Starting phenix.real_space_refine
on Wed Apr 30 06:55:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jkv_36376/04_2025/8jkv_36376.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jkv_36376/04_2025/8jkv_36376.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jkv_36376/04_2025/8jkv_36376.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jkv_36376/04_2025/8jkv_36376.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jkv_36376/04_2025/8jkv_36376.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jkv_36376/04_2025/8jkv_36376.cif"
  }
  resolution = 2.87
  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=   0.000 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    6396      2.51       5
     N    1350      2.21       5
     O    1482      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9266
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4189
          Classifications: {'peptide': 527}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 501}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4189
          Classifications: {'peptide': 527}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 501}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 396
          Unusual residues: {'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 1, 'OCT': 16, 'R16': 1}
          Classifications: {'undetermined': 35}
          Link IDs: {None: 34}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 380
          Unusual residues: {'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 1, 'OCT': 14, 'R16': 1}
          Classifications: {'undetermined': 33}
          Link IDs: {None: 32}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.26, per 1000 atoms: 0.78
  Number of scatterers: 9266
  At special positions: 0
  Unit cell: (110.39, 88.81, 105.41, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1482      8.00
     N    1350      7.00
     C    6396      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 104 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 104 " - pdb=" SG  CYS B 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 151 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 443 " - pdb=" SG  CYS B 462 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 801 " - " ASN A  94 "
      " NAG B 802 " - " ASN B  94 "
      " NAG C   1 " - " ASN A 142 "
      " NAG D   1 " - " ASN A 162 "
      " NAG E   1 " - " ASN B 142 "
      " NAG F   1 " - " ASN B 162 "
  Time building additional restraints: 2.81
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 4 sheets defined
      56.2% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 191 through 215
    Processing helix  chain 'A' and resid 268 through 288
      removed outlier: 3.727A  pdb=" N   ASP A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLY A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 296
      removed outlier: 6.715A  pdb=" N   TRP A 293 " --> pdb=" O   GLY A 290 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   TYR A 294 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LYS A 296 " --> pdb=" O   TRP A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 331
      removed outlier: 3.514A  pdb=" N   TRP A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 356
    Processing helix  chain 'A' and resid 367 through 371
    Processing helix  chain 'A' and resid 375 through 394
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 417 through 437
    Processing helix  chain 'A' and resid 453 through 458
      removed outlier: 3.644A  pdb=" N   PHE A 456 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS A 458 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 476
    Processing helix  chain 'A' and resid 477 through 480
      removed outlier: 3.591A  pdb=" N   LEU A 480 " --> pdb=" O   ASP A 477 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 477 through 480'
    Processing helix  chain 'A' and resid 486 through 491
    Processing helix  chain 'A' and resid 503 through 524
    Processing helix  chain 'A' and resid 527 through 551
      removed outlier: 3.537A  pdb=" N   ILE A 531 " --> pdb=" O   ARG A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 590
      Proline residue:  A 587  - end of helix
    Processing helix  chain 'A' and resid 600 through 605
    Processing helix  chain 'A' and resid 606 through 617
    Processing helix  chain 'A' and resid 632 through 657
      removed outlier: 3.521A  pdb=" N   HIS A 636 " --> pdb=" O   SER A 632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 215
    Processing helix  chain 'B' and resid 268 through 288
      removed outlier: 3.728A  pdb=" N   ASP B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLY B 288 " --> pdb=" O   PHE B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 296
      removed outlier: 6.715A  pdb=" N   TRP B 293 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   TYR B 294 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS B 296 " --> pdb=" O   TRP B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 331
