Starting phenix.real_space_refine
on Fri Sep 11 18:35:55 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6k7l_9939/09_2026/6k7l_9939.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6k7l_9939/09_2026/6k7l_9939.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6k7l_9939/09_2026/6k7l_9939.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6k7l_9939/09_2026/6k7l_9939.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6k7l_9939/09_2026/6k7l_9939.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6k7l_9939/09_2026/6k7l_9939.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6k7l_9939/09_2026/6k7l_9939.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6k7l_9939/09_2026/6k7l_9939.cif"
  }
  resolution = 2.83
  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=   0.005
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: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      54      5.16       5
     Be      1      3.05       5
     C    6881      2.51       5
     N    1756      2.21       5
     O    1919      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10615
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 992, 7893
          Classifications: {'peptide': 992}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 961}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 2615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2615
          Classifications: {'peptide': 325}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 299}
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 40
          Unusual residues: {' MG': 1, 'BEF': 1, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    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 chiralities: 2
  Time building chain proxies: 2.63, per 1000 atoms: 0.25
  Number of scatterers: 10615
  At special positions: 0
  Unit cell: (73.04, 107.07, 166.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      54     16.00
     Mg      1     11.99
     F       3      9.00
     O    1919      8.00
     N    1756      7.00
     C    6881      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  91 " - pdb=" SG  CYS C 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 102 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 157 " - pdb=" SG  CYS C 171 " 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=1, symmetry=0
  Links applied
    ALPHA1-4
      " NAG B   2 " - " MAN B   3 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN C 180 "
      " NAG C 404 " - " ASN C 294 "
      " NAG C 405 " - " ASN C 107 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 420.4 milliseconds
  

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2476

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 11 sheets defined
      49.5% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 74
      removed outlier: 4.137A  pdb=" N   LEU A  65 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      Proline residue:  A  66  - end of helix
    Processing helix  chain 'A' and resid 76 through 88
    Processing helix  chain 'A' and resid 101 through 132
      removed outlier: 4.932A  pdb=" N   ALA A 129 " --> pdb=" O   LYS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 178
      No H-bonds generated for 'chain 'A' and resid 176 through 178'
    Processing helix  chain 'A' and resid 185 through 190
    Processing helix  chain 'A' and resid 200 through 205
    Processing helix  chain 'A' and resid 208 through 215
      removed outlier: 4.437A  pdb=" N   ILE A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 323
    Processing helix  chain 'A' and resid 339 through 351
    Processing helix  chain 'A' and resid 352 through 355
      removed outlier: 3.568A  pdb=" N   ILE A 355 " --> pdb=" O   ASN A 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 352 through 355'
    Processing helix  chain 'A' and resid 358 through 377
    Processing helix  chain 'A' and resid 393 through 397
      removed outlier: 3.996A  pdb=" N   LEU A 396 " --> pdb=" O   THR A 393 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASN A 397 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 393 through 397'
    Processing helix  chain 'A' and resid 398 through 401
    Processing helix  chain 'A' and resid 448 through 455
    Processing helix  chain 'A' and resid 458 through 472
      removed outlier: 3.925A  pdb=" N   ILE A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 503
    Processing helix  chain 'A' and resid 559 through 564
      removed outlier: 3.722A  pdb=" N   TYR A 564 " --> pdb=" O   ASP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 588
    Processing helix  chain 'A' and resid 600 through 617
      removed outlier: 3.892A  pdb=" N   THR A 616 " --> pdb=" O   GLN A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 632
    Processing helix  chain 'A' and resid 651 through 662
    Processing helix  chain 'A' and resid 673 through 684
    Processing helix  chain 'A' and resid 731 through 739
    Processing helix  chain 'A' and resid 742 through 753
    Processing helix  chain 'A' and resid 762 through 775
    Processing helix  chain 'A' and resid 787 through 789
      No H-bonds generated for 'chain 'A' and resid 787 through 789'
    Processing helix  chain 'A' and resid 790 through 797
    Processing helix  chain 'A' and resid 809 through 815
    Processing helix  chain 'A' and resid 823 through 831
      removed outlier: 4.320A  pdb=" N   ASN A 827 " --> pdb=" O   LYS A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 856
      removed outlier: 3.730A  pdb=" N   LEU A 854 " --> pdb=" O   LYS A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 866
      removed outlier: 3.897A  pdb=" N   PHE A 863 " --> pdb=" O   ILE A 859 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   VAL A 864 " --> pdb=" O   TRP A 860 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY A 866 " --> pdb=" O   ALA A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 875 through 881
    Processing helix  chain 'A' and resid 887 through 896
