Starting phenix.real_space_refine
on Wed Mar  4 10:30:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s8v_24927/03_2026/7s8v_24927_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s8v_24927/03_2026/7s8v_24927.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s8v_24927/03_2026/7s8v_24927_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s8v_24927/03_2026/7s8v_24927_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s8v_24927/03_2026/7s8v_24927.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s8v_24927/03_2026/7s8v_24927.map"
  }
  resolution = 3.73
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    4070      2.51       5
     N    1102      2.21       5
     O    1237      1.98       5
     H    6045      0.53       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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12502
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 4190
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 22, 'TRANS': 241}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 8147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 518, 8147
          Classifications: {'peptide': 518}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 485}
          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: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    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: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 2.11, per 1000 atoms: 0.17
  Number of scatterers: 12502
  At special positions: 0
  Unit cell: (95.4, 118.72, 106, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     O    1237      8.00
     N    1102      7.00
     C    4070      6.00
     H    6045      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 633 " - pdb=" SG  CYS A 849 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 776 " - pdb=" SG  CYS A 785 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   8 " - pdb=" SG  CYS B  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 159 " - pdb=" SG  CYS B 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 192 " - pdb=" SG  CYS B 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 196 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS B 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 228 " - pdb=" SG  CYS B 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 259 " - pdb=" SG  CYS B 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 266 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 288 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 647 " - pdb=" SG  CYS B 872 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 798 " - pdb=" SG  CYS B 807 " distance=2.04

  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 D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A6101 " - " ASN A 610 "
      " NAG B1601 " - " ASN B  16 "
      " NAG B1602 " - " ASN B  25 "
      " NAG B1603 " - " ASN B 624 "
      " NAG B1604 " - " ASN B 606 "
      " NAG C   1 " - " ASN A 592 "
      " NAG D   1 " - " ASN B 111 "
      " NAG E   1 " - " ASN B 215 "
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 339.7 milliseconds
  

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1480

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 17 sheets defined
      11.8% alpha, 35.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 625 through 629
    Processing helix  chain 'A' and resid 644 through 649
      removed outlier: 3.700A  pdb=" N   ASP A 649 " --> pdb=" O   GLY A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 684
    Processing helix  chain 'A' and resid 686 through 698
    Processing helix  chain 'A' and resid 852 through 857
      removed outlier: 4.139A  pdb=" N   ARG A 856 " --> pdb=" O   ARG A 852 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LYS A 857 " --> pdb=" O   GLN A 853 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 852 through 857'
    Processing helix  chain 'B' and resid 18 through 24
    Processing helix  chain 'B' and resid 42 through 47
      removed outlier: 3.656A  pdb=" N   PHE B  46 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 153
    Processing helix  chain 'B' and resid 193 through 197
      removed outlier: 3.730A  pdb=" N   CYS B 196 " --> pdb=" O   PRO B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 270
      removed outlier: 3.537A  pdb=" N   HIS B 263 " --> pdb=" O   CYS B 259 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   CYS B 266 " --> pdb=" O   LEU B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 643
    Processing helix  chain 'B' and resid 874 through 881
      removed outlier: 3.729A  pdb=" N   PHE B 878 " --> pdb=" O   SER B 874 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 590
      removed outlier: 5.340A  pdb=" N   ASP A 586 " --> pdb=" O   ASN A 602 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASN A 602 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752
      removed outlier: 3.533A  pdb=" N   HIS A 774 " --> pdb=" O   ILE A 615 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 813
    Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 851
