Starting phenix.real_space_refine
on Wed Mar  4 01:06:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bsv_30168/03_2026/7bsv_30168_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bsv_30168/03_2026/7bsv_30168.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bsv_30168/03_2026/7bsv_30168_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bsv_30168/03_2026/7bsv_30168_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bsv_30168/03_2026/7bsv_30168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bsv_30168/03_2026/7bsv_30168.map"
  }
  resolution = 3.0
  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=   0.004
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: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       1      5.49       5
     Mg      1      5.21       5
     S      45      5.16       5
     C    6081      2.51       5
     N    1504      2.21       5
     O    1702      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9339
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 815, 6596
          Classifications: {'peptide': 815}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 792}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 2613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2613
          Classifications: {'peptide': 324}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'MAN': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Unusual residues: {' MG': 1, 'ALF': 1}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 41
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.14, per 1000 atoms: 0.23
  Number of scatterers: 9339
  At special positions: 0
  Unit cell: (101.26, 93.79, 135.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      45     16.00
     P       1     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1702      8.00
     N    1504      7.00
     C    6081      6.00
    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=2.03
    Simple disulfide: pdb=" SG  CYS C 157 " - pdb=" SG  CYS C 171 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Links applied
    ALPHA1-4
      " NAG B   1 " - " MAN B   2 "
    NAG-ASN
      " NAG C 401 " - " ASN C 180 "
      " NAG C 402 " - " ASN C 294 "
      " NAG C 403 " - " ASN C 107 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 403.2 milliseconds
  

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 10 sheets defined
      46.3% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 64
      removed outlier: 3.515A  pdb=" N   LYS A  58 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   PHE A  61 " --> pdb=" O   PRO A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 82
      removed outlier: 3.574A  pdb=" N   LEU A  73 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 121
      Proline residue:  A  94  - end of helix
      removed outlier: 3.596A  pdb=" N   THR A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   ARG A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLU A 119 " --> pdb=" O   ARG A 115 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 120 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 141
      No H-bonds generated for 'chain 'A' and resid 139 through 141'
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'A' and resid 268 through 273
      removed outlier: 3.681A  pdb=" N   ASN A 273 " --> pdb=" O   LYS A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 314
      removed outlier: 3.503A  pdb=" N   ASN A 289 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE A 297 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 320
      removed outlier: 3.532A  pdb=" N   ASP A 320 " --> pdb=" O   PRO A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 334
    Processing helix  chain 'A' and resid 335 through 352
      removed outlier: 3.550A  pdb=" N   MET A 340 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 341 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 355
      No H-bonds generated for 'chain 'A' and resid 353 through 355'
    Processing helix  chain 'A' and resid 356 through 371
      removed outlier: 4.217A  pdb=" N   TYR A 360 " --> pdb=" O   PRO A 356 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   MET A 365 " --> pdb=" O   VAL A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 377
      removed outlier: 3.925A  pdb=" N   SER A 375 " --> pdb=" O   SER A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 400
      removed outlier: 4.060A  pdb=" N   LEU A 396 " --> pdb=" O   THR A 393 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ASN A 397 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   GLU A 398 " --> pdb=" O   ASP A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 666
      removed outlier: 3.600A  pdb=" N   ILE A 660 " --> pdb=" O   ALA A 656 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 666 " --> pdb=" O   ALA A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 686
      removed outlier: 3.785A  pdb=" N   SER A 683 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR A 684 " --> pdb=" O   THR A 680 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   CYS A 685 " --> pdb=" O   ALA A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 720
      removed outlier: 3.641A  pdb=" N   ASP A 713 " --> pdb=" O   GLU A 709 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   HIS A 716 " --> pdb=" O   GLU A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 762
      removed outlier: 3.910A  pdb=" N   LEU A 758 " --> pdb=" O   SER A 754 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 781
      removed outlier: 3.715A  pdb=" N   ILE A 778 " --> pdb=" O   ILE A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 803
