Starting phenix.real_space_refine
on Fri Oct 10 21:49:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jkv_36376/10_2025/8jkv_36376.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jkv_36376/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jkv_36376/10_2025/8jkv_36376.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jkv_36376/10_2025/8jkv_36376.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jkv_36376/10_2025/8jkv_36376.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jkv_36376/10_2025/8jkv_36376.map"
  }
  resolution = 2.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.37, per 1000 atoms: 0.26
  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: 1.15
  Conformation dependent library (CDL) restraints added in 290.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.27
  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: 1.39

  Time building geometry restraints manager: 1.26 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:             6.120
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.980
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.740
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (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
 ARG   0.002   0.000   ARG B 337 
 TYR   0.043   0.003   TYR A 459 
 PHE   0.044   0.002   PHE B 274 
 TRP   0.014   0.002   TRP B 566 
 HIS   0.011   0.002   HIS A 614 

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

*********************** 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  : 0.326 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.3573
  time to fit residues: 30.1012
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  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.166747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.130694 restraints weight = 9336.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 1.61
r_work: 0.3323 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.0782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9458  Z= 0.156
  Angle     :  0.557   6.477  12628  Z= 0.282
  Chirality :  0.041   0.142   1416
  Planarity :  0.004   0.040   1438
  Dihedral  : 11.930  59.754   1966
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  4.60 %
    Favored  : 94.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.25), residues: 1038
  helix:  2.35 (0.22), residues: 506
  sheet:  1.19 (0.45), residues: 128
  loop : -0.68 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 379 
 TYR   0.022   0.002   TYR B 459 
 PHE   0.023   0.002   PHE B 274 
 TRP   0.013   0.001   TRP A 647 
 HIS   0.003   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9442)
  covalent geometry    : angle       0.54958 (12586)
  SS BOND              : bond        0.00188 (    6)
  SS BOND              : angle       1.38744 (   12)
  hydrogen bonds       : bond        0.05225 (  476)
  hydrogen bonds       : angle       4.92331 ( 1380)
  link_BETA1-4         : bond        0.00375 (    4)
  link_BETA1-4         : angle       1.46962 (   12)
  link_NAG-ASN         : bond        0.00280 (    6)
  link_NAG-ASN         : angle       1.90250 (   18)

*********************** 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
  81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.338 
Fit side-chains
REVERT: B  618 GLU cc_start: 0.8213 (tt0) cc_final: 0.7444 (pt0)
  outliers start: 8
  outliers final: 0
  residues processed: 73
  average time/residue: 0.3734
  time to fit residues: 30.4638
Evaluate side-chains
  69 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 55 optimal weight:    0.0050
   chunk 32 optimal weight:    0.0870
   chunk 10 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.6172

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.168124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.131938 restraints weight = 9255.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.62
r_work: 0.3339 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1102

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= 0.125
  Angle     :  0.499   6.389  12628  Z= 0.253
  Chirality :  0.040   0.134   1416
  Planarity :  0.004   0.039   1438
  Dihedral  : 10.937  59.971   1966
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  6.78 %
    Favored  : 92.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.25), residues: 1038
  helix:  2.83 (0.21), residues: 504
  sheet:  1.05 (0.45), residues: 116
  loop : -0.55 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 379 
 TYR   0.019   0.001   TYR B 570 
 PHE   0.018   0.001   PHE B 274 
 TRP   0.013   0.001   TRP A 647 
 HIS   0.003   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9442)
  covalent geometry    : angle       0.49179 (12586)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       1.09814 (   12)
  hydrogen bonds       : bond        0.04382 (  476)
  hydrogen bonds       : angle       4.54266 ( 1380)
  link_BETA1-4         : bond        0.00355 (    4)
  link_BETA1-4         : angle       1.48817 (   12)
  link_NAG-ASN         : bond        0.00226 (    6)
  link_NAG-ASN         : angle       1.82046 (   18)