      removed outlier: 4.061A  pdb=" N   THR A 872 " --> pdb=" O   GLY A 840 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 851
      removed outlier: 4.061A  pdb=" N   THR A 872 " --> pdb=" O   GLY A 840 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 14
      removed outlier: 4.579A  pdb=" N   VAL B   7 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   GLU B  30 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   HIS B  32 " --> pdb=" O   PRO B   9 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   SER B  27 " --> pdb=" O   MET B  56 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE B  82 " --> pdb=" O   ASN B 111 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 6 through 14
      removed outlier: 4.579A  pdb=" N   VAL B   7 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   GLU B  30 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   HIS B  32 " --> pdb=" O   PRO B   9 " (cutoff:3.500A)
      removed outlier: 8.825A  pdb=" N   LEU B  62 " --> pdb=" O   GLY B  31 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU B  33 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   PHE B  64 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ILE B  35 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   VAL B  66 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   LEU B  37 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU B  61 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 8.224A  pdb=" N   PHE B  96 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   LEU B  63 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   ARG B 118 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL B  94 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   GLU B 120 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   PHE B  96 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ASN B 122 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   TYR B 144 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ASN B 148 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 173
      removed outlier: 3.573A  pdb=" N   THR B 172 " --> pdb=" O   VAL B 179 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL B 179 " --> pdb=" O   THR B 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 182 through 184
      removed outlier: 6.718A  pdb=" N   HIS B 187 " --> pdb=" O   TRP B 183 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 233
    Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254
      removed outlier: 5.990A  pdb=" N   HIS B 247 " --> pdb=" O   CYS B 284 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 293 through 294
    Processing sheet with id=AB4, first strand: chain 'B' and resid 599 through 604
      removed outlier: 5.381A  pdb=" N   ASP B 600 " --> pdb=" O   LYS B 616 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   LYS B 616 " --> pdb=" O   ASP B 600 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 771 through 774
    Processing sheet with id=AB6, first strand: chain 'B' and resid 827 through 832
      removed outlier: 5.291A  pdb=" N   GLN B 845 " --> pdb=" O   PRO B 829 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 869 through 873
      removed outlier: 3.627A  pdb=" N   LEU B 856 " --> pdb=" O   THR B 901 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR B 901 " --> pdb=" O   LEU B 856 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ILE B 898 " --> pdb=" O   TRP B 909 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   TRP B 909 " --> pdb=" O   ILE B 898 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ALA B 900 " --> pdb=" O   GLY B 907 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 869 through 873
      removed outlier: 3.627A  pdb=" N   LEU B 856 " --> pdb=" O   THR B 901 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR B 901 " --> pdb=" O   LEU B 856 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   TYR B 894 " --> pdb=" O   PHE B 915 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE B 915 " --> pdb=" O   TYR B 894 " (cutoff:3.500A)

    194 hydrogen bonds defined for protein.
    474 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: 2.61

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 6041
        1.04 -     1.24: 693
        1.24 -     1.44: 2206
        1.44 -     1.64: 3667
        1.64 -     1.84: 58
  Bond restraints: 12665
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.92e+00
  bond pdb=" C1  NAG A6101 "
       pdb=" O5  NAG A6101 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.01e+00
  bond pdb=" C1  NAG B1601 "
       pdb=" O5  NAG B1601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.74e+00
  bond pdb=" CB  CYS B 288 "
       pdb=" SG  CYS B 288 "
    ideal  model  delta    sigma   weight residual
    1.808  1.765  0.043 3.30e-02 9.18e+02 1.73e+00
  bond pdb=" C1  NAG B1604 "
       pdb=" O5  NAG B1604 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.72e+00
  ... (remaining 12660 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 21911
        1.40 -     2.80: 795
        2.80 -     4.19: 64
        4.19 -     5.59: 7
        5.59 -     6.99: 3
  Bond angle restraints: 22780
  Sorted by residual:
  angle pdb=" CA  CYS B 288 "