      removed outlier: 3.519A  pdb=" N   ARG A 800 " --> pdb=" O   ALA A 796 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS A 803 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 825
    Processing helix  chain 'A' and resid 853 through 860
      removed outlier: 4.380A  pdb=" N   LYS A 857 " --> pdb=" O   LYS A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 891
      removed outlier: 3.621A  pdb=" N   ASN A 881 " --> pdb=" O   PHE A 877 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   PHE A 884 " --> pdb=" O   LYS A 880 " (cutoff:3.500A)
      Proline residue:  A 887  - end of helix
    Processing helix  chain 'A' and resid 892 through 894
      No H-bonds generated for 'chain 'A' and resid 892 through 894'
    Processing helix  chain 'A' and resid 904 through 911
    Processing helix  chain 'A' and resid 918 through 924
    Processing helix  chain 'A' and resid 931 through 936
    Processing helix  chain 'A' and resid 938 through 946
      removed outlier: 3.536A  pdb=" N   LYS A 944 " --> pdb=" O   LEU A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 951
    Processing helix  chain 'A' and resid 952 through 978
      removed outlier: 3.597A  pdb=" N   THR A 968 " --> pdb=" O   ALA A 964 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE A 971 " --> pdb=" O   GLY A 967 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 977 " --> pdb=" O   GLY A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 1015
      removed outlier: 3.530A  pdb=" N   PHE A 995 " --> pdb=" O   GLY A 991 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU A1011 " --> pdb=" O   VAL A1007 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1041
      removed outlier: 3.548A  pdb=" N   LEU A1030 " --> pdb=" O   ILE A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1055 through 1060
    Processing helix  chain 'A' and resid 1063 through 1077
      removed outlier: 3.641A  pdb=" N   PHE A1075 " --> pdb=" O   ILE A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1088
      removed outlier: 3.573A  pdb=" N   VAL A1086 " --> pdb=" O   ILE A1082 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 51
    Processing helix  chain 'C' and resid 52 through 72
      removed outlier: 3.641A  pdb=" N   GLY C  58 " --> pdb=" O   PHE C  54 " (cutoff:3.500A)
      Proline residue:  C  63  - end of helix
      removed outlier: 3.555A  pdb=" N   SER C  72 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 95
      removed outlier: 3.796A  pdb=" N   LYS C  93 " --> pdb=" O   PRO C  90 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU C  95 " --> pdb=" O   ASN C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 136
      removed outlier: 3.688A  pdb=" N   LYS C 136 " --> pdb=" O   ARG C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 152
      removed outlier: 3.783A  pdb=" N   LEU C 151 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN C 152 " --> pdb=" O   SER C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 177
    Processing helix  chain 'C' and resid 206 through 212
    Processing helix  chain 'C' and resid 254 through 262
      removed outlier: 3.738A  pdb=" N   ARG C 262 " --> pdb=" O   ILE C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 305
      removed outlier: 3.640A  pdb=" N   PHE C 304 " --> pdb=" O   VAL C 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 347
      removed outlier: 3.538A  pdb=" N   LEU C 339 " --> pdb=" O   ILE C 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
    Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137
      removed outlier: 4.175A  pdb=" N   TYR A 126 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   VAL A 146 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 160
    Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 188
      removed outlier: 3.955A  pdb=" N   TYR A 172 " --> pdb=" O   LYS A 252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 225
      removed outlier: 3.530A  pdb=" N   LEU A 239 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE A 225 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 382
    Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 391
    Processing sheet with id=AA8, first strand: chain 'A' and resid 696 through 699
      removed outlier: 6.131A  pdb=" N   GLU A 696 " --> pdb=" O   GLY A 748 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   ILE A 750 " --> pdb=" O   GLU A 696 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU A 698 " --> pdb=" O   ILE A 750 " (cutoff:3.500A)
      removed outlier: 8.403A  pdb=" N   ASP A 752 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   VAL A 670 " --> pdb=" O   VAL A 785 " (cutoff:3.500A)
      removed outlier: 8.722A  pdb=" N   CYS A 787 " --> pdb=" O   VAL A 670 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   VAL A 672 " --> pdb=" O   CYS A 787 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   THR A 811 " --> pdb=" O   VAL A 829 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   ILE A 831 " --> pdb=" O   THR A 811 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   SER A 813 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 81
      removed outlier: 6.029A  pdb=" N   TYR C 122 " --> pdb=" O   LEU C 272 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   LEU C 272 " --> pdb=" O   TYR C 122 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   LEU C 124 " --> pdb=" O   ARG C 270 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   ARG C 270 " --> pdb=" O   LEU C 124 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 110
      removed outlier: 3.514A  pdb=" N   PHE C 108 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   ARG C 290 " --> pdb=" O   ILE C 188 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   THR C 182 " --> pdb=" O   THR C 296 " (cutoff:3.500A)

    362 hydrogen bonds defined for protein.