*********************** 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
  82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.7794 (p-80)
REVERT: A  618 GLU cc_start: 0.8282 (tt0) cc_final: 0.7526 (pt0)
REVERT: B  614 HIS cc_start: 0.8936 (OUTLIER) cc_final: 0.7797 (p-80)
REVERT: B  618 GLU cc_start: 0.8271 (tt0) cc_final: 0.7501 (pt0)
  outliers start: 10
  outliers final: 3
  residues processed: 74
  average time/residue: 0.3531
  time to fit residues: 29.4530
Evaluate side-chains
  74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 79 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0060
   chunk 23 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0980
   chunk 41 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 69 optimal weight:    0.2980
   overall best weight:    0.4796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.169305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.133229 restraints weight = 9349.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.62
r_work: 0.3348 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9458  Z= 0.108
  Angle     :  0.473   6.438  12628  Z= 0.240
  Chirality :  0.039   0.132   1416
  Planarity :  0.004   0.041   1438
  Dihedral  : 10.205  59.456   1966
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.22 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.25), residues: 1038
  helix:  3.09 (0.21), residues: 504
  sheet:  1.01 (0.44), residues: 116
  loop : -0.40 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.018   0.001   TYR B 570 
 PHE   0.015   0.001   PHE B 315 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.002   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9442)
  covalent geometry    : angle       0.46682 (12586)
  SS BOND              : bond        0.00164 (    6)
  SS BOND              : angle       0.79426 (   12)
  hydrogen bonds       : bond        0.03929 (  476)
  hydrogen bonds       : angle       4.33891 ( 1380)
  link_BETA1-4         : bond        0.00387 (    4)
  link_BETA1-4         : angle       1.39525 (   12)
  link_NAG-ASN         : bond        0.00215 (    6)
  link_NAG-ASN         : angle       1.70917 (   18)

*********************** 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
  80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  618 GLU cc_start: 0.8330 (tt0) cc_final: 0.7569 (pt0)
REVERT: B  618 GLU cc_start: 0.8286 (tt0) cc_final: 0.7516 (pt0)
  outliers start: 9
  outliers final: 1
  residues processed: 73
  average time/residue: 0.3465
  time to fit residues: 28.5134
Evaluate side-chains
  69 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0000
   chunk 13 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.1188

-------------------------------------------------------------------------------
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 = 0.3906 r_free = 0.3906 target = 0.166795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.129882 restraints weight = 9337.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.85
r_work: 0.3297 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1189

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     :  0.550   6.421  12628  Z= 0.276
  Chirality :  0.042   0.145   1416
  Planarity :  0.004   0.038   1438
  Dihedral  : 10.482  59.993   1966
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  7.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.25), residues: 1038
  helix:  2.70 (0.21), residues: 508
  sheet:  0.87 (0.44), residues: 116
  loop : -0.48 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 379 
 TYR   0.020   0.002   TYR B 570 
 PHE   0.017   0.002   PHE B 315 
 TRP   0.014   0.002   TRP A 647 
 HIS   0.003   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 9442)
  covalent geometry    : angle       0.54326 (12586)
  SS BOND              : bond        0.00339 (    6)
  SS BOND              : angle       0.93690 (   12)
  hydrogen bonds       : bond        0.05083 (  476)
  hydrogen bonds       : angle       4.61612 ( 1380)
  link_BETA1-4         : bond        0.00386 (    4)
  link_BETA1-4         : angle       1.40746 (   12)
  link_NAG-ASN         : bond        0.00208 (    6)
  link_NAG-ASN         : angle       1.91716 (   18)

*********************** 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  : 0.382 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.7675 (p-80)
REVERT: A  618 GLU cc_start: 0.8201 (tt0) cc_final: 0.7263 (pt0)
REVERT: B  614 HIS cc_start: 0.8880 (OUTLIER) cc_final: 0.7666 (p-80)
REVERT: B  618 GLU cc_start: 0.8223 (tt0) cc_final: 0.7287 (pt0)
  outliers start: 14
  outliers final: 6
  residues processed: 76
  average time/residue: 0.3549
  time to fit residues: 30.3566
Evaluate side-chains
  77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
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 6 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 100 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.167973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.130947 restraints weight = 9347.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.84
r_work: 0.3309 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9458  Z= 0.144
  Angle     :  0.506   6.439  12628  Z= 0.255
  Chirality :  0.040   0.137   1416
  Planarity :  0.004   0.040   1438
  Dihedral  : 10.158  59.907   1966
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  8.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.25), residues: 1038
  helix:  2.85 (0.21), residues: 508
  sheet:  0.86 (0.44), residues: 116
  loop : -0.45 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 379 
 TYR   0.019   0.001   TYR B 570 
 PHE   0.014   0.001   PHE B 315 
 TRP   0.012   0.001   TRP A 647 
 HIS   0.003   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9442)
  covalent geometry    : angle       0.49907 (12586)
  SS BOND              : bond        0.00241 (    6)
  SS BOND              : angle       0.93201 (   12)
  hydrogen bonds       : bond        0.04513 (  476)
  hydrogen bonds       : angle       4.49639 ( 1380)
  link_BETA1-4         : bond        0.00411 (    4)
  link_BETA1-4         : angle       1.41278 (   12)
  link_NAG-ASN         : bond        0.00184 (    6)
  link_NAG-ASN         : angle       1.82793 (   18)