        pdb=" CB  CYS B 288 "
        pdb=" SG  CYS B 288 "
      ideal   model   delta    sigma   weight residual
     114.40  121.39   -6.99 2.30e+00 1.89e-01 9.24e+00
  angle pdb=" N   CYS B 288 "
        pdb=" CA  CYS B 288 "
        pdb=" CB  CYS B 288 "
      ideal   model   delta    sigma   weight residual
     110.14  114.02   -3.88 1.41e+00 5.03e-01 7.56e+00
  angle pdb=" C   LEU B 599 "
        pdb=" N   ASP B 600 "
        pdb=" CA  ASP B 600 "
      ideal   model   delta    sigma   weight residual
     121.80  128.06   -6.26 2.44e+00 1.68e-01 6.58e+00
  angle pdb=" CA  CYS B 301 "
        pdb=" CB  CYS B 301 "
        pdb=" SG  CYS B 301 "
      ideal   model   delta    sigma   weight residual
     114.40  109.02    5.38 2.30e+00 1.89e-01 5.48e+00
  angle pdb=" C   CYS B 288 "
        pdb=" CA  CYS B 288 "
        pdb=" CB  CYS B 288 "
      ideal   model   delta    sigma   weight residual
     109.26  112.58   -3.32 1.47e+00 4.63e-01 5.11e+00
  ... (remaining 22775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.93: 5792
       21.93 -    43.86: 356
       43.86 -    65.80: 85
       65.80 -    87.73: 14
       87.73 -   109.66: 5
  Dihedral angle restraints: 6252
    sinusoidal: 3511
      harmonic: 2741
  Sorted by residual:
  dihedral pdb=" CA  LEU B 305 "
           pdb=" C   LEU B 305 "
           pdb=" N   GLY B 306 "
           pdb=" CA  GLY B 306 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.11   30.89     0      5.00e+00 4.00e-02 3.82e+01
  dihedral pdb=" CB  CYS B   8 "
           pdb=" SG  CYS B   8 "
           pdb=" SG  CYS B  26 "
           pdb=" CB  CYS B  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.03  -50.03     1      1.00e+01 1.00e-02 3.43e+01
  dihedral pdb=" CB  CYS B 798 "
           pdb=" SG  CYS B 798 "
           pdb=" SG  CYS B 807 "
           pdb=" CB  CYS B 807 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.02   46.98     1      1.00e+01 1.00e-02 3.05e+01
  ... (remaining 6249 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.330: 990
       0.330 -    0.661: 0
       0.661 -    0.991: 0
       0.991 -    1.322: 1
       1.322 -    1.652: 2
  Chirality restraints: 993
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.75   -1.65 2.00e-02 2.50e+03 6.82e+03
  chirality pdb=" C1  BMA D   3 "
            pdb=" O4  NAG D   2 "
            pdb=" C2  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.77   -1.63 2.00e-02 2.50e+03 6.61e+03
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.30   -1.10 2.00e-02 2.50e+03 3.01e+03
  ... (remaining 990 not shown)

  Planarity restraints: 1890
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 306 "    0.036 5.00e-02 4.00e+02   5.46e-02 4.78e+00
        pdb=" N   PRO B 307 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 307 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 307 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 842 "    0.004 2.00e-02 2.50e+03   1.15e-02 1.98e+00
        pdb=" CD  GLN A 842 "   -0.023 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 842 "    0.013 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 842 "    0.003 2.00e-02 2.50e+03
        pdb="HE21 GLN A 842 "    0.007 2.00e-02 2.50e+03
        pdb="HE22 GLN A 842 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 616 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.52e+00
        pdb=" N   PRO B 617 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B 617 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 617 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1887 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 608
        2.15 -     2.76: 23669
        2.76 -     3.37: 34404
        3.37 -     3.99: 45992
        3.99 -     4.60: 69424
  Nonbonded interactions: 174097
  Sorted by model distance:
  nonbonded pdb=" H   PHE A 766 "
            pdb=" OG1 THR A 795 "
     model   vdw
     1.535 2.450
  nonbonded pdb="HE21 GLN A 876 "
            pdb=" O   GLY A 884 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" O   TRP A 822 "
            pdb=" HH  TYR A 855 "
     model   vdw
     1.555 2.450
  nonbonded pdb=" O   ALA A 644 "
            pdb=" HG1 THR A 647 "
     model   vdw
     1.556 2.450
  nonbonded pdb=" O   CYS B 266 "
            pdb="HH11 ARG B 270 "
     model   vdw
     1.572 2.450
  ... (remaining 174092 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 'C'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  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:             0.070
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.140
  Find NCS groups from input model:        0.040
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
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      :  0.004   0.066   6649  Z= 0.184
  Angle     :  1.413  60.368   9056  Z= 0.532
  Chirality :  0.093   1.652    993
  Planarity :  0.004   0.055   1160
  Dihedral  : 13.875 109.661   2664
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.81 %
    Favored  : 96.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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 are not related in a simple way.