    1005 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1465
        1.30 -     1.43: 2578
        1.43 -     1.56: 5449
        1.56 -     1.68: 1
        1.68 -     1.81: 71
  Bond restraints: 9564
  Sorted by residual:
  bond pdb=" F4  ALF A1101 "
       pdb="AL   ALF A1101 "
    ideal  model  delta    sigma   weight residual
    1.686  1.800 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" F1  ALF A1101 "
       pdb="AL   ALF A1101 "
    ideal  model  delta    sigma   weight residual
    1.684  1.796 -0.112 2.00e-02 2.50e+03 3.15e+01
  bond pdb=" F3  ALF A1101 "
       pdb="AL   ALF A1101 "
    ideal  model  delta    sigma   weight residual
    1.685  1.796 -0.111 2.00e-02 2.50e+03 3.07e+01
  bond pdb=" F2  ALF A1101 "
       pdb="AL   ALF A1101 "
    ideal  model  delta    sigma   weight residual
    1.685  1.793 -0.108 2.00e-02 2.50e+03 2.93e+01
  bond pdb=" C17 P5S A1103 "
       pdb=" O19 P5S A1103 "
    ideal  model  delta    sigma   weight residual
    1.351  1.453 -0.102 2.00e-02 2.50e+03 2.60e+01
  ... (remaining 9559 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.20: 12962
       14.20 -    28.41: 4
       28.41 -    42.61: 0
       42.61 -    56.81: 0
       56.81 -    71.01: 2
  Bond angle restraints: 12968
  Sorted by residual:
  angle pdb=" F1  ALF A1101 "
        pdb="AL   ALF A1101 "
        pdb=" F2  ALF A1101 "
      ideal   model   delta    sigma   weight residual
     108.68  179.69  -71.01 3.00e+00 1.11e-01 5.60e+02
  angle pdb=" F3  ALF A1101 "
        pdb="AL   ALF A1101 "
        pdb=" F4  ALF A1101 "
      ideal   model   delta    sigma   weight residual
     109.63  179.28  -69.65 3.00e+00 1.11e-01 5.39e+02
  angle pdb=" F2  ALF A1101 "
        pdb="AL   ALF A1101 "
        pdb=" F4  ALF A1101 "
      ideal   model   delta    sigma   weight residual
     110.21   90.09   20.12 3.00e+00 1.11e-01 4.50e+01
  angle pdb=" F2  ALF A1101 "
        pdb="AL   ALF A1101 "
        pdb=" F3  ALF A1101 "
      ideal   model   delta    sigma   weight residual
     109.59   89.52   20.07 3.00e+00 1.11e-01 4.48e+01
  angle pdb=" F1  ALF A1101 "
        pdb="AL   ALF A1101 "
        pdb=" F3  ALF A1101 "
      ideal   model   delta    sigma   weight residual
     109.69   90.20   19.49 3.00e+00 1.11e-01 4.22e+01
  ... (remaining 12963 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.93: 5397
       29.93 -    59.85: 294
       59.85 -    89.78: 40
       89.78 -   119.71: 6
      119.71 -   149.64: 6
  Dihedral angle restraints: 5743
    sinusoidal: 2398
      harmonic: 3345
  Sorted by residual:
  dihedral pdb=" CA  THR C 100 "
           pdb=" C   THR C 100 "
           pdb=" N   PRO C 101 "
           pdb=" CA  PRO C 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  121.36   58.64     0      5.00e+00 4.00e-02 1.38e+02
  dihedral pdb=" CB  CYS C  91 "
           pdb=" SG  CYS C  91 "
           pdb=" SG  CYS C 104 "
           pdb=" CB  CYS C 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.74  -60.74     1      1.00e+01 1.00e-02 4.91e+01
  dihedral pdb=" CA  VAL C  99 "
           pdb=" C   VAL C  99 "
           pdb=" N   THR C 100 "
           pdb=" CA  THR C 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.71  -29.29     0      5.00e+00 4.00e-02 3.43e+01
  ... (remaining 5740 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 1462
       0.148 -    0.295: 0
       0.295 -    0.443: 0
       0.443 -    0.591: 1
       0.591 -    0.738: 2
  Chirality restraints: 1465
  Sorted by residual:
  chirality pdb=" C1  MAN B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  MAN B   2 "
            pdb=" O5  MAN B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    1.91    0.49 2.00e-02 2.50e+03 6.00e+02
  chirality pdb=" C1  NAG C 402 "
            pdb=" ND2 ASN C 294 "
            pdb=" C2  NAG C 402 "
            pdb=" O5  NAG C 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.66   -0.74 2.00e-01 2.50e+01 1.36e+01
  chirality pdb=" C1  NAG C 403 "
            pdb=" ND2 ASN C 107 "
            pdb=" C2  NAG C 403 "
            pdb=" O5  NAG C 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.71   -0.69 2.00e-01 2.50e+01 1.18e+01
  ... (remaining 1462 not shown)

  Planarity restraints: 1615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 403 "    0.342 2.00e-02 2.50e+03   2.92e-01 1.07e+03
        pdb=" C7  NAG C 403 "   -0.086 2.00e-02 2.50e+03
        pdb=" C8  NAG C 403 "    0.172 2.00e-02 2.50e+03
        pdb=" N2  NAG C 403 "   -0.515 2.00e-02 2.50e+03
        pdb=" O7  NAG C 403 "    0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 107 "    0.124 2.00e-02 2.50e+03   2.34e-01 6.83e+02