      removed outlier: 3.514A  pdb=" N   TRP B 312 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 356
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 375 through 394
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 417 through 437
    Processing helix  chain 'B' and resid 453 through 458
      removed outlier: 3.645A  pdb=" N   PHE B 456 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS B 458 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 476
    Processing helix  chain 'B' and resid 477 through 480
      removed outlier: 3.591A  pdb=" N   LEU B 480 " --> pdb=" O   ASP B 477 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 477 through 480'
    Processing helix  chain 'B' and resid 486 through 491
    Processing helix  chain 'B' and resid 503 through 524
    Processing helix  chain 'B' and resid 527 through 551
      removed outlier: 3.536A  pdb=" N   ILE B 531 " --> pdb=" O   ARG B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 590
      Proline residue:  B 587  - end of helix
    Processing helix  chain 'B' and resid 600 through 605
    Processing helix  chain 'B' and resid 606 through 617
    Processing helix  chain 'B' and resid 632 through 657
      removed outlier: 3.522A  pdb=" N   HIS B 636 " --> pdb=" O   SER B 632 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132
      removed outlier: 8.989A  pdb=" N   TYR A 163 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   LEU A  83 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   LEU A  85 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   HIS A  87 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ASN A 162 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ALA A 178 " --> pdb=" O   LYS A 168 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115
      removed outlier: 6.825A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   ASN A 114 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   LEU A  95 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   CYS A 151 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132
      removed outlier: 8.989A  pdb=" N   TYR B 163 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   LEU B  83 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   LEU B 165 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   LEU B  85 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   HIS B  87 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ASN B 162 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ALA B 178 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115
      removed outlier: 6.824A  pdb=" N   VAL B  97 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   ASN B 114 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   LEU B  95 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   CYS B 151 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.48

  Time building geometry restraints manager: 3.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2529
        1.34 -     1.46: 1871
        1.46 -     1.58: 4992
        1.58 -     1.70: 0
        1.70 -     1.82: 50
  Bond restraints: 9442
  Sorted by residual:
  bond pdb=" CB  PRO A 311 "
       pdb=" CG  PRO A 311 "
    ideal  model  delta    sigma   weight residual
    1.492  1.413  0.079 5.00e-02 4.00e+02 2.53e+00
  bond pdb=" CB  PRO B 311 "
       pdb=" CG  PRO B 311 "
    ideal  model  delta    sigma   weight residual
    1.492  1.413  0.079 5.00e-02 4.00e+02 2.50e+00
  bond pdb=" C1  NAG B 802 "
       pdb=" O5  NAG B 802 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.36e+00
  bond pdb=" C1  NAG A 801 "
       pdb=" O5  NAG A 801 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.32e+00
  bond pdb=" CB  CYS A 104 "
       pdb=" SG  CYS A 104 "
    ideal  model  delta    sigma   weight residual
    1.808  1.760  0.048 3.30e-02 9.18e+02 2.14e+00
  ... (remaining 9437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 12033
        1.42 -     2.83: 446
        2.83 -     4.25: 79
        4.25 -     5.66: 24
        5.66 -     7.08: 4
  Bond angle restraints: 12586
  Sorted by residual:
  angle pdb=" C   GLY B 613 "
        pdb=" N   HIS B 614 "
        pdb=" CA  HIS B 614 "
      ideal   model   delta    sigma   weight residual
     121.14  116.42    4.72 1.75e+00 3.27e-01 7.27e+00
  angle pdb=" C   GLY A 613 "
        pdb=" N   HIS A 614 "
        pdb=" CA  HIS A 614 "
      ideal   model   delta    sigma   weight residual
     121.14  116.44    4.70 1.75e+00 3.27e-01 7.21e+00
  angle pdb=" C   LYS A 551 "
        pdb=" N   VAL A 552 "
        pdb=" CA  VAL A 552 "
      ideal   model   delta    sigma   weight residual
     121.97  126.62   -4.65 1.80e+00 3.09e-01 6.66e+00
  angle pdb=" C   LYS B 551 "
        pdb=" N   VAL B 552 "
        pdb=" CA  VAL B 552 "
      ideal   model   delta    sigma   weight residual