  whole: -3.48 (0.27), residues: 768
  helix: -3.77 (0.47), residues: 54
  sheet: -1.79 (0.32), residues: 216
  loop : -2.50 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 806 
 TYR   0.011   0.001   TYR A 689 
 PHE   0.012   0.001   PHE B  51 
 TRP   0.006   0.001   TRP A 822 
 HIS   0.003   0.001   HIS B 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6620)
  covalent geometry    : angle       0.64612 ( 8986)
  SS BOND              : bond        0.00412 (   17)
  SS BOND              : angle       1.57304 (   34)
  hydrogen bonds       : bond        0.25967 (  165)
  hydrogen bonds       : angle      10.36512 (  474)
  link_BETA1-4         : bond        0.06525 (    4)
  link_BETA1-4         : angle      34.34311 (   12)
  link_NAG-ASN         : bond        0.00328 (    8)
  link_NAG-ASN         : angle       1.92474 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  585 LEU cc_start: 0.8520 (mt) cc_final: 0.8211 (mt)
REVERT: A  602 ASN cc_start: 0.8310 (m-40) cc_final: 0.7727 (m110)
REVERT: A  691 LYS cc_start: 0.9275 (tptt) cc_final: 0.8951 (tppt)
REVERT: A  778 HIS cc_start: 0.6277 (m90) cc_final: 0.5981 (p90)
REVERT: A  834 MET cc_start: 0.7055 (ptm) cc_final: 0.6636 (ptp)
REVERT: B   90 ASN cc_start: 0.9082 (t0) cc_final: 0.8371 (t0)
REVERT: B  110 MET cc_start: 0.6111 (mmt) cc_final: 0.5608 (mmt)
REVERT: B  611 ILE cc_start: 0.8117 (mt) cc_final: 0.7774 (mt)
REVERT: B  845 GLN cc_start: 0.8265 (tp40) cc_final: 0.6922 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2482
  time to fit residues: 39.8141
Evaluate side-chains
  92 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
B  32 HIS
B  34 GLN
B 123 ASN
B 594 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.085360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.072009 restraints weight = 98560.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.074151 restraints weight = 49424.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.075464 restraints weight = 30730.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.076194 restraints weight = 22779.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.076654 restraints weight = 18906.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6616
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6649  Z= 0.143
  Angle     :  0.707   8.932   9056  Z= 0.348
  Chirality :  0.047   0.173    993
  Planarity :  0.005   0.087   1160
  Dihedral  :  9.598  65.709   1110
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  8.60 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -2.96 (0.28), residues: 768
  helix: -3.23 (0.51), residues: 62
  sheet: -1.40 (0.32), residues: 228
  loop : -2.15 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 236 
 TYR   0.014   0.001   TYR A 689 
 PHE   0.016   0.002   PHE B  96 
 TRP   0.007   0.001   TRP A 618 
 HIS   0.005   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6620)
  covalent geometry    : angle       0.67853 ( 8986)
  SS BOND              : bond        0.00541 (   17)
  SS BOND              : angle       1.43133 (   34)
  hydrogen bonds       : bond        0.05451 (  165)
  hydrogen bonds       : angle       7.60955 (  474)
  link_BETA1-4         : bond        0.00231 (    4)
  link_BETA1-4         : angle       4.45139 (   12)
  link_NAG-ASN         : bond        0.00569 (    8)
  link_NAG-ASN         : angle       1.89125 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  691 LYS cc_start: 0.9252 (tptt) cc_final: 0.9003 (tppt)
REVERT: A  834 MET cc_start: 0.7349 (ptm) cc_final: 0.6819 (ptp)
REVERT: B   34 GLN cc_start: 0.7017 (mt0) cc_final: 0.6686 (mp10)
REVERT: B  287 GLU cc_start: 0.8019 (mp0) cc_final: 0.6602 (tp30)
REVERT: B  845 GLN cc_start: 0.8392 (tp40) cc_final: 0.7345 (mp10)
  outliers start: 8
  outliers final: 4
  residues processed: 100
  average time/residue: 0.2334
  time to fit residues: 29.2376
Evaluate side-chains
  84 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  614 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
A 699 ASN
A 870 ASN
B 148 ASN
** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 877 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.083083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.070006 restraints weight = 100688.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.072071 restraints weight = 50618.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.073319 restraints weight = 31706.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.074004 restraints weight = 23736.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.074485 restraints weight = 19726.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088   6649  Z= 0.237
  Angle     :  0.728   8.128   9056  Z= 0.369
  Chirality :  0.047   0.250    993
  Planarity :  0.006   0.087   1160
  Dihedral  :  8.104  59.666   1110
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 10.86 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -2.81 (0.27), residues: 768
  helix: -2.83 (0.50), residues: 62
  sheet: -1.25 (0.32), residues: 233
  loop : -2.12 (0.26), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 118 
 TYR   0.023   0.002   TYR A 689 
 PHE   0.018   0.002   PHE B  88 
 TRP   0.007   0.001   TRP A 618 
 HIS   0.007   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 6620)
