Starting phenix.real_space_refine
on Mon May 12 19:44:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jkv_36376/05_2025/8jkv_36376.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jkv_36376/05_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_36376/05_2025/8jkv_36376.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jkv_36376/05_2025/8jkv_36376.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jkv_36376/05_2025/8jkv_36376.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jkv_36376/05_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-5687/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: 6.85, per 1000 atoms: 0.74
  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: 2.53
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.83
  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: 2.54

  Time building geometry restraints manager: 2.84 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:             3.940
  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:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.080
  Find NCS groups from input model:        0.450
  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:12.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.490
-------------------------------------------------------------------------------
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  : 0.947 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.7704
  time to fit residues: 65.3807
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  : 0.975 
-------------------------------------------------------------------------------
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: 2.53 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
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  : 1.095 
Fit side-chains
REVERT: B  618 GLU cc_start: 0.8232 (tt0) cc_final: 0.7456 (pt0)
  outliers start: 8
  outliers final: 0
  residues processed: 72
  average time/residue: 0.6867
  time to fit residues: 56.2492
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  : 0.922 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   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:    1.0984

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.165935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.130308 restraints weight = 9419.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.79
r_work: 0.3273 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9458  Z= 0.185
  Angle     :  0.565   6.342  12628  Z= 0.285
  Chirality :  0.042   0.147   1416
  Planarity :  0.004   0.039   1438
  Dihedral  : 11.493  59.971   1966
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  6.78 %
    Favored  : 91.90 %
  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:  1.52 (0.25), residues: 1038
  helix:  2.27 (0.21), residues: 520
  sheet:  0.98 (0.45), residues: 116
  loop : -0.70 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 647 
 HIS   0.004   0.001   HIS A 614 
 PHE   0.019   0.002   PHE B 274 
 TYR   0.021   0.002   TYR A 570 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    6)
  link_NAG-ASN         : angle       1.96901 (   18)
  link_BETA1-4         : bond        0.00338 (    4)
  link_BETA1-4         : angle       1.51233 (   12)
  hydrogen bonds       : bond        0.05346 (  476)
  hydrogen bonds       : angle       4.80745 ( 1380)
  SS BOND              : bond        0.00238 (    6)
  SS BOND              : angle       1.18574 (   12)
  covalent geometry    : bond        0.00459 ( 9442)
  covalent geometry    : angle       0.55799 (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
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.7838 (p-80)
REVERT: B  614 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.7853 (p-80)
REVERT: B  618 GLU cc_start: 0.8312 (tt0) cc_final: 0.7486 (pt0)
  outliers start: 12
  outliers final: 4
  residues processed: 71
  average time/residue: 0.7261
  time to fit residues: 58.6864
Evaluate side-chains
  72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   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:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.166106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.130753 restraints weight = 9330.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.56
r_work: 0.3285 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   9458  Z= 0.187
  Angle     :  0.554   6.390  12628  Z= 0.280
  Chirality :  0.042   0.145   1416
  Planarity :  0.004   0.039   1438
  Dihedral  : 11.204  59.773   1966
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  7.11 %
    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:  1.59 (0.25), residues: 1038
  helix:  2.37 (0.21), residues: 520
  sheet:  0.85 (0.44), residues: 116
  loop : -0.67 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 647 
 HIS   0.003   0.001   HIS B 614 
 PHE   0.018   0.002   PHE B 315 
 TYR   0.021   0.002   TYR A 570 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00208 (    6)
  link_NAG-ASN         : angle       1.96289 (   18)
  link_BETA1-4         : bond        0.00366 (    4)
  link_BETA1-4         : angle       1.47856 (   12)
  hydrogen bonds       : bond        0.05161 (  476)
  hydrogen bonds       : angle       4.72399 ( 1380)
  SS BOND              : bond        0.00243 (    6)
  SS BOND              : angle       1.02421 (   12)
  covalent geometry    : bond        0.00463 ( 9442)
  covalent geometry    : angle       0.54721 (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
  87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.7790 (p-80)
REVERT: B  614 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.7793 (p-80)
  outliers start: 16
  outliers final: 6
  residues processed: 77
  average time/residue: 0.6716
  time to fit residues: 58.7447
Evaluate side-chains
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    0.1980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 95 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.167985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.132036 restraints weight = 9256.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.64
r_work: 0.3332 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9458  Z= 0.118
  Angle     :  0.485   6.422  12628  Z= 0.247
  Chirality :  0.039   0.130   1416
  Planarity :  0.004   0.044   1438
  Dihedral  : 10.422  59.926   1966
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.77 %
    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:  1.96 (0.25), residues: 1038
  helix:  2.73 (0.21), residues: 518
  sheet:  0.86 (0.44), residues: 116
  loop : -0.51 (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   0.015   0.001   PHE B 315 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.002   0.000   ARG B 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00191 (    6)
  link_NAG-ASN         : angle       1.76625 (   18)
  link_BETA1-4         : bond        0.00401 (    4)
  link_BETA1-4         : angle       1.43047 (   12)
  hydrogen bonds       : bond        0.04217 (  476)
  hydrogen bonds       : angle       4.46222 ( 1380)
  SS BOND              : bond        0.00179 (    6)
  SS BOND              : angle       0.95329 (   12)
  covalent geometry    : bond        0.00276 ( 9442)
  covalent geometry    : angle       0.47870 (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
  81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.929 
Fit side-chains
REVERT: B  618 GLU cc_start: 0.8273 (tt0) cc_final: 0.7443 (pt0)
  outliers start: 10
  outliers final: 4
  residues processed: 73
  average time/residue: 0.7070
  time to fit residues: 58.5828
Evaluate side-chains
  73 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  630 ASN
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:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.166617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.130375 restraints weight = 9266.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.62
r_work: 0.3308 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9458  Z= 0.168
  Angle     :  0.532   6.419  12628  Z= 0.269
  Chirality :  0.041   0.140   1416
  Planarity :  0.004   0.046   1438
  Dihedral  : 10.358  59.833   1966
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  7.88 %
    Favored  : 90.37 %
  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:  1.77 (0.25), residues: 1038
  helix:  2.55 (0.21), residues: 520
  sheet:  0.76 (0.44), residues: 116
  loop : -0.59 (0.29), residues: 402