        pdb=" CG  ASN C 107 "   -0.066 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 107 "    0.094 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 107 "   -0.417 2.00e-02 2.50e+03
        pdb=" C1  NAG C 403 "    0.265 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 401 "   -0.068 2.00e-02 2.50e+03   5.76e-02 4.15e+01
        pdb=" C7  NAG C 401 "    0.015 2.00e-02 2.50e+03
        pdb=" C8  NAG C 401 "    0.019 2.00e-02 2.50e+03
        pdb=" N2  NAG C 401 "    0.091 2.00e-02 2.50e+03
        pdb=" O7  NAG C 401 "   -0.056 2.00e-02 2.50e+03
  ... (remaining 1612 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 64
        2.43 -     3.05: 6095
        3.05 -     3.66: 13205
        3.66 -     4.28: 22947
        4.28 -     4.90: 37488
  Nonbonded interactions: 79799
  Sorted by model distance:
  nonbonded pdb=" F4  ALF A1101 "
            pdb="MG    MG A1102 "
     model   vdw
     1.809 2.120
  nonbonded pdb=" OG1 THR A 175 "
            pdb=" OD2 ASP A 179 "
     model   vdw
     2.042 3.040
  nonbonded pdb=" O   GLY C  84 "
            pdb=" OG1 THR C  85 "
     model   vdw
     2.054 3.040
  nonbonded pdb=" O   TYR A 188 "
            pdb=" ND2 ASN A 243 "
     model   vdw
     2.079 3.120
  nonbonded pdb=" ND2 ASN C 216 "
            pdb=" O   GLY C 251 "
     model   vdw
     2.101 3.120
  ... (remaining 79794 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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.720
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
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      :  0.009   0.747   9572  Z= 0.803
  Angle     :  1.186  71.014  12986  Z= 0.470
  Chirality :  0.049   0.738   1465
  Planarity :  0.008   0.292   1612
  Dihedral  : 19.273 149.635   3576
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 30.62
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.62 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 22.12 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.02 (0.17), residues: 1129
  helix: -4.44 (0.12), residues: 497
  sheet: -2.74 (0.37), residues: 166
  loop : -3.76 (0.21), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 262 
 TYR   0.011   0.001   TYR A 324 
 PHE   0.014   0.001   PHE A 894 
 TRP   0.016   0.001   TRP A 323 
 HIS   0.004   0.001   HIS A 929 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 9564)
  covalent geometry    : angle       1.14888 (12968)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       0.88274 (    6)
  hydrogen bonds       : bond        0.29104 (  362)
  hydrogen bonds       : angle      12.10350 ( 1005)
  Misc. bond           : bond        0.74735 (    1)
  link_ALPHA1-4        : bond        0.01875 (    1)
  link_ALPHA1-4        : angle       7.57103 (    3)
  link_NAG-ASN         : bond        0.01419 (    3)
  link_NAG-ASN         : angle      10.44374 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 144
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ARG cc_start: 0.7850 (ptm-80) cc_final: 0.7524 (ptt180)
REVERT: A  191 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7011 (mmp-170)
REVERT: A  256 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8614 (pttp)
REVERT: A  329 GLN cc_start: 0.8014 (tp40) cc_final: 0.7624 (mm-40)
REVERT: A  676 ASP cc_start: 0.7872 (t0) cc_final: 0.7440 (t0)
REVERT: A  703 LYS cc_start: 0.7720 (mtpm) cc_final: 0.6858 (mtmm)
REVERT: A  774 ILE cc_start: 0.8693 (mt) cc_final: 0.8480 (mt)
REVERT: A  926 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8127 (pp)
REVERT: C   27 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5779 (tpp80)
REVERT: C  343 LEU cc_start: 0.8246 (pp) cc_final: 0.7948 (pt)
  outliers start: 63
  outliers final: 21
  residues processed: 195
  average time/residue: 0.5359
  time to fit residues: 112.0938
Evaluate side-chains
  142 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  695 THR
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  754 SER
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  895 CYS
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue  994 THR
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   68 ILE
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  132 ARG
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  342 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
A 106 GLN
A 121 ASN
A 226 ASN
A 386 ASN
A 392 ASN
A 397 ASN
A 764 GLN
A 777 GLN
A 819 ASN
A 862 HIS
A 872 HIS
C  36 GLN
C 129 GLN
C 142 GLN
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 ASN
C 298 ASN
C 347 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.144217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.103996 restraints weight = 10241.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 1.80