  covalent geometry    : angle       0.69471 ( 8986)
  SS BOND              : bond        0.00757 (   17)
  SS BOND              : angle       2.29953 (   34)
  hydrogen bonds       : bond        0.04602 (  165)
  hydrogen bonds       : angle       6.99284 (  474)
  link_BETA1-4         : bond        0.00382 (    4)
  link_BETA1-4         : angle       3.54650 (   12)
  link_NAG-ASN         : bond        0.00699 (    8)
  link_NAG-ASN         : angle       2.36556 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  691 LYS cc_start: 0.9293 (tptt) cc_final: 0.9062 (tppt)
REVERT: A  834 MET cc_start: 0.7959 (ptm) cc_final: 0.7411 (ptp)
REVERT: A  891 PHE cc_start: 0.6341 (p90) cc_final: 0.6099 (p90)
REVERT: B  287 GLU cc_start: 0.8151 (mp0) cc_final: 0.6589 (tp30)
REVERT: B  845 GLN cc_start: 0.8291 (tp40) cc_final: 0.7121 (mp10)
  outliers start: 11
  outliers final: 9
  residues processed: 88
  average time/residue: 0.2197
  time to fit residues: 24.3949
Evaluate side-chains
  81 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  614 LYS
Chi-restraints excluded: chain B residue  782 ILE
Chi-restraints excluded: chain B residue  896 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 70 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0970
   chunk 11 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0170
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.4816

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

Flipped N/Q/H residues before XYZ refinement:
B 260 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.084278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.071195 restraints weight = 98039.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.073267 restraints weight = 50087.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.074479 restraints weight = 31061.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.075153 restraints weight = 23291.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.075592 restraints weight = 19415.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6649  Z= 0.112
  Angle     :  0.614   6.335   9056  Z= 0.308
  Chirality :  0.046   0.192    993
  Planarity :  0.005   0.087   1160
  Dihedral  :  6.792  56.662   1110
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.00 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -2.46 (0.28), residues: 768
  helix: -2.68 (0.52), residues: 62
  sheet: -0.89 (0.34), residues: 227
  loop : -1.93 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 874 
 TYR   0.015   0.001   TYR B  60 
 PHE   0.010   0.001   PHE B 788 
 TRP   0.007   0.001   TRP A 618 
 HIS   0.003   0.001   HIS B 787 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6620)
  covalent geometry    : angle       0.59526 ( 8986)
  SS BOND              : bond        0.00529 (   17)
  SS BOND              : angle       1.25441 (   34)
  hydrogen bonds       : bond        0.04020 (  165)
  hydrogen bonds       : angle       6.38931 (  474)
  link_BETA1-4         : bond        0.00384 (    4)
  link_BETA1-4         : angle       2.87838 (   12)
  link_NAG-ASN         : bond        0.00339 (    8)
  link_NAG-ASN         : angle       1.82483 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  691 LYS cc_start: 0.9263 (tptt) cc_final: 0.9013 (tppt)
REVERT: A  834 MET cc_start: 0.7818 (ptm) cc_final: 0.7342 (ptp)
REVERT: A  891 PHE cc_start: 0.6295 (p90) cc_final: 0.6057 (p90)
REVERT: B  287 GLU cc_start: 0.8265 (mp0) cc_final: 0.6895 (tp30)
REVERT: B  845 GLN cc_start: 0.8426 (tp40) cc_final: 0.7356 (mp10)
  outliers start: 10
  outliers final: 7
  residues processed: 81
  average time/residue: 0.1875
  time to fit residues: 19.9548
Evaluate side-chains
  80 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  614 LYS
Chi-restraints excluded: chain B residue  871 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 17 optimal weight:    0.0270
   chunk 18 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.8046

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

Flipped N/Q/H residues before XYZ refinement:
A 631 ASN
A 827 ASN
B 282 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.081705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.068828 restraints weight = 101588.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.070850 restraints weight = 51352.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.072032 restraints weight = 32086.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.072670 restraints weight = 24081.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.073114 restraints weight = 20055.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.4993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   6649  Z= 0.245
  Angle     :  0.714   6.873   9056  Z= 0.364
  Chirality :  0.046   0.197    993
  Planarity :  0.006   0.089   1160
  Dihedral  :  7.054  58.246   1110
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 13.68 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -2.57 (0.28), residues: 768
  helix: -2.51 (0.53), residues: 63
  sheet: -1.02 (0.35), residues: 218
  loop : -2.01 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 118 
 TYR   0.023   0.002   TYR A 689 
 PHE   0.014   0.002   PHE A 747 
 TRP   0.011   0.002   TRP B 183 
 HIS   0.006   0.002   HIS B 787 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 6620)