     121.97  126.58   -4.61 1.80e+00 3.09e-01 6.55e+00
  angle pdb=" CA  TYR A 570 "
        pdb=" CB  TYR A 570 "
        pdb=" CG  TYR A 570 "
      ideal   model   delta    sigma   weight residual
     113.90  118.35   -4.45 1.80e+00 3.09e-01 6.12e+00
  ... (remaining 12581 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.02: 5163
       19.02 -    38.05: 519
       38.05 -    57.07: 112
       57.07 -    76.09: 20
       76.09 -    95.11: 10
  Dihedral angle restraints: 5824
    sinusoidal: 2782
      harmonic: 3042
  Sorted by residual:
  dihedral pdb=" CB  CYS B 151 "
           pdb=" SG  CYS B 151 "
           pdb=" SG  CYS B 179 "
           pdb=" CB  CYS B 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.52  -88.48     1      1.00e+01 1.00e-02 9.35e+01
  dihedral pdb=" CB  CYS A 151 "
           pdb=" SG  CYS A 151 "
           pdb=" SG  CYS A 179 "
           pdb=" CB  CYS A 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.59  -88.41     1      1.00e+01 1.00e-02 9.33e+01
  dihedral pdb=" CB  CYS B 443 "
           pdb=" SG  CYS B 443 "
           pdb=" SG  CYS B 462 "
           pdb=" CB  CYS B 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.43  -77.43     1      1.00e+01 1.00e-02 7.51e+01
  ... (remaining 5821 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 627
       0.028 -    0.055: 476
       0.055 -    0.083: 210
       0.083 -    0.111: 75
       0.111 -    0.139: 28
  Chirality restraints: 1416
  Sorted by residual:
  chirality pdb=" CA  ILE A 559 "
            pdb=" N   ILE A 559 "
            pdb=" C   ILE A 559 "
            pdb=" CB  ILE A 559 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.81e-01
  chirality pdb=" CA  ILE B 559 "
            pdb=" N   ILE B 559 "
            pdb=" C   ILE B 559 "
            pdb=" CB  ILE B 559 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  PRO B 622 "
            pdb=" N   PRO B 622 "
            pdb=" C   PRO B 622 "
            pdb=" CB  PRO B 622 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 1413 not shown)

  Planarity restraints: 1444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 274 "   -0.022 2.00e-02 2.50e+03   1.91e-02 6.39e+00
        pdb=" CG  PHE B 274 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 274 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 274 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 274 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 274 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 274 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 274 "    0.022 2.00e-02 2.50e+03   1.90e-02 6.31e+00
        pdb=" CG  PHE A 274 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 274 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 274 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 274 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 274 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 459 "    0.021 2.00e-02 2.50e+03   1.75e-02 6.11e+00
        pdb=" CG  TYR A 459 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 459 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 459 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 459 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 459 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 459 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 459 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1441 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1829
        2.78 -     3.31: 7883
        3.31 -     3.84: 14333
        3.84 -     4.37: 18409
        4.37 -     4.90: 31863
  Nonbonded interactions: 74317
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 546 "
            pdb=" OG1 THR A 573 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG  SER B 546 "
            pdb=" OG1 THR B 573 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   LYS B 296 "
            pdb=" OG1 THR B 304 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   LYS A 296 "
            pdb=" OG1 THR A 304 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR B 447 "
            pdb=" OD2 ASP B 455 "
     model   vdw
     2.323 3.040
  ... (remaining 74312 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 75 through 663 or resid 804 or (resid 806 and (name C03 or \ 
 name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C1 \ 
0 or name C11 or name C12 or name C13 or name C14)) or resid 807 through 809 or  \ 
resid 816 or resid 821 through 833))
  selection = (chain 'B' and (resid 75 through 663 or resid 804 or resid 806 through 809 or re \ 
sid 816 or resid 821 through 833))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.900
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.630
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
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      :  0.007   0.079   9458  Z= 0.270
  Angle     :  0.665   7.077  12628  Z= 0.333