*********************** 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
  83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.7645 (p-80)
REVERT: A  618 GLU cc_start: 0.8204 (tt0) cc_final: 0.7286 (pt0)
REVERT: B  614 HIS cc_start: 0.8866 (OUTLIER) cc_final: 0.7643 (p-80)
REVERT: B  618 GLU cc_start: 0.8193 (tt0) cc_final: 0.7270 (pt0)
  outliers start: 13
  outliers final: 4
  residues processed: 75
  average time/residue: 0.3493
  time to fit residues: 29.5346
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  : 0.351 
-------------------------------------------------------------------------------
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  113 VAL
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  630 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 82 optimal weight:    0.2980
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.167408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.131163 restraints weight = 9329.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.61
r_work: 0.3318 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9458  Z= 0.145
  Angle     :  0.506   6.439  12628  Z= 0.256
  Chirality :  0.041   0.136   1416
  Planarity :  0.004   0.040   1438
  Dihedral  :  9.879  59.501   1966
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.10 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.25), residues: 1038
  helix:  2.69 (0.21), residues: 520
  sheet:  0.83 (0.44), residues: 116
  loop : -0.47 (0.30), residues: 402

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9442)
  covalent geometry    : angle       0.49965 (12586)
  SS BOND              : bond        0.00224 (    6)
  SS BOND              : angle       1.02496 (   12)
  hydrogen bonds       : bond        0.04489 (  476)
  hydrogen bonds       : angle       4.46318 ( 1380)
  link_BETA1-4         : bond        0.00411 (    4)
  link_BETA1-4         : angle       1.40921 (   12)
  link_NAG-ASN         : bond        0.00200 (    6)
  link_NAG-ASN         : angle       1.77930 (   18)

*********************** 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
  81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.7785 (p-80)
REVERT: A  618 GLU cc_start: 0.8339 (tt0) cc_final: 0.7517 (pt0)
REVERT: B  614 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.7781 (p-80)
REVERT: B  618 GLU cc_start: 0.8321 (tt0) cc_final: 0.7500 (pt0)
  outliers start: 12
  outliers final: 4
  residues processed: 76
  average time/residue: 0.3371
  time to fit residues: 28.8605
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  : 0.353 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3888 r_free = 0.3888 target = 0.165399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.129794 restraints weight = 9380.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.60
r_work: 0.3254 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   9458  Z= 0.235
  Angle     :  0.588   6.460  12628  Z= 0.296
  Chirality :  0.044   0.149   1416
  Planarity :  0.005   0.060   1438
  Dihedral  : 10.387  57.129   1966
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  8.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.25), residues: 1038
  helix:  2.38 (0.21), residues: 520
  sheet:  0.73 (0.44), residues: 116
  loop : -0.67 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 379 
 TYR   0.021   0.002   TYR B 570 
 PHE   0.018   0.002   PHE A 315 
 TRP   0.015   0.002   TRP B 647 
 HIS   0.003   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 9442)
  covalent geometry    : angle       0.58144 (12586)
  SS BOND              : bond        0.00484 (    6)
  SS BOND              : angle       1.20482 (   12)
  hydrogen bonds       : bond        0.05531 (  476)
  hydrogen bonds       : angle       4.71622 ( 1380)
  link_BETA1-4         : bond        0.00421 (    4)
  link_BETA1-4         : angle       1.46427 (   12)
  link_NAG-ASN         : bond        0.00186 (    6)
  link_NAG-ASN         : angle       1.93268 (   18)