r_work: 0.2924 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9572  Z= 0.150
  Angle     :  0.902  32.497  12986  Z= 0.400
  Chirality :  0.046   0.477   1465
  Planarity :  0.005   0.062   1612
  Dihedral  : 13.428 142.101   1428
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 20.94 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.85 (0.21), residues: 1129
  helix: -2.39 (0.18), residues: 500
  sheet: -1.68 (0.39), residues: 157
  loop : -2.94 (0.24), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 689 
 TYR   0.014   0.002   TYR A 324 
 PHE   0.015   0.001   PHE A 894 
 TRP   0.017   0.001   TRP A 323 
 HIS   0.004   0.001   HIS A 864 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9564)
  covalent geometry    : angle       0.89246 (12968)
  SS BOND              : bond        0.00265 (    3)
  SS BOND              : angle       1.81745 (    6)
  hydrogen bonds       : bond        0.04793 (  362)
  hydrogen bonds       : angle       5.73630 ( 1005)
  Misc. bond           : bond        0.00333 (    1)
  link_ALPHA1-4        : bond        0.01832 (    1)
  link_ALPHA1-4        : angle       4.63326 (    3)
  link_NAG-ASN         : bond        0.01281 (    3)
  link_NAG-ASN         : angle       4.26054 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 137
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ARG cc_start: 0.7963 (ptm-80) cc_final: 0.7409 (tmt-80)
REVERT: A  224 ARG cc_start: 0.7339 (ttm170) cc_final: 0.6653 (ttt90)
REVERT: A  252 LYS cc_start: 0.8390 (mptt) cc_final: 0.8131 (mmtp)
REVERT: A  256 LYS cc_start: 0.8749 (ptmm) cc_final: 0.8475 (pttp)
REVERT: A  329 GLN cc_start: 0.8107 (tp40) cc_final: 0.7670 (mm-40)
REVERT: A  364 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8009 (mp0)
REVERT: A  385 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7783 (pt)
REVERT: A  676 ASP cc_start: 0.8273 (t0) cc_final: 0.8068 (t0)
REVERT: A  703 LYS cc_start: 0.7528 (mtpm) cc_final: 0.6614 (mtmm)
REVERT: A  717 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6521 (tm-30)
REVERT: A  895 CYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8152 (p)
REVERT: A  926 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8342 (pp)
REVERT: A  928 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.6804 (mp10)
REVERT: C  343 LEU cc_start: 0.7611 (pp) cc_final: 0.7398 (pt)
  outliers start: 61
  outliers final: 17
  residues processed: 186
  average time/residue: 0.4865
  time to fit residues: 97.6252
Evaluate side-chains
  140 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  364 GLU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  408 THR
Chi-restraints excluded: chain A residue  708 SER
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  895 CYS
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  928 GLN
Chi-restraints excluded: chain A residue  936 THR
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue 1065 SER
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  228 LYS
Chi-restraints excluded: chain C residue  234 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
A 777 GLN
A 840 GLN
C 142 GLN
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 152 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.140393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.099763 restraints weight = 10287.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.78
r_work: 0.2840 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   9572  Z= 0.255
  Angle     :  0.925  34.022  12986  Z= 0.412
  Chirality :  0.049   0.348   1465
  Planarity :  0.005   0.064   1612
  Dihedral  : 12.155 141.380   1400
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.64 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 22.32 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.22), residues: 1129
  helix: -1.40 (0.20), residues: 505
  sheet: -1.07 (0.40), residues: 157
  loop : -2.77 (0.25), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 723 
 TYR   0.015   0.002   TYR A 847 
 PHE   0.017   0.002   PHE C 108 
 TRP   0.021   0.002   TRP C 236 
 HIS   0.005   0.001   HIS A 929 

Details of bonding type rmsd
  covalent geometry    : bond        0.00618 ( 9564)
  covalent geometry    : angle       0.91871 (12968)
  SS BOND              : bond        0.00466 (    3)
  SS BOND              : angle       2.01712 (    6)
  hydrogen bonds       : bond        0.04963 (  362)
  hydrogen bonds       : angle       5.34726 ( 1005)
  Misc. bond           : bond        0.00223 (    1)
  link_ALPHA1-4        : bond        0.01474 (    1)
  link_ALPHA1-4        : angle       4.52567 (    3)