  Chirality :  0.046   0.139   1416
  Planarity :  0.005   0.039   1438
  Dihedral  : 15.121  95.113   3858
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.73 (0.25), residues: 1038
  helix:  1.38 (0.21), residues: 502
  sheet:  1.28 (0.47), residues: 128
  loop : -0.92 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 566 
 HIS   0.011   0.002   HIS A 614 
 PHE   0.044   0.002   PHE B 274 
 TYR   0.043   0.003   TYR A 459 
 ARG   0.002   0.000   ARG B 337 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00104 (    6)
  link_NAG-ASN         : angle       2.29246 (   18)
  link_BETA1-4         : bond        0.00372 (    4)
  link_BETA1-4         : angle       1.57903 (   12)
  hydrogen bonds       : bond        0.15432 (  476)
  hydrogen bonds       : angle       6.73615 ( 1380)
  SS BOND              : bond        0.00279 (    6)
  SS BOND              : angle       2.65320 (   12)
  covalent geometry    : bond        0.00667 ( 9442)
  covalent geometry    : angle       0.65385 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.036 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.7611
  time to fit residues: 64.6203
Evaluate side-chains
  68 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 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 = 0.3905 r_free = 0.3905 target = 0.166838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.130774 restraints weight = 9260.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.62
r_work: 0.3323 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.0761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9458  Z= 0.152
  Angle     :  0.553   6.586  12628  Z= 0.281
  Chirality :  0.041   0.143   1416
  Planarity :  0.004   0.041   1438
  Dihedral  : 11.909  59.983   1966
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  4.16 %
    Favored  : 94.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.65 (0.26), residues: 1038
  helix:  2.40 (0.22), residues: 506
  sheet:  1.21 (0.46), residues: 128
  loop : -0.68 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 647 
 HIS   0.004   0.001   HIS B 614 
 PHE   0.023   0.002   PHE B 274 
 TYR   0.023   0.002   TYR A 459 
 ARG   0.004   0.000   ARG B 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00253 (    6)
  link_NAG-ASN         : angle       1.88645 (   18)
  link_BETA1-4         : bond        0.00338 (    4)
  link_BETA1-4         : angle       1.51712 (   12)
  hydrogen bonds       : bond        0.05212 (  476)
  hydrogen bonds       : angle       4.93615 ( 1380)
  SS BOND              : bond        0.00168 (    6)
  SS BOND              : angle       1.37291 (   12)
  covalent geometry    : bond        0.00356 ( 9442)
  covalent geometry    : angle       0.54609 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 1.266 
Fit side-chains
REVERT: B  618 GLU cc_start: 0.8215 (tt0) cc_final: 0.7445 (pt0)
  outliers start: 8
  outliers final: 0
  residues processed: 72
  average time/residue: 0.8635
  time to fit residues: 70.6460
Evaluate side-chains
  68 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0060
   chunk 53 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    1.0600

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
B 286 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.166081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.130449 restraints weight = 9420.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.81
r_work: 0.3275 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.0974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9458  Z= 0.181
  Angle     :  0.560   6.336  12628  Z= 0.282
  Chirality :  0.042   0.144   1416
  Planarity :  0.004   0.039   1438
  Dihedral  : 11.455  59.795   1966
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  6.67 %
    Favored  : 92.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.25), residues: 1038
  helix:  2.30 (0.21), residues: 520
  sheet:  0.99 (0.45), residues: 116
  loop : -0.69 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 647 
 HIS   0.004   0.001   HIS A 614 
 PHE   0.021   0.002   PHE B 274 
 TYR   0.021   0.002   TYR B 459 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00218 (    6)
  link_NAG-ASN         : angle       1.95244 (   18)
  link_BETA1-4         : bond        0.00376 (    4)
  link_BETA1-4         : angle       1.50419 (   12)
  hydrogen bonds       : bond        0.05255 (  476)
  hydrogen bonds       : angle       4.78159 ( 1380)
  SS BOND              : bond        0.00238 (    6)
  SS BOND              : angle       1.16949 (   12)
  covalent geometry    : bond        0.00448 ( 9442)
  covalent geometry    : angle       0.55294 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8961 (OUTLIER) cc_final: 0.7826 (p-80)
REVERT: B  614 HIS cc_start: 0.8962 (OUTLIER) cc_final: 0.7839 (p-80)
REVERT: B  618 GLU cc_start: 0.8305 (tt0) cc_final: 0.7479 (pt0)
  outliers start: 12
  outliers final: 4
  residues processed: 71