      removed outlier: 3.914A  pdb=" N   LEU A 891 " --> pdb=" O   ALA A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 908
    Processing helix  chain 'A' and resid 910 through 919
      removed outlier: 3.574A  pdb=" N   THR A 914 " --> pdb=" O   GLU A 910 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN A 916 " --> pdb=" O   TYR A 912 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA A 918 " --> pdb=" O   THR A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 948
      Proline residue:  A 944  - end of helix
    Processing helix  chain 'A' and resid 961 through 985
      removed outlier: 3.835A  pdb=" N   LEU A 965 " --> pdb=" O   ASP A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 1011
    Processing helix  chain 'A' and resid 1020 through 1024
      removed outlier: 3.547A  pdb=" N   MET A1023 " --> pdb=" O   ALA A1020 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A1024 " --> pdb=" O   PRO A1021 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1020 through 1024'
    Processing helix  chain 'A' and resid 1025 through 1032
    Processing helix  chain 'A' and resid 1033 through 1062
      removed outlier: 4.055A  pdb=" N   LEU A1041 " --> pdb=" O   TRP A1037 " (cutoff:3.500A)
      Proline residue:  A1044  - end of helix
      removed outlier: 5.102A  pdb=" N   LEU A1050 " --> pdb=" O   ALA A1046 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   ASP A1051 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 74
      Proline residue:  C  52  - end of helix
      Proline residue:  C  63  - end of helix
    Processing helix  chain 'C' and resid 91 through 95
      removed outlier: 3.562A  pdb=" N   CYS C  94 " --> pdb=" O   CYS C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 136
    Processing helix  chain 'C' and resid 139 through 144
    Processing helix  chain 'C' and resid 146 through 152
    Processing helix  chain 'C' and resid 172 through 177
    Processing helix  chain 'C' and resid 206 through 212
    Processing helix  chain 'C' and resid 222 through 227
    Processing helix  chain 'C' and resid 239 through 243
      removed outlier: 3.515A  pdb=" N   LEU C 243 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 246 through 253
      removed outlier: 3.865A  pdb=" N   ASN C 250 " --> pdb=" O   PRO C 247 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   GLY C 251 " --> pdb=" O   ASP C 248 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   PHE C 252 " --> pdb=" O   ASN C 249 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ILE C 253 " --> pdb=" O   ASN C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 262
    Processing helix  chain 'C' and resid 323 through 350
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40
    Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160
      removed outlier: 6.556A  pdb=" N   TRP A 262 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   SER A 174 " --> pdb=" O   TRP A 262 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   HIS A 264 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ASP A 168 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 198
      removed outlier: 3.645A  pdb=" N   TYR A 182 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 382
    Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391
      removed outlier: 6.697A  pdb=" N   THR A 781 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   VAL A 801 " --> pdb=" O   THR A 781 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   ALA A 783 " --> pdb=" O   VAL A 801 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   ILE A 803 " --> pdb=" O   ALA A 783 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   GLY A 785 " --> pdb=" O   ILE A 803 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   VAL A 403 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   LEU A 782 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   TYR A 405 " --> pdb=" O   LEU A 782 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ILE A 784 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   PHE A 407 " --> pdb=" O   ILE A 784 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ILE A 666 " --> pdb=" O   VAL A 756 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   CYS A 758 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ILE A 668 " --> pdb=" O   CYS A 758 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU A 727 " --> pdb=" O   ILE A 757 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   CYS A 759 " --> pdb=" O   LEU A 727 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ILE A 729 " --> pdb=" O   CYS A 759 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   ILE A 694 " --> pdb=" O   ILE A 728 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   ASP A 730 " --> pdb=" O   ILE A 694 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   ILE A 696 " --> pdb=" O   ASP A 730 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431
      removed outlier: 3.638A  pdb=" N   VAL A 429 " --> pdb=" O   ILE A 426 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   CYS A 424 " --> pdb=" O   TYR A 431 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   VAL A 418 " --> pdb=" O   LYS A 647 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   ALA A 643 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 514 through 517
    Processing sheet with id=AA8, first strand: chain 'A' and resid 531 through 532
      removed outlier: 3.970A  pdb=" N   THR A 547 " --> pdb=" O   LYS A 551 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS A 551 " --> pdb=" O   THR A 547 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 79
      removed outlier: 7.056A  pdb=" N   VAL C 118 " --> pdb=" O   LEU C 275 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   LEU C 275 " --> pdb=" O   VAL C 118 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   MET C 120 " --> pdb=" O   TYR C 273 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 110
      removed outlier: 4.749A  pdb=" N   ARG C 290 " --> pdb=" O   ILE C 188 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163