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   0.017   0.001   PHE B 315 
 TYR   0.020   0.002   TYR A 570 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00192 (    6)
  link_NAG-ASN         : angle       1.84913 (   18)
  link_BETA1-4         : bond        0.00394 (    4)
  link_BETA1-4         : angle       1.41527 (   12)
  hydrogen bonds       : bond        0.04859 (  476)
  hydrogen bonds       : angle       4.58211 ( 1380)
  SS BOND              : bond        0.00298 (    6)
  SS BOND              : angle       1.04447 (   12)
  covalent geometry    : bond        0.00415 ( 9442)
  covalent geometry    : angle       0.52581 (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
  84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8953 (OUTLIER) cc_final: 0.7792 (p-80)
REVERT: B  614 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.7782 (p-80)
  outliers start: 16
  outliers final: 4
  residues processed: 74
  average time/residue: 0.7729
  time to fit residues: 64.5666
Evaluate side-chains
  72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 18 optimal weight:    0.1980
   chunk 55 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 4 optimal weight:    7.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.168860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.130473 restraints weight = 9307.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.66
r_work: 0.3289 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
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   0.042   9458  Z= 0.113
  Angle     :  0.475   6.458  12628  Z= 0.241
  Chirality :  0.039   0.129   1416
  Planarity :  0.004   0.040   1438
  Dihedral  :  9.695  58.104   1966
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  8.75 %
    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:  2.08 (0.25), residues: 1038
  helix:  2.83 (0.21), residues: 520
  sheet:  0.86 (0.44), residues: 116
  loop : -0.46 (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   0.013   0.001   PHE A 315 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.001   0.000   ARG B 269 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00181 (    6)
  link_NAG-ASN         : angle       1.66954 (   18)
  link_BETA1-4         : bond        0.00418 (    4)
  link_BETA1-4         : angle       1.39432 (   12)
  hydrogen bonds       : bond        0.04023 (  476)
  hydrogen bonds       : angle       4.36289 ( 1380)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       1.07969 (   12)
  covalent geometry    : bond        0.00262 ( 9442)
  covalent geometry    : angle       0.46837 (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
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.7630 (p-80)
REVERT: B  614 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.7627 (p-80)
REVERT: B  618 GLU cc_start: 0.8242 (tt0) cc_final: 0.7299 (pt0)
  outliers start: 7
  outliers final: 3
  residues processed: 77
  average time/residue: 0.7471
  time to fit residues: 64.9220
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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  614 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.165183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.129666 restraints weight = 9435.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.59
r_work: 0.3243 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073   9458  Z= 0.239
  Angle     :  0.593   6.453  12628  Z= 0.298
  Chirality :  0.045   0.148   1416
  Planarity :  0.004   0.038   1438
  Dihedral  : 10.383  59.910   1966
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.52 %
    Favored  : 89.50 %
  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:  1.53 (0.25), residues: 1038
  helix:  2.35 (0.21), residues: 520
  sheet:  0.72 (0.44), residues: 116
  loop : -0.72 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 647 
 HIS   0.003   0.001   HIS A 614 
 PHE   0.017   0.002   PHE B 315 
 TYR   0.021   0.002   TYR B 570 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00172 (    6)
  link_NAG-ASN         : angle       1.92694 (   18)
  link_BETA1-4         : bond        0.00422 (    4)
  link_BETA1-4         : angle       1.45572 (   12)
  hydrogen bonds       : bond        0.05609 (  476)
  hydrogen bonds       : angle       4.73799 ( 1380)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       1.20188 (   12)
  covalent geometry    : bond        0.00601 ( 9442)
  covalent geometry    : angle       0.58668 (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
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.7750 (p-80)
REVERT: B  614 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.7748 (p-80)
  outliers start: 9
  outliers final: 5
  residues processed: 74
  average time/residue: 0.7425
  time to fit residues: 62.1359
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  : 1.024 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 103 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.167420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.131966 restraints weight = 9243.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.84
r_work: 0.3298 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1383