  average time/residue: 0.9243
  time to fit residues: 74.5445
Evaluate side-chains
  73 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0020
   chunk 17 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.7390

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.167767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.131543 restraints weight = 9305.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.65
r_work: 0.3327 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9458  Z= 0.137
  Angle     :  0.503   6.428  12628  Z= 0.256
  Chirality :  0.040   0.137   1416
  Planarity :  0.004   0.039   1438
  Dihedral  : 10.818  59.900   1966
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  7.55 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.89 (0.25), residues: 1038
  helix:  2.65 (0.21), residues: 518
  sheet:  0.88 (0.44), residues: 116
  loop : -0.53 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.003   0.001   HIS A 614 
 PHE   0.016   0.001   PHE B 315 
 TYR   0.019   0.001   TYR A 570 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    6)
  link_NAG-ASN         : angle       1.82661 (   18)
  link_BETA1-4         : bond        0.00376 (    4)
  link_BETA1-4         : angle       1.45587 (   12)
  hydrogen bonds       : bond        0.04467 (  476)
  hydrogen bonds       : angle       4.53166 ( 1380)
  SS BOND              : bond        0.00202 (    6)
  SS BOND              : angle       0.92858 (   12)
  covalent geometry    : bond        0.00331 ( 9442)
  covalent geometry    : angle       0.49660 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A  618 GLU cc_start: 0.8265 (tt0) cc_final: 0.7472 (pt0)
REVERT: B  618 GLU cc_start: 0.8273 (tt0) cc_final: 0.7472 (pt0)
  outliers start: 11
  outliers final: 3
  residues processed: 75
  average time/residue: 0.8021
  time to fit residues: 67.7447
Evaluate side-chains
  75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  630 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 97 optimal weight:    0.3980
   chunk 53 optimal weight:    0.2980
   chunk 39 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
B 184 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.167337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.131149 restraints weight = 9275.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.63
r_work: 0.3324 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9458  Z= 0.149
  Angle     :  0.514   6.412  12628  Z= 0.260
  Chirality :  0.041   0.137   1416
  Planarity :  0.004   0.044   1438
  Dihedral  : 10.461  59.392   1966
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  7.33 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.94 (0.25), residues: 1038
  helix:  2.78 (0.21), residues: 508
  sheet:  0.82 (0.43), residues: 116
  loop : -0.51 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 647 
 HIS   0.003   0.001   HIS A 614 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.020   0.002   TYR B 570 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00196 (    6)
  link_NAG-ASN         : angle       1.83822 (   18)
  link_BETA1-4         : bond        0.00371 (    4)
  link_BETA1-4         : angle       1.41852 (   12)
  hydrogen bonds       : bond        0.04615 (  476)
  hydrogen bonds       : angle       4.53349 ( 1380)
  SS BOND              : bond        0.00268 (    6)
  SS BOND              : angle       0.95579 (   12)
  covalent geometry    : bond        0.00362 ( 9442)
  covalent geometry    : angle       0.50697 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8924 (OUTLIER) cc_final: 0.7763 (p-80)
REVERT: B  614 HIS cc_start: 0.8924 (OUTLIER) cc_final: 0.7767 (p-80)
REVERT: B  618 GLU cc_start: 0.8261 (tt0) cc_final: 0.7444 (pt0)
  outliers start: 14
  outliers final: 6
  residues processed: 76
  average time/residue: 0.7022
  time to fit residues: 60.6933
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.166908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.131856 restraints weight = 9251.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.54
r_work: 0.3309 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9458  Z= 0.160
  Angle     :  0.523   6.428  12628  Z= 0.264
  Chirality :  0.041   0.139   1416
  Planarity :  0.004   0.039   1438
  Dihedral  : 10.213  58.988   1966
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  7.77 %
    Favored  : 90.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.82 (0.25), residues: 1038
  helix:  2.60 (0.21), residues: 520
  sheet:  0.79 (0.44), residues: 116
  loop : -0.56 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.003   0.001   HIS B 614 
 PHE   0.016   0.001   PHE B 315 
 TYR   0.020   0.002   TYR B 570 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    6)
  link_NAG-ASN         : angle       1.83466 (   18)
  link_BETA1-4         : bond        0.00410 (    4)
  link_BETA1-4         : angle       1.41265 (   12)
