
  covalent geometry    : angle       0.53624 ( 8632)
  Misc. bond           : bond        0.00029 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 VAL cc_start: 0.8907 (p) cc_final: 0.8704 (t)
REVERT: A  306 TRP cc_start: 0.7256 (t-100) cc_final: 0.6711 (p-90)
REVERT: A  370 MET cc_start: 0.7245 (mmp) cc_final: 0.7020 (mmt)
REVERT: A  385 TYR cc_start: 0.6844 (OUTLIER) cc_final: 0.6564 (t80)
REVERT: B   53 MET cc_start: 0.8143 (tpt) cc_final: 0.7937 (mmt)
  outliers start: 21
  outliers final: 19
  residues processed: 91
  average time/residue: 0.1763
  time to fit residues: 22.0773
Evaluate side-chains
  89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0870
   chunk 27 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 145 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.226254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.192525 restraints weight = 7684.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.196816 restraints weight = 5043.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.199645 restraints weight = 3818.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6409  Z= 0.121
  Angle     :  0.557   9.377   8644  Z= 0.281
  Chirality :  0.042   0.260    942
  Planarity :  0.003   0.033   1044
  Dihedral  :  4.968  57.428   1001
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 20.00 %
    Favored  : 76.09 %
  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 (0.32), residues: 761
  helix:  0.80 (0.28), residues: 361
  sheet: -0.91 (0.60), residues: 97
  loop : -2.25 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.011   0.001   PHE A 133 
 TYR   0.027   0.002   TYR A 110 
 ARG   0.005   0.000   ARG A 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00208 (    1)
  link_NAG-ASN         : angle       2.62980 (    3)
  link_BETA1-4         : bond        0.00428 (    1)
  link_BETA1-4         : angle       0.59920 (    3)
  hydrogen bonds       : bond        0.03314 (  260)
  hydrogen bonds       : angle       4.15202 (  765)
  SS BOND              : bond        0.00215 (    3)
  SS BOND              : angle       1.79911 (    6)
  covalent geometry    : bond        0.00290 ( 6403)
  covalent geometry    : angle       0.55301 ( 8632)
  Misc. bond           : bond        0.00031 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 VAL cc_start: 0.8978 (p) cc_final: 0.8737 (t)
REVERT: A  306 TRP cc_start: 0.7306 (t-100) cc_final: 0.6568 (p-90)
REVERT: A  370 MET cc_start: 0.7302 (mmp) cc_final: 0.7058 (mmt)
REVERT: B   53 MET cc_start: 0.8114 (tpt) cc_final: 0.7912 (mmt)
  outliers start: 25
  outliers final: 20
  residues processed: 86
  average time/residue: 0.1875
  time to fit residues: 22.2006
Evaluate side-chains
  82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 2 optimal weight:    0.0270
   chunk 38 optimal weight:    0.0570
   chunk 59 optimal weight:    0.0970
   chunk 69 optimal weight:    0.0170
   chunk 67 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0870
   chunk 24 optimal weight:    0.0570
   overall best weight:    0.0490

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 416 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.166194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.144130 restraints weight = 7153.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.144628 restraints weight = 5741.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.147022 restraints weight = 5091.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108   6409  Z= 0.181
  Angle     :  0.983  59.123   8644  Z= 0.582
  Chirality :  0.044   0.490    942
  Planarity :  0.004   0.033   1044
  Dihedral  :  5.026  57.426   1001
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 20.16 %
    Favored  : 76.09 %
  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: -0.87 (0.32), residues: 761
  helix:  0.82 (0.28), residues: 361
  sheet: -0.91 (0.60), residues: 97
  loop : -2.23 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.016   0.001   PHE A 423 
 TYR   0.024   0.002   TYR A 110 
 ARG   0.004   0.000   ARG A 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00238 (    1)
  link_NAG-ASN         : angle       2.62149 (    3)
  link_BETA1-4         : bond        0.00530 (    1)
  link_BETA1-4         : angle       0.87623 (    3)
  hydrogen bonds       : bond        0.03255 (  260)
  hydrogen bonds       : angle       4.15477 (  765)
  SS BOND              : bond        0.00231 (    3)
  SS BOND              : angle       1.80325 (    6)
  covalent geometry    : bond        0.00384 ( 6403)
  covalent geometry    : angle       0.98166 ( 8632)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 VAL cc_start: 0.8916 (p) cc_final: 0.8712 (t)
REVERT: A  306 TRP cc_start: 0.7280 (t-100) cc_final: 0.6650 (p-90)
REVERT: A  370 MET cc_start: 0.7289 (mmp) cc_final: 0.7054 (mmt)
REVERT: B   53 MET cc_start: 0.8166 (tpt) cc_final: 0.7924 (mmt)
  outliers start: 24
  outliers final: 22
  residues processed: 81
  average time/residue: 0.1769
  time to fit residues: 19.6624
Evaluate side-chains
  84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0170
   chunk 7 optimal weight:    0.3980
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0070
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.166512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.144179 restraints weight = 7287.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.145163 restraints weight = 5718.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.147188 restraints weight = 5031.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103   6409  Z= 0.175
  Angle     :  0.982  59.200   8644  Z= 0.576
  Chirality :  0.043   0.367    942
  Planarity :  0.003   0.033   1044
  Dihedral  :  5.018  57.428   1001
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.62 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.87 (0.32), residues: 761
  helix:  0.82 (0.28), residues: 361
  sheet: -0.91 (0.60), residues: 97
  loop : -2.23 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.015   0.001   PHE A 423 
 TYR   0.023   0.002   TYR A 110 
 ARG   0.004   0.000   ARG A 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00235 (    1)
  link_NAG-ASN         : angle       2.62083 (    3)
  link_BETA1-4         : bond        0.00279 (    1)
  link_BETA1-4         : angle       0.41889 (    3)
  hydrogen bonds       : bond        0.03259 (  260)
  hydrogen bonds       : angle       4.15433 (  765)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       1.80288 (    6)
  covalent geometry    : bond        0.00377 ( 6403)
  covalent geometry    : angle       0.98004 ( 8632)
  Misc. bond           : bond        0.00012 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3097.43 seconds
wall clock time: 54 minutes 53.11 seconds (3293.11 seconds total)