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= 0.134
  Angle     :  0.497   6.463  12628  Z= 0.252
  Chirality :  0.040   0.134   1416
  Planarity :  0.004   0.041   1438
  Dihedral  :  9.860  58.399   1966
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  8.86 %
    Favored  : 89.61 %
  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:  1.83 (0.25), residues: 1038
  helix:  2.68 (0.21), residues: 520
  sheet:  0.74 (0.44), residues: 116
  loop : -0.64 (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 A 614 
 PHE   0.015   0.001   PHE A 315 
 TYR   0.019   0.001   TYR B 570 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00174 (    6)
  link_NAG-ASN         : angle       1.70811 (   18)
  link_BETA1-4         : bond        0.00436 (    4)
  link_BETA1-4         : angle       1.43103 (   12)
  hydrogen bonds       : bond        0.04417 (  476)
  hydrogen bonds       : angle       4.48162 ( 1380)
  SS BOND              : bond        0.00215 (    6)
  SS BOND              : angle       1.03031 (   12)
  covalent geometry    : bond        0.00324 ( 9442)
  covalent geometry    : angle       0.49094 (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
  82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 1.047 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.7743 (p-80)
REVERT: B  614 HIS cc_start: 0.8930 (OUTLIER) cc_final: 0.7736 (p-80)
  outliers start: 14
  outliers final: 4
  residues processed: 80
  average time/residue: 0.7108
  time to fit residues: 64.4751
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  : 0.940 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0270
   chunk 40 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.7038

-------------------------------------------------------------------------------
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 = 0.167864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.132056 restraints weight = 9438.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.78
r_work: 0.3310 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1441

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= 0.134
  Angle     :  0.497   6.428  12628  Z= 0.253
  Chirality :  0.040   0.133   1416
  Planarity :  0.004   0.040   1438
  Dihedral  :  9.534  57.277   1966
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.41 %
    Favored  : 89.61 %
  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:  1.90 (0.25), residues: 1038
  helix:  2.73 (0.21), residues: 520
  sheet:  0.74 (0.45), residues: 116
  loop : -0.60 (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 A 614 
 PHE   0.016   0.001   PHE B 315 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.002   0.000   ARG A 372 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00198 (    6)
  link_NAG-ASN         : angle       1.62687 (   18)
  link_BETA1-4         : bond        0.00433 (    4)
  link_BETA1-4         : angle       1.41430 (   12)
  hydrogen bonds       : bond        0.04338 (  476)
  hydrogen bonds       : angle       4.42329 ( 1380)
  SS BOND              : bond        0.00185 (    6)
  SS BOND              : angle       1.11126 (   12)
  covalent geometry    : bond        0.00324 ( 9442)
  covalent geometry    : angle       0.49102 (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
  76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 1.035 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.7728 (p-80)
REVERT: B  614 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.7701 (p-80)
  outliers start: 9
  outliers final: 6
  residues processed: 73
  average time/residue: 0.7496
  time to fit residues: 61.7191
Evaluate side-chains
  74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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=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:    0.5980
   chunk 76 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   chunk 89 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.168234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.131482 restraints weight = 9292.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.70
r_work: 0.3338 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9458  Z= 0.127
  Angle     :  0.486   6.427  12628  Z= 0.248
  Chirality :  0.040   0.132   1416
  Planarity :  0.004   0.047   1438
  Dihedral  :  9.341  56.185   1966
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.63 %
    Favored  : 89.39 %
  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:  1.95 (0.25), residues: 1038
  helix:  2.78 (0.21), residues: 520
  sheet:  0.79 (0.45), residues: 116
  loop : -0.61 (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 A 614 
 PHE   0.015   0.001   PHE A 315 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.001   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00177 (    6)
  link_NAG-ASN         : angle       1.57079 (   18)
  link_BETA1-4         : bond        0.00453 (    4)
  link_BETA1-4         : angle       1.39121 (   12)
  hydrogen bonds       : bond        0.04225 (  476)
  hydrogen bonds       : angle       4.37713 ( 1380)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       1.10649 (   12)
  covalent geometry    : bond        0.00304 ( 9442)
  covalent geometry    : angle       0.48044 (12586)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5663.29 seconds
wall clock time: 98 minutes 50.71 seconds (5930.71 seconds total)