  covalent geometry    : angle       0.68836 ( 8986)
  SS BOND              : bond        0.00663 (   17)
  SS BOND              : angle       1.84420 (   34)
  hydrogen bonds       : bond        0.03978 (  165)
  hydrogen bonds       : angle       6.22786 (  474)
  link_BETA1-4         : bond        0.00305 (    4)
  link_BETA1-4         : angle       2.53102 (   12)
  link_NAG-ASN         : bond        0.00662 (    8)
  link_NAG-ASN         : angle       2.60788 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  834 MET cc_start: 0.8334 (ptm) cc_final: 0.7877 (ptp)
REVERT: B   13 ILE cc_start: 0.8126 (mp) cc_final: 0.7905 (mp)
REVERT: B  110 MET cc_start: 0.7759 (mmt) cc_final: 0.7448 (mmt)
  outliers start: 11
  outliers final: 6
  residues processed: 78
  average time/residue: 0.1831
  time to fit residues: 18.7969
Evaluate side-chains
  73 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  782 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.082143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.069190 restraints weight = 100273.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.071167 restraints weight = 51582.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.072397 restraints weight = 31868.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.073089 restraints weight = 23642.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.073510 restraints weight = 19789.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.5488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6649  Z= 0.160
  Angle     :  0.639   5.726   9056  Z= 0.322
  Chirality :  0.046   0.174    993
  Planarity :  0.005   0.088   1160
  Dihedral  :  6.717  59.792   1110
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.82 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -2.48 (0.28), residues: 768
  helix: -2.44 (0.53), residues: 63
  sheet: -0.98 (0.35), residues: 212
  loop : -1.92 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 874 
 TYR   0.016   0.001   TYR A 689 
 PHE   0.013   0.002   PHE B 788 
 TRP   0.007   0.001   TRP B 183 
 HIS   0.006   0.001   HIS B 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6620)
  covalent geometry    : angle       0.62117 ( 8986)
  SS BOND              : bond        0.00618 (   17)
  SS BOND              : angle       1.23969 (   34)
  hydrogen bonds       : bond        0.03728 (  165)
  hydrogen bonds       : angle       6.04403 (  474)
  link_BETA1-4         : bond        0.00350 (    4)
  link_BETA1-4         : angle       2.39844 (   12)
  link_NAG-ASN         : bond        0.00463 (    8)
  link_NAG-ASN         : angle       2.10595 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  834 MET cc_start: 0.8309 (ptm) cc_final: 0.7788 (ptp)
REVERT: A  893 TYR cc_start: 0.5586 (OUTLIER) cc_final: 0.4479 (m-10)
REVERT: B  110 MET cc_start: 0.7894 (mmt) cc_final: 0.7617 (mmt)
  outliers start: 13
  outliers final: 10
  residues processed: 75
  average time/residue: 0.2174
  time to fit residues: 20.9724
Evaluate side-chains
  73 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  694 GLU
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  796 MET
Chi-restraints excluded: chain A residue  816 ASN
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  893 TYR
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  782 ILE
Chi-restraints excluded: chain B residue  871 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 2 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.082337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.069296 restraints weight = 99404.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.071320 restraints weight = 50716.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.072501 restraints weight = 31581.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.073219 restraints weight = 23743.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.073621 restraints weight = 19954.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.5771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6649  Z= 0.138
  Angle     :  0.605   5.479   9056  Z= 0.305
  Chirality :  0.045   0.181    993
  Planarity :  0.005   0.086   1160
  Dihedral  :  6.481  59.981   1110
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.39 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -2.33 (0.29), residues: 768
  helix: -2.35 (0.54), residues: 63
  sheet: -0.92 (0.36), residues: 209
  loop : -1.79 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 874 
 TYR   0.015   0.001   TYR A 689 
 PHE   0.015   0.002   PHE B 231 
 TRP   0.006   0.001   TRP A 618 
 HIS   0.005   0.001   HIS B 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6620)
  covalent geometry    : angle       0.58768 ( 8986)
  SS BOND              : bond        0.00465 (   17)
  SS BOND              : angle       1.16426 (   34)
  hydrogen bonds       : bond        0.03530 (  165)
  hydrogen bonds       : angle       5.82414 (  474)
  link_BETA1-4         : bond        0.00337 (    4)
  link_BETA1-4         : angle       2.27222 (   12)
  link_NAG-ASN         : bond        0.00425 (    8)
  link_NAG-ASN         : angle       2.09920 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  834 MET cc_start: 0.8375 (ptm) cc_final: 0.7854 (ptp)
REVERT: A  893 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.4643 (m-10)