    497 hydrogen bonds defined for protein.
    1437 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: 2.16

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1815
        1.32 -     1.44: 2878
        1.44 -     1.57: 6083
        1.57 -     1.69: 0
        1.69 -     1.81: 85
  Bond restraints: 10861
  Sorted by residual:
  bond pdb=" F2  BEF A1801 "
       pdb="BE   BEF A1801 "
    ideal  model  delta    sigma   weight residual
    1.476  1.760 -0.284 2.00e-02 2.50e+03 2.02e+02
  bond pdb=" F1  BEF A1801 "
       pdb="BE   BEF A1801 "
    ideal  model  delta    sigma   weight residual
    1.476  1.758 -0.282 2.00e-02 2.50e+03 1.99e+02
  bond pdb=" F3  BEF A1801 "
       pdb="BE   BEF A1801 "
    ideal  model  delta    sigma   weight residual
    1.476  1.756 -0.280 2.00e-02 2.50e+03 1.96e+02
  bond pdb=" C   ARG C 215 "
       pdb=" N   ASN C 216 "
    ideal  model  delta    sigma   weight residual
    1.329  1.218  0.111 1.86e-02 2.89e+03 3.53e+01
  bond pdb=" CB  VAL A 853 "
       pdb=" CG1 VAL A 853 "
    ideal  model  delta    sigma   weight residual
    1.521  1.423  0.098 3.30e-02 9.18e+02 8.79e+00
  ... (remaining 10856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 13956
        2.31 -     4.62: 673
        4.62 -     6.93: 73
        6.93 -     9.25: 23
        9.25 -    11.56: 14
  Bond angle restraints: 14739
  Sorted by residual:
  angle pdb=" C   LEU A 330 "
        pdb=" N   ASN A 331 "
        pdb=" CA  ASN A 331 "
      ideal   model   delta    sigma   weight residual
     121.54  133.10  -11.56 1.91e+00 2.74e-01 3.66e+01
  angle pdb=" N   SER A 223 "
        pdb=" CA  SER A 223 "
        pdb=" C   SER A 223 "
      ideal   model   delta    sigma   weight residual
     109.81  120.43  -10.62 2.21e+00 2.05e-01 2.31e+01
  angle pdb=" N   SER A1024 "
        pdb=" CA  SER A1024 "
        pdb=" C   SER A1024 "
      ideal   model   delta    sigma   weight residual
     112.38  117.89   -5.51 1.22e+00 6.72e-01 2.04e+01
  angle pdb=" C   ILE A 235 "
        pdb=" N   ARG A 236 "
        pdb=" CA  ARG A 236 "
      ideal   model   delta    sigma   weight residual
     121.70  129.52   -7.82 1.80e+00 3.09e-01 1.89e+01
  angle pdb=" N   THR A 135 "
        pdb=" CA  THR A 135 "
        pdb=" C   THR A 135 "
      ideal   model   delta    sigma   weight residual
     114.75  109.56    5.19 1.26e+00 6.30e-01 1.70e+01
  ... (remaining 14734 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 5658
       17.59 -    35.18: 597
       35.18 -    52.77: 120
       52.77 -    70.36: 21
       70.36 -    87.95: 11
  Dihedral angle restraints: 6407
    sinusoidal: 2568
      harmonic: 3839
  Sorted by residual:
  dihedral pdb=" CA  ILE A 485 "
           pdb=" C   ILE A 485 "
           pdb=" N   TYR A 486 "
           pdb=" CA  TYR A 486 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.47  -49.53     0      5.00e+00 4.00e-02 9.81e+01
  dihedral pdb=" CA  THR A 535 "
           pdb=" C   THR A 535 "
           pdb=" N   SER A 536 "
           pdb=" CA  SER A 536 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -134.93  -45.07     0      5.00e+00 4.00e-02 8.12e+01
  dihedral pdb=" CA  GLY A 336 "
           pdb=" C   GLY A 336 "
           pdb=" N   ALA A 337 "
           pdb=" CA  ALA A 337 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.63  -32.37     0      5.00e+00 4.00e-02 4.19e+01
  ... (remaining 6404 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1259
       0.071 -    0.142: 379
       0.142 -    0.213: 38
       0.213 -    0.284: 5
       0.284 -    0.355: 3
  Chirality restraints: 1684
  Sorted by residual:
  chirality pdb=" C1  NAG C 404 "
            pdb=" ND2 ASN C 294 "
            pdb=" C2  NAG C 404 "
            pdb=" O5  NAG C 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.16e+00
  chirality pdb=" CB  ILE A 485 "
            pdb=" CA  ILE A 485 "
            pdb=" CG1 ILE A 485 "
            pdb=" CG2 ILE A 485 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CG  LEU A 529 "
            pdb=" CB  LEU A 529 "
            pdb=" CD1 LEU A 529 "
            pdb=" CD2 LEU A 529 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.10e+00
  ... (remaining 1681 not shown)

  Planarity restraints: 1844
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 405 "   -0.262 2.00e-02 2.50e+03   2.20e-01 6.06e+02
        pdb=" C7  NAG C 405 "    0.068 2.00e-02 2.50e+03
        pdb=" C8  NAG C 405 "   -0.175 2.00e-02 2.50e+03
        pdb=" N2  NAG C 405 "    0.372 2.00e-02 2.50e+03
        pdb=" O7  NAG C 405 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "    0.132 2.00e-02 2.50e+03   1.14e-01 1.64e+02
        pdb=" C7  NAG B   1 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "   -0.021 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "   -0.189 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "    0.106 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   2 "    0.067 2.00e-02 2.50e+03   5.53e-02 3.82e+01
        pdb=" C7  NAG B   2 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8  NAG B   2 "    0.051 2.00e-02 2.50e+03
        pdb=" N2  NAG B   2 "   -0.088 2.00e-02 2.50e+03
        pdb=" O7  NAG B   2 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1841 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 70
        2.56 -     3.15: 7857
        3.15 -     3.73: 16812
        3.73 -     4.32: 24631
        4.32 -     4.90: 40210
  Nonbonded interactions: 89580
  Sorted by model distance:
  nonbonded pdb=" F3  BEF A1801 "
            pdb="MG    MG A1802 "
     model   vdw
     1.976 2.120
  nonbonded pdb=" OD1 ASP A 786 "
            pdb="MG    MG A1802 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" OD2 ASP A 409 "
            pdb="MG    MG A1802 "
     model   vdw
     2.096 2.170
  nonbonded pdb=" O   THR A 411 "
            pdb="MG    MG A1802 "
     model   vdw
     2.132 2.170
  nonbonded pdb=" OD2 ASP A 409 "
            pdb=" F3  BEF A1801 "
     model   vdw
     2.187 2.990