  link_NAG-ASN         : bond        0.00824 (    3)
  link_NAG-ASN         : angle       3.17298 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 120
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ARG cc_start: 0.8014 (ptm-80) cc_final: 0.7390 (tmt-80)
REVERT: A  224 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6663 (ttt90)
REVERT: A  252 LYS cc_start: 0.8388 (mptt) cc_final: 0.7974 (mmtt)
REVERT: A  256 LYS cc_start: 0.8796 (ptmm) cc_final: 0.8540 (pttp)
REVERT: A  329 GLN cc_start: 0.8191 (tp40) cc_final: 0.7749 (mm-40)
REVERT: A  703 LYS cc_start: 0.7546 (mtpm) cc_final: 0.6646 (mtmm)
REVERT: A  717 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6488 (tm-30)
REVERT: A  774 ILE cc_start: 0.8257 (mt) cc_final: 0.7966 (mp)
REVERT: A  790 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8622 (mmp)
REVERT: A  895 CYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7782 (m)
REVERT: A  926 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8477 (pp)
REVERT: A  928 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7174 (mp10)
  outliers start: 54
  outliers final: 28
  residues processed: 164
  average time/residue: 0.4909
  time to fit residues: 86.9233
Evaluate side-chains
  145 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  408 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  708 SER
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  752 ASP
Chi-restraints excluded: chain A residue  790 MET
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  895 CYS
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  928 GLN
Chi-restraints excluded: chain A residue  936 THR
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1065 SER
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   68 ILE
Chi-restraints excluded: chain C residue   92 ASN
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  228 LYS
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  286 LEU
Chi-restraints excluded: chain C residue  339 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 13 optimal weight:    7.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
A 777 GLN
C 142 GLN
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 152 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.146421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.106636 restraints weight = 10210.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.74
r_work: 0.2932 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9572  Z= 0.130
  Angle     :  0.847  30.193  12986  Z= 0.367
  Chirality :  0.044   0.258   1465
  Planarity :  0.004   0.077   1612
  Dihedral  : 10.793 127.906   1400
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 23.01 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.23), residues: 1129
  helix: -0.49 (0.22), residues: 505
  sheet: -0.57 (0.42), residues: 157
  loop : -2.53 (0.25), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 723 
 TYR   0.015   0.001   TYR A 318 
 PHE   0.015   0.001   PHE A 894 
 TRP   0.017   0.001   TRP A 323 
 HIS   0.004   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9564)
  covalent geometry    : angle       0.83990 (12968)
  SS BOND              : bond        0.00433 (    3)
  SS BOND              : angle       3.44107 (    6)
  hydrogen bonds       : bond        0.03828 (  362)
  hydrogen bonds       : angle       4.86584 ( 1005)
  Misc. bond           : bond        0.00093 (    1)
  link_ALPHA1-4        : bond        0.01529 (    1)
  link_ALPHA1-4        : angle       4.10172 (    3)
  link_NAG-ASN         : bond        0.00755 (    3)
  link_NAG-ASN         : angle       2.47416 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 129
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7345 (ttp-170)
REVERT: A   91 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8539 (p)
REVERT: A  135 ARG cc_start: 0.8031 (ptm-80) cc_final: 0.7531 (tmt-80)
REVERT: A  191 ARG cc_start: 0.7509 (mmm160) cc_final: 0.6639 (mmm160)
REVERT: A  252 LYS cc_start: 0.8347 (mptt) cc_final: 0.8128 (mmtp)
REVERT: A  256 LYS cc_start: 0.8772 (ptmm) cc_final: 0.8528 (pttp)
REVERT: A  329 GLN cc_start: 0.8065 (tp40) cc_final: 0.7612 (mm-40)
REVERT: A  385 ILE cc_start: 0.7948 (pt) cc_final: 0.7726 (pt)
REVERT: A  678 MET cc_start: 0.5337 (tmm) cc_final: 0.5129 (tpp)
REVERT: A  717 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6634 (tm-30)
REVERT: A  774 ILE cc_start: 0.8120 (mt) cc_final: 0.7854 (mp)
REVERT: A  926 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8348 (pp)
REVERT: A  928 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.6931 (mp10)
REVERT: C  155 LYS cc_start: 0.8269 (mttp) cc_final: 0.7618 (pttm)