  hydrogen bonds       : bond        0.04759 (  476)
  hydrogen bonds       : angle       4.55694 ( 1380)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       1.00691 (   12)
  covalent geometry    : bond        0.00393 ( 9442)
  covalent geometry    : angle       0.51637 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.979 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8937 (OUTLIER) cc_final: 0.7760 (p-80)
REVERT: B  614 HIS cc_start: 0.8945 (OUTLIER) cc_final: 0.7761 (p-80)
  outliers start: 16
  outliers final: 4
  residues processed: 77
  average time/residue: 0.7040
  time to fit residues: 61.5091
Evaluate side-chains
  74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0980
   chunk 55 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 4 optimal weight:    5.9990
   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 114 ASN
B 114 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.168704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130361 restraints weight = 9310.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.65
r_work: 0.3285 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9458  Z= 0.119
  Angle     :  0.478   6.453  12628  Z= 0.243
  Chirality :  0.039   0.130   1416
  Planarity :  0.004   0.046   1438
  Dihedral  :  9.670  57.396   1966
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.86 %
    Favored  : 90.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  2.07 (0.25), residues: 1038
  helix:  2.84 (0.21), residues: 520
  sheet:  0.84 (0.44), residues: 116
  loop : -0.47 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.003   0.001   HIS B 614 
 PHE   0.013   0.001   PHE A 315 
 TYR   0.018   0.001   TYR A 570 
 ARG   0.002   0.000   ARG B 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00178 (    6)
  link_NAG-ASN         : angle       1.67667 (   18)
  link_BETA1-4         : bond        0.00415 (    4)
  link_BETA1-4         : angle       1.40617 (   12)
  hydrogen bonds       : bond        0.04113 (  476)
  hydrogen bonds       : angle       4.38121 ( 1380)
  SS BOND              : bond        0.00206 (    6)
  SS BOND              : angle       1.06369 (   12)
  covalent geometry    : bond        0.00281 ( 9442)
  covalent geometry    : angle       0.47193 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.7641 (p-80)
REVERT: B  614 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.7645 (p-80)
REVERT: B  618 GLU cc_start: 0.8245 (tt0) cc_final: 0.7306 (pt0)
  outliers start: 8
  outliers final: 5
  residues processed: 74
  average time/residue: 0.7834
  time to fit residues: 65.1670
Evaluate side-chains
  77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.164445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.128670 restraints weight = 9448.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.61
r_work: 0.3248 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.081   9458  Z= 0.277
  Angle     :  0.629   6.483  12628  Z= 0.315
  Chirality :  0.046   0.153   1416
  Planarity :  0.005   0.042   1438
  Dihedral  : 10.612  59.760   1966
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  8.10 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.38 (0.25), residues: 1038
  helix:  2.22 (0.21), residues: 520
  sheet:  0.65 (0.43), residues: 116
  loop : -0.79 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 647 
 HIS   0.004   0.001   HIS B 614 
 PHE   0.018   0.002   PHE A 315 
 TYR   0.021   0.002   TYR B 570 
 ARG   0.003   0.000   ARG B 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    6)
  link_NAG-ASN         : angle       1.99225 (   18)
  link_BETA1-4         : bond        0.00416 (    4)
  link_BETA1-4         : angle       1.48489 (   12)
  hydrogen bonds       : bond        0.06019 (  476)
  hydrogen bonds       : angle       4.83233 ( 1380)
  SS BOND              : bond        0.00399 (    6)
  SS BOND              : angle       1.14505 (   12)
  covalent geometry    : bond        0.00695 ( 9442)
  covalent geometry    : angle       0.62272 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.928 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.7827 (p-80)
REVERT: B  614 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.7817 (p-80)
  outliers start: 16
  outliers final: 5
  residues processed: 83
  average time/residue: 0.7431
  time to fit residues: 69.6286
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 103 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 11 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.167761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.130869 restraints weight = 9241.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.63
r_work: 0.3295 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9458  Z= 0.129
  Angle     :  0.494   6.462  12628  Z= 0.252
  Chirality :  0.040   0.132   1416
  Planarity :  0.004   0.048   1438
  Dihedral  :  9.888  57.282   1966