*********************** 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
  83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.7802 (p-80)
REVERT: B  614 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.7796 (p-80)
  outliers start: 14
  outliers final: 6
  residues processed: 77
  average time/residue: 0.3553
  time to fit residues: 30.6317
Evaluate side-chains
  77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  153 LEU
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 7 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 48 optimal weight:    0.2980
   chunk 83 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0770
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.168072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.131599 restraints weight = 9279.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.64
r_work: 0.3340 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9458  Z= 0.122
  Angle     :  0.482   6.453  12628  Z= 0.246
  Chirality :  0.040   0.130   1416
  Planarity :  0.004   0.058   1438
  Dihedral  :  9.725  58.751   1966
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  8.86 %
    Favored  : 90.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.25), residues: 1038
  helix:  2.74 (0.21), residues: 520
  sheet:  0.84 (0.45), residues: 116
  loop : -0.57 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.019   0.001   TYR B 570 
 PHE   0.014   0.001   PHE B 315 
 TRP   0.012   0.001   TRP A 647 
 HIS   0.002   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9442)
  covalent geometry    : angle       0.47610 (12586)
  SS BOND              : bond        0.00189 (    6)
  SS BOND              : angle       1.02234 (   12)
  hydrogen bonds       : bond        0.04187 (  476)
  hydrogen bonds       : angle       4.41416 ( 1380)
  link_BETA1-4         : bond        0.00451 (    4)
  link_BETA1-4         : angle       1.42097 (   12)
  link_NAG-ASN         : bond        0.00188 (    6)
  link_NAG-ASN         : angle       1.66077 (   18)

*********************** 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: 10
    poor density    : 66
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.7704 (p-80)
REVERT: B  614 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.7701 (p-80)
  outliers start: 10
  outliers final: 6
  residues processed: 74
  average time/residue: 0.3392
  time to fit residues: 28.2811
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  : 0.271 
-------------------------------------------------------------------------------
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 61 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 79 optimal weight:    0.4980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3910 r_free = 0.3910 target = 0.167510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.130973 restraints weight = 9294.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.63
r_work: 0.3325 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1416

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= 0.140
  Angle     :  0.501   6.434  12628  Z= 0.254
  Chirality :  0.040   0.134   1416
  Planarity :  0.004   0.058   1438
  Dihedral  :  9.604  59.463   1966
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  9.19 %
    Favored  : 89.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.25), residues: 1038
  helix:  2.71 (0.21), residues: 520
  sheet:  0.83 (0.45), residues: 116
  loop : -0.55 (0.30), residues: 402

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9442)
  covalent geometry    : angle       0.49420 (12586)
  SS BOND              : bond        0.00223 (    6)
  SS BOND              : angle       1.14730 (   12)
  hydrogen bonds       : bond        0.04411 (  476)
  hydrogen bonds       : angle       4.43695 ( 1380)
  link_BETA1-4         : bond        0.00448 (    4)
  link_BETA1-4         : angle       1.40921 (   12)
  link_NAG-ASN         : bond        0.00193 (    6)
  link_NAG-ASN         : angle       1.66910 (   18)

********************** 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: 10
    poor density    : 66
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  614 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.7751 (p-80)
REVERT: B  614 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.7742 (p-80)
  outliers start: 10
  outliers final: 5
  residues processed: 72
  average time/residue: 0.3621
  time to fit residues: 29.2514
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  : 0.257 
-------------------------------------------------------------------------------
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   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 75 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 46 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.165925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130017 restraints weight = 9265.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.80
r_work: 0.3278 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   9458  Z= 0.204
  Angle     :  0.562   6.460  12628  Z= 0.283
  Chirality :  0.043   0.144   1416
  Planarity :  0.004   0.059   1438
  Dihedral  : 10.071  56.268   1966
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.41 %
    Favored  : 89.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.25), residues: 1038
  helix:  2.48 (0.21), residues: 520
  sheet:  0.77 (0.44), residues: 116
  loop : -0.71 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 379 
 TYR   0.020   0.002   TYR B 570 
 PHE   0.017   0.002   PHE B 315 
 TRP   0.014   0.002   TRP B 647 
 HIS   0.003   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9442)
  covalent geometry    : angle       0.55607 (12586)
  SS BOND              : bond        0.00317 (    6)
  SS BOND              : angle       1.19309 (   12)
  hydrogen bonds       : bond        0.05226 (  476)
  hydrogen bonds       : angle       4.63635 ( 1380)
  link_BETA1-4         : bond        0.00444 (    4)
  link_BETA1-4         : angle       1.44519 (   12)
  link_NAG-ASN         : bond        0.00185 (    6)
  link_NAG-ASN         : angle       1.80011 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3040.27 seconds
wall clock time: 52 minutes 38.89 seconds (3158.89 seconds total)