REVERT: C  184 GLU cc_start: 0.7195 (pm20) cc_final: 0.6893 (mp0)
REVERT: C  238 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7838 (pttp)
REVERT: C  270 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8310 (mtm-85)
  outliers start: 47
  outliers final: 17
  residues processed: 167
  average time/residue: 0.5193
  time to fit residues: 93.3057
Evaluate side-chains
  137 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ARG
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  708 SER
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  928 GLN
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1065 SER
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  228 LYS
Chi-restraints excluded: chain C residue  339 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 83 optimal weight:    0.0170
   chunk 23 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0370
   chunk 27 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9698

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
C 142 GLN
C 144 ASN
C 152 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.146131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.105390 restraints weight = 10226.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.75
r_work: 0.2942 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9572  Z= 0.138
  Angle     :  0.850  31.090  12986  Z= 0.366
  Chirality :  0.044   0.228   1465
  Planarity :  0.004   0.073   1612
  Dihedral  :  9.863 118.365   1398
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 23.60 %
    Favored  : 71.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.09 %

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: -1.52 (0.24), residues: 1129
  helix: -0.08 (0.23), residues: 510
  sheet: -0.37 (0.41), residues: 163
  loop : -2.33 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 290 
 TYR   0.014   0.001   TYR A 318 
 PHE   0.016   0.001   PHE C 108 
 TRP   0.015   0.001   TRP A 323 
 HIS   0.004   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9564)
  covalent geometry    : angle       0.84378 (12968)
  SS BOND              : bond        0.00346 (    3)
  SS BOND              : angle       2.68444 (    6)
  hydrogen bonds       : bond        0.03819 (  362)
  hydrogen bonds       : angle       4.71144 ( 1005)
  Misc. bond           : bond        0.00092 (    1)
  link_ALPHA1-4        : bond        0.01877 (    1)
  link_ALPHA1-4        : angle       4.37518 (    3)
  link_NAG-ASN         : bond        0.00673 (    3)
  link_NAG-ASN         : angle       2.22594 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 120
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  124 THR cc_start: 0.8572 (m) cc_final: 0.8277 (t)
REVERT: A  135 ARG cc_start: 0.8035 (ptm-80) cc_final: 0.7591 (tmt-80)
REVERT: A  191 ARG cc_start: 0.7461 (mmm160) cc_final: 0.6563 (mmm160)
REVERT: A  252 LYS cc_start: 0.8352 (mptt) cc_final: 0.8101 (mmtp)
REVERT: A  256 LYS cc_start: 0.8779 (ptmm) cc_final: 0.8508 (pttp)
REVERT: A  329 GLN cc_start: 0.8124 (tp40) cc_final: 0.7715 (mm-40)
REVERT: A  385 ILE cc_start: 0.7979 (pt) cc_final: 0.7743 (pt)
REVERT: A  678 MET cc_start: 0.5563 (tmm) cc_final: 0.5247 (tpp)
REVERT: A  717 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6792 (tm-30)
REVERT: A  721 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5876 (mp0)
REVERT: A  774 ILE cc_start: 0.8258 (mt) cc_final: 0.7967 (mp)
REVERT: A  926 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8417 (pp)
REVERT: A  928 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.7081 (mp10)
REVERT: C  155 LYS cc_start: 0.8310 (mttp) cc_final: 0.7652 (pttm)
REVERT: C  184 GLU cc_start: 0.7258 (pm20) cc_final: 0.6950 (mp0)
REVERT: C  238 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7786 (pttp)
REVERT: C  270 ARG cc_start: 0.8788 (mtt180) cc_final: 0.8251 (mtm-85)
REVERT: C  290 ARG cc_start: 0.7835 (mtp180) cc_final: 0.7339 (mtm110)
  outliers start: 50
  outliers final: 14
  residues processed: 161
  average time/residue: 0.5073
  time to fit residues: 88.0565
Evaluate side-chains
  135 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  708 SER
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  928 GLN
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1065 SER
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  228 LYS
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  339 LEU
Chi-restraints excluded: chain C residue  343 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 93 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
A 386 ASN
C  36 GLN
C 142 GLN