  ... (remaining 89575 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.290
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
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      :  0.015   0.900  10870  Z= 1.004
  Angle     :  1.167  16.286  14760  Z= 0.616
  Chirality :  0.065   0.355   1684
  Planarity :  0.011   0.220   1841
  Dihedral  : 15.287  87.949   3922
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.46 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  7.21 %
    Favored  : 92.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.27 (0.19), residues: 1301
  helix: -2.16 (0.16), residues: 612
  sheet: -0.76 (0.39), residues: 181
  loop : -2.54 (0.23), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C  37 
 TYR   0.030   0.004   TYR C 297 
 PHE   0.027   0.004   PHE C 179 
 TRP   0.034   0.004   TRP A 607 
 HIS   0.012   0.002   HIS A 147 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01209 /  0.51 (10861)
  covalent geometry    : angle       1.15075 /  0.61 (14739)
  SS BOND              : bond        0.00831 /  0.41 (    3)
  SS BOND              : angle       3.73710 /  1.83 (    6)
  hydrogen bonds       : bond        0.11942 /  7.45 (  497)
  hydrogen bonds       : angle       6.63560 /  4.40 ( 1437)
  Misc. bond           : bond        0.90047 / 47.39 (    1)
  link_ALPHA1-4        : bond        0.01855 /  0.98 (    1)
  link_ALPHA1-4        : angle       6.06332 /  3.20 (    3)
  link_BETA1-4         : bond        0.00123 /  0.06 (    1)
  link_BETA1-4         : angle       1.71954 /  0.98 (    3)
  link_NAG-ASN         : bond        0.01499 /  0.73 (    3)
  link_NAG-ASN         : angle       6.60432 /  3.09 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 133
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6186 (tt0)
REVERT: A  184 GLU cc_start: 0.8204 (tp30) cc_final: 0.7898 (tp30)
REVERT: A  187 ASN cc_start: 0.8318 (t0) cc_final: 0.8070 (t0)
REVERT: A  191 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7154 (mm-30)
REVERT: A  253 ARG cc_start: 0.7054 (ttt-90) cc_final: 0.6776 (ttt-90)
REVERT: A  256 GLN cc_start: 0.7425 (tt0) cc_final: 0.7217 (tt0)
REVERT: A  390 MET cc_start: 0.7829 (ttt) cc_final: 0.7298 (tpp)
REVERT: A  469 MET cc_start: 0.6715 (mtp) cc_final: 0.6320 (mtp)
REVERT: A  560 ASP cc_start: 0.7189 (p0) cc_final: 0.6709 (t70)
REVERT: A  582 GLU cc_start: 0.5960 (pp20) cc_final: 0.5725 (mt-10)
REVERT: A 1041 LEU cc_start: 0.8504 (tp) cc_final: 0.8245 (tt)
REVERT: A 1059 ARG cc_start: 0.6662 (mtp85) cc_final: 0.6430 (tpt170)
REVERT: C   59 LEU cc_start: 0.8534 (mt) cc_final: 0.8218 (mp)
REVERT: C  112 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7434 (mtmt)
REVERT: C  136 LYS cc_start: 0.8655 (ptmt) cc_final: 0.8072 (pttp)
REVERT: C  242 MET cc_start: 0.8171 (mmm) cc_final: 0.7842 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 135
  average time/residue: 0.6273
  time to fit residues: 90.8799
Evaluate side-chains
  101 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:   10.0000
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 147 HIS
A 187 ASN
A 249 GLN
A 323 HIS
A 352 ASN
A 765 GLN
** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1127 ASN
C  36 GLN
C 176 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.191025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.154596 restraints weight = 10057.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.28
r_work: 0.3114 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10870  Z= 0.130
  Angle     :  0.667  11.938  14760  Z= 0.344
  Chirality :  0.045   0.474   1684
  Planarity :  0.006   0.079   1841
  Dihedral  :  6.616  56.623   1434
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.38 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.69 %
    Favored  : 87.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.73 (0.22), residues: 1301
  helix: -0.54 (0.20), residues: 612
  sheet: -0.40 (0.39), residues: 185
  loop : -2.12 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 898 
 TYR   0.013   0.001   TYR A 611 
 PHE   0.020   0.002   PHE A 968 
 TRP   0.017   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 147 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 (10861)
  covalent geometry    : angle       0.65413 /  0.34 (14739)
  SS BOND              : bond        0.01081 /  0.52 (    3)
  SS BOND              : angle       1.80761 /  0.92 (    6)
  hydrogen bonds       : bond        0.05027 /  3.20 (  497)
  hydrogen bonds       : angle       5.38484 /  3.54 ( 1437)
  Misc. bond           : bond        0.00063 /  0.03 (    1)
  link_ALPHA1-4        : bond        0.01302 /  0.69 (    1)
  link_ALPHA1-4        : angle       2.76632 /  1.45 (    3)
  link_BETA1-4         : bond        0.00092 /  0.05 (    1)
  link_BETA1-4         : angle       1.18079 /  0.65 (    3)
  link_NAG-ASN         : bond        0.01026 /  0.51 (    3)
  link_NAG-ASN         : angle       4.81537 /  2.29 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7053 (tt0)
REVERT: A  180 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5135 (mpm)
REVERT: A  187 ASN cc_start: 0.8673 (t0) cc_final: 0.8300 (t0)
REVERT: A  191 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7788 (mm-30)
REVERT: A  390 MET cc_start: 0.9098 (ttt) cc_final: 0.8743 (tpp)
REVERT: A  469 MET cc_start: 0.6609 (mtp) cc_final: 0.6226 (mtp)
REVERT: A  560 ASP cc_start: 0.7376 (p0) cc_final: 0.6760 (t70)
REVERT: A  582 GLU cc_start: 0.6145 (pp20) cc_final: 0.5760 (mt-10)
REVERT: A  772 MET cc_start: 0.8904 (tmm) cc_final: 0.8699 (ttp)
REVERT: A  776 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6867 (mt0)
REVERT: C  136 LYS cc_start: 0.9119 (ptmt) cc_final: 0.8842 (ptmm)
REVERT: C  155 LYS cc_start: 0.8762 (pttp) cc_final: 0.8403 (mtmt)
REVERT: C  242 MET cc_start: 0.8900 (mmm) cc_final: 0.8546 (mmm)
  outliers start: 19
  outliers final: 5
  residues processed: 129
  average time/residue: 0.5493
  time to fit residues: 76.8986
Evaluate side-chains
  116 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  776 GLN