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.08 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.80 (0.25), residues: 1038
  helix:  2.67 (0.21), residues: 520
  sheet:  0.67 (0.43), residues: 116
  loop : -0.67 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 647 
 HIS   0.003   0.001   HIS B 614 
 PHE   0.015   0.001   PHE A 315 
 TYR   0.019   0.001   TYR B 570 
 ARG   0.002   0.000   ARG B 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00187 (    6)
  link_NAG-ASN         : angle       1.68760 (   18)
  link_BETA1-4         : bond        0.00422 (    4)
  link_BETA1-4         : angle       1.43663 (   12)
  hydrogen bonds       : bond        0.04346 (  476)
  hydrogen bonds       : angle       4.46879 ( 1380)
  SS BOND              : bond        0.00191 (    6)
  SS BOND              : angle       1.15205 (   12)
  covalent geometry    : bond        0.00308 ( 9442)
  covalent geometry    : angle       0.48737 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.7643 (p-80)
REVERT: B  614 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.7637 (p-80)
  outliers start: 7
  outliers final: 5
  residues processed: 74
  average time/residue: 0.7585
  time to fit residues: 62.9885
Evaluate side-chains
  75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0470
   chunk 40 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.5278

-------------------------------------------------------------------------------
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 = 0.3923 r_free = 0.3923 target = 0.168811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.133157 restraints weight = 9425.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.80
r_work: 0.3318 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9458  Z= 0.115
  Angle     :  0.473   6.445  12628  Z= 0.241
  Chirality :  0.039   0.130   1416
  Planarity :  0.004   0.053   1438
  Dihedral  :  9.214  55.781   1966
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.30 %
    Favored  : 89.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  2.06 (0.25), residues: 1038
  helix:  2.88 (0.21), residues: 520
  sheet:  0.75 (0.44), residues: 116
  loop : -0.53 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 647 
 HIS   0.002   0.001   HIS A 614 
 PHE   0.015   0.001   PHE B 315 
 TYR   0.018   0.001   TYR A 570 
 ARG   0.001   0.000   ARG A 269 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    6)
  link_NAG-ASN         : angle       1.51585 (   18)
  link_BETA1-4         : bond        0.00443 (    4)
  link_BETA1-4         : angle       1.38796 (   12)
  hydrogen bonds       : bond        0.03962 (  476)
  hydrogen bonds       : angle       4.29832 ( 1380)
  SS BOND              : bond        0.00211 (    6)
  SS BOND              : angle       1.08191 (   12)
  covalent geometry    : bond        0.00271 ( 9442)
  covalent geometry    : angle       0.46665 (12586)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 1.037 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.7725 (p-80)
REVERT: B  614 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.7748 (p-80)
REVERT: B  618 GLU cc_start: 0.8310 (tt0) cc_final: 0.7448 (pt0)
  outliers start: 8
  outliers final: 5
  residues processed: 70
  average time/residue: 0.7985
  time to fit residues: 62.7865
Evaluate side-chains
  74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
B 114 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.166382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.130757 restraints weight = 9330.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.83
r_work: 0.3278 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9458  Z= 0.180
  Angle     :  0.535   6.448  12628  Z= 0.271
  Chirality :  0.042   0.137   1416
  Planarity :  0.004   0.056   1438
  Dihedral  :  9.708  55.003   1966
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.08 %
    Favored  : 89.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.76 (0.25), residues: 1038
  helix:  2.61 (0.21), residues: 520
  sheet:  0.72 (0.44), residues: 116
  loop : -0.68 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 647 
 HIS   0.003   0.001   HIS A 614 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.019   0.002   TYR A 570 
 ARG   0.002   0.000   ARG B 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    6)
  link_NAG-ASN         : angle       1.70423 (   18)
  link_BETA1-4         : bond        0.00472 (    4)
  link_BETA1-4         : angle       1.41806 (   12)
  hydrogen bonds       : bond        0.04929 (  476)
  hydrogen bonds       : angle       4.53908 ( 1380)
  SS BOND              : bond        0.00277 (    6)
  SS BOND              : angle       1.05507 (   12)
  covalent geometry    : bond        0.00446 ( 9442)
  covalent geometry    : angle       0.52896 (12586)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6300.92 seconds
wall clock time: 109 minutes 56.19 seconds (6596.19 seconds total)