REVERT: B   38 MET cc_start: 0.6731 (tpp) cc_final: 0.5984 (tpp)
REVERT: B  110 MET cc_start: 0.7884 (mmt) cc_final: 0.7643 (mmt)
REVERT: B  844 TRP cc_start: 0.4075 (p90) cc_final: 0.3041 (p90)
  outliers start: 10
  outliers final: 8
  residues processed: 73
  average time/residue: 0.2153
  time to fit residues: 19.9198
Evaluate side-chains
  70 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 VAL
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  893 TYR
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  782 ILE
Chi-restraints excluded: chain B residue  855 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 47 optimal weight:    0.0970
   chunk 3 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 69 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.082621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.069564 restraints weight = 98706.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.071593 restraints weight = 49933.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.072787 restraints weight = 31428.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.073515 restraints weight = 23389.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.073962 restraints weight = 19516.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.6081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6649  Z= 0.115
  Angle     :  0.586   5.322   9056  Z= 0.296
  Chirality :  0.045   0.180    993
  Planarity :  0.005   0.085   1160
  Dihedral  :  6.101  56.235   1110
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 15.80 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -2.12 (0.30), residues: 768
  helix: -2.15 (0.55), residues: 63
  sheet: -0.81 (0.36), residues: 209
  loop : -1.63 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 882 
 TYR   0.014   0.001   TYR A 689 
 PHE   0.027   0.001   PHE B 231 
 TRP   0.006   0.001   TRP B 632 
 HIS   0.005   0.001   HIS B 841 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6620)
  covalent geometry    : angle       0.57053 ( 8986)
  SS BOND              : bond        0.00413 (   17)
  SS BOND              : angle       1.01218 (   34)
  hydrogen bonds       : bond        0.03373 (  165)
  hydrogen bonds       : angle       5.62679 (  474)
  link_BETA1-4         : bond        0.00327 (    4)
  link_BETA1-4         : angle       2.16572 (   12)
  link_NAG-ASN         : bond        0.00329 (    8)
  link_NAG-ASN         : angle       1.92981 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  834 MET cc_start: 0.8418 (ptm) cc_final: 0.7892 (ptp)
REVERT: B   34 GLN cc_start: 0.8234 (mt0) cc_final: 0.7919 (mt0)
REVERT: B   38 MET cc_start: 0.6558 (tpp) cc_final: 0.5688 (tpp)
REVERT: B  844 TRP cc_start: 0.4096 (p90) cc_final: 0.3084 (p90)
  outliers start: 6
  outliers final: 6
  residues processed: 72
  average time/residue: 0.2118
  time to fit residues: 19.5570
Evaluate side-chains
  68 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 VAL
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  871 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 72 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.080693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.067961 restraints weight = 101327.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.069929 restraints weight = 51944.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.071078 restraints weight = 32233.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.071773 restraints weight = 24159.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.072069 restraints weight = 20333.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.6845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   6649  Z= 0.215
  Angle     :  0.681   5.929   9056  Z= 0.349
  Chirality :  0.045   0.186    993
  Planarity :  0.006   0.088   1160
  Dihedral  :  6.855  59.866   1110
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 15.94 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -2.33 (0.29), residues: 768
  helix: -2.12 (0.57), residues: 63
  sheet: -1.00 (0.36), residues: 216
  loop : -1.79 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 882 
 TYR   0.019   0.002   TYR A 689 
 PHE   0.032   0.002   PHE B 231 
 TRP   0.014   0.002   TRP A 810 
 HIS   0.012   0.002   HIS B 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 6620)
  covalent geometry    : angle       0.66159 ( 8986)
  SS BOND              : bond        0.00598 (   17)
  SS BOND              : angle       1.38210 (   34)
  hydrogen bonds       : bond        0.03747 (  165)
  hydrogen bonds       : angle       5.76720 (  474)
  link_BETA1-4         : bond        0.00368 (    4)
  link_BETA1-4         : angle       2.27539 (   12)
  link_NAG-ASN         : bond        0.00558 (    8)
  link_NAG-ASN         : angle       2.44897 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  834 MET cc_start: 0.8580 (ptm) cc_final: 0.8154 (ptp)
REVERT: A  893 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.4638 (m-10)
REVERT: B   34 GLN cc_start: 0.8335 (mt0) cc_final: 0.8022 (mt0)
REVERT: B   38 MET cc_start: 0.6667 (tpp) cc_final: 0.5622 (tpp)
REVERT: B   98 MET cc_start: 0.8225 (mmm) cc_final: 0.7984 (mmt)
REVERT: B  305 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8417 (tt)
REVERT: B  818 MET cc_start: 0.7899 (mtp) cc_final: 0.7545 (mtp)