Chi-restraints excluded: chain A residue  875 ARG
Chi-restraints excluded: chain C residue  215 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 126 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 107 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 134 GLN
A 433 GLN
A 679 ASN
A 776 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.190313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.153877 restraints weight = 10084.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 1.29
r_work: 0.3238 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10870  Z= 0.143
  Angle     :  0.643  12.347  14760  Z= 0.329
  Chirality :  0.045   0.448   1684
  Planarity :  0.005   0.076   1841
  Dihedral  :  6.124  51.626   1434
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.92 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.86 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.03 (0.23), residues: 1301
  helix:  0.21 (0.21), residues: 607
  sheet: -0.18 (0.40), residues: 184
  loop : -1.94 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1059 
 TYR   0.015   0.001   TYR C 297 
 PHE   0.020   0.002   PHE A 968 
 TRP   0.016   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 (10861)
  covalent geometry    : angle       0.62890 /  0.33 (14739)
  SS BOND              : bond        0.00342 /  0.17 (    3)
  SS BOND              : angle       1.74586 /  0.88 (    6)
  hydrogen bonds       : bond        0.04936 /  3.16 (  497)
  hydrogen bonds       : angle       5.10079 /  3.35 ( 1437)
  Misc. bond           : bond        0.00096 /  0.05 (    1)
  link_ALPHA1-4        : bond        0.01287 /  0.68 (    1)
  link_ALPHA1-4        : angle       2.90349 /  1.52 (    3)
  link_BETA1-4         : bond        0.00194 /  0.10 (    1)
  link_BETA1-4         : angle       1.00959 /  0.56 (    3)
  link_NAG-ASN         : bond        0.01025 /  0.51 (    3)
  link_NAG-ASN         : angle       4.91302 /  2.32 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6973 (tt0)
REVERT: A  180 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.5729 (mpm)
REVERT: A  187 ASN cc_start: 0.8830 (t0) cc_final: 0.8490 (t0)
REVERT: A  322 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7469 (ttp80)
REVERT: A  390 MET cc_start: 0.8993 (ttt) cc_final: 0.8737 (tpp)
REVERT: C  136 LYS cc_start: 0.9059 (ptmt) cc_final: 0.8840 (ptmm)
REVERT: C  242 MET cc_start: 0.8938 (mmm) cc_final: 0.8680 (mmt)
  outliers start: 20
  outliers final: 8
  residues processed: 133
  average time/residue: 0.5474
  time to fit residues: 78.8718
Evaluate side-chains
  115 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  875 ARG
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  215 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 49 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 456 HIS
A 776 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.188682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.145482 restraints weight = 10238.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.38
r_work: 0.3037 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8942
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10870  Z= 0.151
  Angle     :  0.637  12.290  14760  Z= 0.327
  Chirality :  0.045   0.453   1684
  Planarity :  0.005   0.074   1841
  Dihedral  :  5.912  46.406   1434
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.61 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.94 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.76 (0.23), residues: 1301
  helix:  0.51 (0.21), residues: 607
  sheet: -0.13 (0.40), residues: 184
  loop : -1.88 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1059 
 TYR   0.014   0.001   TYR C 122 
 PHE   0.020   0.002   PHE A 968 
 TRP   0.016   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 (10861)
  covalent geometry    : angle       0.62282 /  0.32 (14739)
  SS BOND              : bond        0.00376 /  0.19 (    3)
  SS BOND              : angle       1.94021 /  0.99 (    6)
  hydrogen bonds       : bond        0.04867 /  3.11 (  497)
  hydrogen bonds       : angle       5.03710 /  3.31 ( 1437)
  Misc. bond           : bond        0.00105 /  0.06 (    1)
  link_ALPHA1-4        : bond        0.01072 /  0.56 (    1)
  link_ALPHA1-4        : angle       2.79571 /  1.46 (    3)
  link_BETA1-4         : bond        0.00219 /  0.12 (    1)
  link_BETA1-4         : angle       1.04141 /  0.58 (    3)
  link_NAG-ASN         : bond        0.01016 /  0.51 (    3)
  link_NAG-ASN         : angle       4.87218 /  2.30 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7008 (tt0)
REVERT: A  180 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5293 (mpm)
REVERT: A  187 ASN cc_start: 0.8732 (t0) cc_final: 0.8365 (t0)
REVERT: A  322 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7452 (ttp80)
REVERT: A  390 MET cc_start: 0.9111 (ttt) cc_final: 0.8754 (tpp)
REVERT: C  136 LYS cc_start: 0.9154 (ptmt) cc_final: 0.8860 (ptmm)
  outliers start: 25
  outliers final: 9
  residues processed: 130
  average time/residue: 0.5396
  time to fit residues: 75.7738
Evaluate side-chains
  121 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  215 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 125 optimal weight:    2.9990
   chunk 44 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0170
   chunk 57 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 105 optimal weight:    0.0770
   chunk 110 optimal weight:    5.9990
   overall best weight:    2.6182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 776 GLN
A 851 ASN
A1118 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.188774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.146436 restraints weight = 10011.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.23
r_work: 0.3037 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8978
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  10870  Z= 0.238
  Angle     :  0.700  13.110  14760  Z= 0.359
  Chirality :  0.049   0.455   1684
  Planarity :  0.005   0.074   1841
  Dihedral  :  6.103  44.040   1434
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.69 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.86 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.84 (0.23), residues: 1301
  helix:  0.39 (0.21), residues: 611
  sheet: -0.07 (0.40), residues: 184
  loop : -1.91 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1059 
 TYR   0.020   0.002   TYR C 297 
 PHE   0.023   0.002   PHE A 968 
 TRP   0.018   0.002   TRP C 260 
 HIS   0.007   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00578 /  0.24 (10861)
  covalent geometry    : angle       0.68513 /  0.35 (14739)
  SS BOND              : bond        0.00436 /  0.22 (    3)
  SS BOND              : angle       2.37555 /  1.20 (    6)
  hydrogen bonds       : bond        0.05681 /  3.65 (  497)
  hydrogen bonds       : angle       5.15419 /  3.39 ( 1437)
  Misc. bond           : bond        0.00177 /  0.09 (    1)
  link_ALPHA1-4        : bond        0.01191 /  0.63 (    1)
  link_ALPHA1-4        : angle       3.53453 /  1.86 (    3)
  link_BETA1-4         : bond        0.00289 /  0.15 (    1)
  link_BETA1-4         : angle       1.20225 /  0.69 (    3)
  link_NAG-ASN         : bond        0.01076 /  0.54 (    3)
  link_NAG-ASN         : angle       5.23976 /  2.48 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7131 (tt0)
REVERT: A  180 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5373 (mpm)
REVERT: A  187 ASN cc_start: 0.8781 (t0) cc_final: 0.8416 (t0)
REVERT: A  322 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7716 (ttp80)
REVERT: A  390 MET cc_start: 0.9101 (ttt) cc_final: 0.8751 (tpp)
REVERT: A  638 LEU cc_start: 0.5164 (OUTLIER) cc_final: 0.4891 (mm)
REVERT: A  691 MET cc_start: 0.5719 (OUTLIER) cc_final: 0.4382 (mtm)
REVERT: A  734 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7184 (tm)
REVERT: C  242 MET cc_start: 0.8873 (mmm) cc_final: 0.8574 (mmt)
  outliers start: 34
  outliers final: 10
  residues processed: 137
  average time/residue: 0.5482
  time to fit residues: 81.4097
Evaluate side-chains
  118 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  683 SER
Chi-restraints excluded: chain A residue  691 MET
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  814 SER
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  215 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 130 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 1 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 77 optimal weight:    0.6980
   chunk 109 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 104 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.190022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.150977 restraints weight = 10162.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.34
r_work: 0.3120 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10870  Z= 0.124
  Angle     :  0.617  12.026  14760  Z= 0.318
  Chirality :  0.044   0.455   1684
  Planarity :  0.005   0.073   1841
  Dihedral  :  5.707  40.904   1434
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.94 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.59 (0.24), residues: 1301
  helix:  0.67 (0.21), residues: 610
  sheet: -0.00 (0.40), residues: 187
  loop : -1.87 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1059 
 TYR   0.012   0.001   TYR C 297 
 PHE   0.019   0.001   PHE A 968 
 TRP   0.017   0.001   TRP A 927 
 HIS   0.005   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 (10861)
  covalent geometry    : angle       0.60412 /  0.31 (14739)
  SS BOND              : bond        0.00312 /  0.16 (    3)
  SS BOND              : angle       1.52369 /  0.76 (    6)
  hydrogen bonds       : bond        0.04624 /  2.94 (  497)
  hydrogen bonds       : angle       4.96205 /  3.26 ( 1437)
  Misc. bond           : bond        0.00066 /  0.03 (    1)
  link_ALPHA1-4        : bond        0.01123 /  0.59 (    1)
  link_ALPHA1-4        : angle       2.57000 /  1.34 (    3)
  link_BETA1-4         : bond        0.00373 /  0.20 (    1)
  link_BETA1-4         : angle       0.96413 /  0.53 (    3)
  link_NAG-ASN         : bond        0.01003 /  0.50 (    3)
  link_NAG-ASN         : angle       4.76572 /  2.25 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7026 (tt0)
REVERT: A  180 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5278 (mpm)
REVERT: A  187 ASN cc_start: 0.8755 (t0) cc_final: 0.8402 (t0)
REVERT: A  390 MET cc_start: 0.9131 (ttt) cc_final: 0.8762 (tpp)
REVERT: A  452 LEU cc_start: 0.5607 (OUTLIER) cc_final: 0.5377 (pp)
REVERT: A  638 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.4712 (mm)
REVERT: A  691 MET cc_start: 0.5376 (OUTLIER) cc_final: 0.4092 (mtm)
REVERT: A  734 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7255 (tm)
REVERT: C  158 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7741 (mp0)
REVERT: C  242 MET cc_start: 0.8866 (mmm) cc_final: 0.8588 (mmm)
  outliers start: 23
  outliers final: 7
  residues processed: 127
  average time/residue: 0.5477
  time to fit residues: 75.7222
Evaluate side-chains
  119 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  691 MET
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  215 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0970
   chunk 26 optimal weight:    0.7980
   chunk 14 optimal weight:    7.9990
   chunk 17 optimal weight:   30.0000
   chunk 40 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    2.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.189376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.147342 restraints weight = 10039.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.36
r_work: 0.2996 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8971
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10870  Z= 0.204
  Angle     :  0.673  12.822  14760  Z= 0.344
  Chirality :  0.047   0.455   1684
  Planarity :  0.005   0.073   1841
  Dihedral  :  5.821  40.141   1434
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.46 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.60 (0.23), residues: 1301