REVERT: B  844 TRP cc_start: 0.4136 (p90) cc_final: 0.3004 (p90)
  outliers start: 10
  outliers final: 8
  residues processed: 72
  average time/residue: 0.2033
  time to fit residues: 19.0343
Evaluate side-chains
  69 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 VAL
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  893 TYR
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  782 ILE
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  871 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0370
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.6258

-------------------------------------------------------------------------------
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 = 0.4007 r_free = 0.4007 target = 0.081695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.068637 restraints weight = 98221.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.070670 restraints weight = 50509.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.071865 restraints weight = 31489.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.072529 restraints weight = 23621.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.072927 restraints weight = 19713.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.6935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6649  Z= 0.115
  Angle     :  0.601   5.272   9056  Z= 0.303
  Chirality :  0.045   0.175    993
  Planarity :  0.005   0.081   1160
  Dihedral  :  6.312  57.421   1110
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 16.22 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -2.03 (0.30), residues: 768
  helix: -1.89 (0.60), residues: 63
  sheet: -0.73 (0.36), residues: 214
  loop : -1.62 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 882 
 TYR   0.012   0.001   TYR A 689 
 PHE   0.017   0.002   PHE B 231 
 TRP   0.006   0.001   TRP B 632 
 HIS   0.009   0.001   HIS B 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6620)
  covalent geometry    : angle       0.58739 ( 8986)
  SS BOND              : bond        0.00462 (   17)
  SS BOND              : angle       0.95405 (   34)
  hydrogen bonds       : bond        0.03360 (  165)
  hydrogen bonds       : angle       5.57246 (  474)
  link_BETA1-4         : bond        0.00273 (    4)
  link_BETA1-4         : angle       2.08622 (   12)
  link_NAG-ASN         : bond        0.00367 (    8)
  link_NAG-ASN         : angle       1.96015 (   24)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  834 MET cc_start: 0.8513 (ptm) cc_final: 0.8031 (ptp)
REVERT: A  891 PHE cc_start: 0.6171 (p90) cc_final: 0.5933 (p90)
REVERT: A  893 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.4577 (m-10)
REVERT: B   34 GLN cc_start: 0.8306 (mt0) cc_final: 0.7985 (mt0)
REVERT: B   38 MET cc_start: 0.6513 (tpp) cc_final: 0.5617 (tpp)
REVERT: B   98 MET cc_start: 0.8185 (mmm) cc_final: 0.7957 (mmt)
REVERT: B  818 MET cc_start: 0.7882 (mtp) cc_final: 0.7429 (mtp)
  outliers start: 8
  outliers final: 6
  residues processed: 66
  average time/residue: 0.1960
  time to fit residues: 16.8887
Evaluate side-chains
  66 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 VAL
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  893 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  855 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0270
   chunk 64 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.7040

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.081757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.068813 restraints weight = 99144.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.070871 restraints weight = 50864.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.072053 restraints weight = 31309.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.072757 restraints weight = 23364.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.073180 restraints weight = 19561.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.7155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6649  Z= 0.121
  Angle     :  0.592   5.354   9056  Z= 0.298
  Chirality :  0.044   0.180    993
  Planarity :  0.005   0.083   1160
  Dihedral  :  6.008  54.666   1110
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 16.36 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 are not related in a simple way.
  whole: -1.91 (0.30), residues: 768
  helix: -1.73 (0.63), residues: 63
  sheet: -0.67 (0.37), residues: 214
  loop : -1.52 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 882 
 TYR   0.014   0.001   TYR A 689 
 PHE   0.017   0.001   PHE B 231 
 TRP   0.007   0.001   TRP B 632 
 HIS   0.010   0.001   HIS B 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6620)
  covalent geometry    : angle       0.57740 ( 8986)
  SS BOND              : bond        0.00456 (   17)
  SS BOND              : angle       1.03183 (   34)
  hydrogen bonds       : bond        0.03259 (  165)
  hydrogen bonds       : angle       5.44809 (  474)
  link_BETA1-4         : bond        0.00294 (    4)
  link_BETA1-4         : angle       2.12204 (   12)
  link_NAG-ASN         : bond        0.00363 (    8)
  link_NAG-ASN         : angle       1.95802 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2599.07 seconds
wall clock time: 44 minutes 49.97 seconds (2689.97 seconds total)