  helix:  0.58 (0.21), residues: 612
  sheet:  0.06 (0.40), residues: 184
  loop : -1.77 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1059 
 TYR   0.019   0.002   TYR C 297 
 PHE   0.021   0.002   PHE A 968 
 TRP   0.016   0.002   TRP C 260 
 HIS   0.005   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00490 /  0.20 (10861)
  covalent geometry    : angle       0.65853 /  0.34 (14739)
  SS BOND              : bond        0.00405 /  0.20 (    3)
  SS BOND              : angle       2.00729 /  1.00 (    6)
  hydrogen bonds       : bond        0.05329 /  3.42 (  497)
  hydrogen bonds       : angle       5.03111 /  3.31 ( 1437)
  Misc. bond           : bond        0.00149 /  0.08 (    1)
  link_ALPHA1-4        : bond        0.01226 /  0.65 (    1)
  link_ALPHA1-4        : angle       3.26357 /  1.71 (    3)
  link_BETA1-4         : bond        0.00038 /  0.02 (    1)
  link_BETA1-4         : angle       1.17808 /  0.68 (    3)
  link_NAG-ASN         : bond        0.01052 /  0.52 (    3)
  link_NAG-ASN         : angle       5.11003 /  2.42 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7085 (tt0)
REVERT: A  180 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5322 (mpm)
REVERT: A  187 ASN cc_start: 0.8775 (t0) cc_final: 0.8416 (t0)
REVERT: A  390 MET cc_start: 0.9132 (ttt) cc_final: 0.8770 (tpp)
REVERT: A  452 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5431 (pp)
REVERT: A  638 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4746 (mm)
REVERT: A  734 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7214 (tm)
REVERT: A  772 MET cc_start: 0.8779 (ttp) cc_final: 0.8424 (ttm)
REVERT: C  242 MET cc_start: 0.8860 (mmm) cc_final: 0.8564 (mmm)
  outliers start: 23
  outliers final: 9
  residues processed: 123
  average time/residue: 0.5286
  time to fit residues: 70.7208
Evaluate side-chains
  118 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  334 TYR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  215 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 122 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 74 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 36 optimal weight:    9.9990
   chunk 84 optimal weight:    0.7980
   chunk 77 optimal weight:    0.4980
   chunk 105 optimal weight:    0.0060
   chunk 124 optimal weight:    2.9990
   chunk 117 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   overall best weight:    0.4996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 776 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.193562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.156780 restraints weight = 10002.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 1.29
r_work: 0.3278 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10870  Z= 0.112
  Angle     :  0.592  11.615  14760  Z= 0.305
  Chirality :  0.044   0.451   1684
  Planarity :  0.004   0.071   1841
  Dihedral  :  5.325  39.281   1434
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.16 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.34 (0.24), residues: 1301
  helix:  0.88 (0.22), residues: 614
  sheet:  0.12 (0.40), residues: 187
  loop : -1.77 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1059 
 TYR   0.011   0.001   TYR C 122 
 PHE   0.017   0.001   PHE A 968 
 TRP   0.017   0.001   TRP A 927 
 HIS   0.005   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 (10861)
  covalent geometry    : angle       0.58041 /  0.30 (14739)
  SS BOND              : bond        0.00234 /  0.12 (    3)
  SS BOND              : angle       1.25950 /  0.63 (    6)
  hydrogen bonds       : bond        0.04169 /  2.65 (  497)
  hydrogen bonds       : angle       4.80362 /  3.16 ( 1437)
  Misc. bond           : bond        0.00048 /  0.03 (    1)
  link_ALPHA1-4        : bond        0.00835 /  0.44 (    1)
  link_ALPHA1-4        : angle       2.24759 /  1.17 (    3)
  link_BETA1-4         : bond        0.00176 /  0.09 (    1)
  link_BETA1-4         : angle       0.86830 /  0.46 (    3)
  link_NAG-ASN         : bond        0.01000 /  0.50 (    3)
  link_NAG-ASN         : angle       4.57792 /  2.16 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.5747 (mpm)
REVERT: A  187 ASN cc_start: 0.8827 (t0) cc_final: 0.8550 (t0)
REVERT: A  390 MET cc_start: 0.8952 (ttt) cc_final: 0.8709 (tpp)
REVERT: A  452 LEU cc_start: 0.5556 (OUTLIER) cc_final: 0.5268 (pp)
REVERT: A  638 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5592 (mm)
REVERT: C  215 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7919 (mmp-170)
  outliers start: 22
  outliers final: 10
  residues processed: 134
  average time/residue: 0.5696
  time to fit residues: 82.8066
Evaluate side-chains
  125 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  334 TYR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  776 GLN
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  215 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 114 optimal weight:    1.9990
   chunk 102 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 776 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.188591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.151372 restraints weight = 10064.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.27
r_work: 0.3068 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10870  Z= 0.202
  Angle     :  0.669  12.762  14760  Z= 0.342
  Chirality :  0.047   0.457   1684
  Planarity :  0.005   0.071   1841
  Dihedral  :  5.600  38.834   1434
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.20 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.42 (0.24), residues: 1301
  helix:  0.72 (0.21), residues: 614
  sheet:  0.16 (0.40), residues: 184
  loop : -1.70 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1059 
 TYR   0.019   0.002   TYR C 297 
 PHE   0.020   0.002   PHE A 968 
 TRP   0.015   0.002   TRP C 260 
 HIS   0.005   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00485 /  0.20 (10861)
  covalent geometry    : angle       0.65440 /  0.34 (14739)
  SS BOND              : bond        0.00404 /  0.20 (    3)
  SS BOND              : angle       2.01762 /  1.00 (    6)
  hydrogen bonds       : bond        0.05230 /  3.36 (  497)
  hydrogen bonds       : angle       4.95635 /  3.26 ( 1437)
  Misc. bond           : bond        0.00142 /  0.07 (    1)
  link_ALPHA1-4        : bond        0.01227 /  0.65 (    1)
  link_ALPHA1-4        : angle       3.21495 /  1.68 (    3)
  link_BETA1-4         : bond        0.00014 /  0.01 (    1)
  link_BETA1-4         : angle       1.19553 /  0.68 (    3)
  link_NAG-ASN         : bond        0.01073 /  0.53 (    3)
  link_NAG-ASN         : angle       5.07519 /  2.40 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5313 (mpm)
REVERT: A  187 ASN cc_start: 0.8812 (t0) cc_final: 0.8444 (t0)
REVERT: A  390 MET cc_start: 0.9123 (ttt) cc_final: 0.8767 (tpp)
REVERT: A  452 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5321 (pp)
REVERT: A  638 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.4691 (mm)
  outliers start: 17
  outliers final: 9
  residues processed: 123
  average time/residue: 0.5348
  time to fit residues: 71.7211
Evaluate side-chains
  116 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  334 TYR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  215 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 101 optimal weight:    0.4980
   chunk 120 optimal weight:    1.9990
   chunk 121 optimal weight:    0.6980
   chunk 95 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 13 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.190288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.152122 restraints weight = 10061.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 1.29
r_work: 0.3105 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10870  Z= 0.122
  Angle     :  0.608  11.813  14760  Z= 0.311
  Chirality :  0.044   0.454   1684
  Planarity :  0.005   0.071   1841
  Dihedral  :  5.337  38.433   1434
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 19.72 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.28 (0.24), residues: 1301
  helix:  0.90 (0.21), residues: 613
  sheet:  0.17 (0.40), residues: 187
  loop : -1.71 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A1059 
 TYR   0.013   0.001   TYR C 122 
 PHE   0.017   0.001   PHE A 968 
 TRP   0.017   0.001   TRP A 927 
 HIS   0.005   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 (10861)
  covalent geometry    : angle       0.59524 /  0.31 (14739)
  SS BOND              : bond        0.00274 /  0.14 (    3)
  SS BOND              : angle       1.44701 /  0.72 (    6)
  hydrogen bonds       : bond        0.04388 /  2.80 (  497)
  hydrogen bonds       : angle       4.82846 /  3.17 ( 1437)
  Misc. bond           : bond        0.00073 /  0.04 (    1)
  link_ALPHA1-4        : bond        0.01007 /  0.53 (    1)
  link_ALPHA1-4        : angle       2.47191 /  1.29 (    3)
  link_BETA1-4         : bond        0.00225 /  0.12 (    1)
  link_BETA1-4         : angle       0.89917 /  0.50 (    3)
  link_NAG-ASN         : bond        0.00998 /  0.50 (    3)
  link_NAG-ASN         : angle       4.66037 /  2.20 (    9)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.5363 (mpm)
REVERT: A  187 ASN cc_start: 0.8736 (t0) cc_final: 0.8376 (t0)
REVERT: A  390 MET cc_start: 0.9106 (ttt) cc_final: 0.8750 (tpp)
REVERT: A  416 CYS cc_start: 0.6731 (m) cc_final: 0.6526 (m)
REVERT: A  452 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5329 (pp)
REVERT: A  638 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4760 (mm)
REVERT: A 1059 ARG cc_start: 0.7545 (ttm110) cc_final: 0.6779 (ttm170)
REVERT: C  215 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7776 (mmp-170)
  outliers start: 13
  outliers final: 8
  residues processed: 123
  average time/residue: 0.5695
  time to fit residues: 76.0735
Evaluate side-chains
  118 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  334 TYR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  215 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 118 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 123 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 124 HIS
** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.192090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.155294 restraints weight = 10079.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.29
r_work: 0.3107 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8925
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10870  Z= 0.133
  Angle     :  0.610  11.994  14760  Z= 0.313
  Chirality :  0.045   0.455   1684
  Planarity :  0.004   0.071   1841
  Dihedral  :  5.297  38.208   1434
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 19.46 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.20 (0.24), residues: 1301
  helix:  0.94 (0.22), residues: 614
  sheet:  0.25 (0.40), residues: 184
  loop : -1.64 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1059 
 TYR   0.014   0.001   TYR C 297 
 PHE   0.018   0.001   PHE A 968 
 TRP   0.016   0.001   TRP A 927 
 HIS   0.005   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 (10861)
  covalent geometry    : angle       0.59755 /  0.31 (14739)
  SS BOND              : bond        0.00305 /  0.15 (    3)
  SS BOND              : angle       1.52407 /  0.76 (    6)
  hydrogen bonds       : bond        0.04482 /  2.87 (  497)
  hydrogen bonds       : angle       4.80624 /  3.16 ( 1437)
  Misc. bond           : bond        0.00082 /  0.04 (    1)
  link_ALPHA1-4        : bond        0.00980 /  0.52 (    1)
  link_ALPHA1-4        : angle       2.57930 /  1.35 (    3)
  link_BETA1-4         : bond        0.00187 /  0.10 (    1)
  link_BETA1-4         : angle       0.92295 /  0.51 (    3)
  link_NAG-ASN         : bond        0.01017 /  0.51 (    3)
  link_NAG-ASN         : angle       4.73670 /  2.24 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3799.35 seconds
wall clock time: 65 minutes 39.01 seconds (3939.01 seconds total)