C 152 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.142459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.102497 restraints weight = 10238.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 1.75
r_work: 0.2886 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9572  Z= 0.221
  Angle     :  0.891  32.817  12986  Z= 0.392
  Chirality :  0.047   0.238   1465
  Planarity :  0.004   0.067   1612
  Dihedral  :  9.896 124.964   1396
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.55 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 24.88 %
    Favored  : 70.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.09 %

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: -1.57 (0.24), residues: 1129
  helix: -0.21 (0.22), residues: 508
  sheet: -0.22 (0.42), residues: 163
  loop : -2.29 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 723 
 TYR   0.015   0.002   TYR A 311 
 PHE   0.016   0.002   PHE C 108 
 TRP   0.017   0.002   TRP C 236 
 HIS   0.005   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 9564)
  covalent geometry    : angle       0.88261 (12968)
  SS BOND              : bond        0.00510 (    3)
  SS BOND              : angle       3.48168 (    6)
  hydrogen bonds       : bond        0.04345 (  362)
  hydrogen bonds       : angle       4.78770 ( 1005)
  Misc. bond           : bond        0.00196 (    1)
  link_ALPHA1-4        : bond        0.01680 (    1)
  link_ALPHA1-4        : angle       5.51348 (    3)
  link_NAG-ASN         : bond        0.00705 (    3)
  link_NAG-ASN         : angle       2.39505 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 112
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  124 THR cc_start: 0.8603 (m) cc_final: 0.8300 (t)
REVERT: A  135 ARG cc_start: 0.7969 (ptm-80) cc_final: 0.7557 (tmt-80)
REVERT: A  191 ARG cc_start: 0.7426 (mmm160) cc_final: 0.6524 (mmm160)
REVERT: A  212 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7769 (pm20)
REVERT: A  256 LYS cc_start: 0.8768 (ptmm) cc_final: 0.8508 (pttp)
REVERT: A  329 GLN cc_start: 0.8201 (tp40) cc_final: 0.7799 (mm-40)
REVERT: A  385 ILE cc_start: 0.8022 (pt) cc_final: 0.7794 (pt)
REVERT: A  678 MET cc_start: 0.5599 (tmm) cc_final: 0.5276 (tpp)
REVERT: A  717 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6584 (tm-30)
REVERT: A  721 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5954 (mp0)
REVERT: A  774 ILE cc_start: 0.8265 (mt) cc_final: 0.7981 (mp)
REVERT: A  926 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8430 (pp)
REVERT: A  928 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.7168 (mp10)
REVERT: C  155 LYS cc_start: 0.8398 (mttp) cc_final: 0.7698 (pttm)
REVERT: C  238 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7823 (pttp)
REVERT: C  270 ARG cc_start: 0.8891 (mtt180) cc_final: 0.8308 (mtm-85)
REVERT: C  290 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7367 (mtm110)
  outliers start: 47
  outliers final: 22
  residues processed: 149
  average time/residue: 0.5097
  time to fit residues: 81.8745
Evaluate side-chains
  138 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  708 SER
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  814 ILE
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  928 GLN
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1065 SER
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain C residue  228 LYS
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  339 LEU
Chi-restraints excluded: chain C residue  343 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 105 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
A 386 ASN
C 152 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.147052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.107437 restraints weight = 10163.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.79
r_work: 0.2983 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9572  Z= 0.130
  Angle     :  0.840  30.365  12986  Z= 0.361
  Chirality :  0.044   0.237   1465
  Planarity :  0.004   0.068   1612
  Dihedral  :  9.093 107.445   1396
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 24.98 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.25), residues: 1129
  helix:  0.18 (0.23), residues: 501
  sheet: -0.02 (0.43), residues: 156
  loop : -2.11 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 723 
 TYR   0.014   0.001   TYR A 324 
 PHE   0.015   0.001   PHE C 108 
 TRP   0.017   0.001   TRP A 323 
 HIS   0.005   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9564)
  covalent geometry    : angle       0.83306 (12968)
  SS BOND              : bond        0.00308 (    3)
  SS BOND              : angle       2.62561 (    6)
  hydrogen bonds       : bond        0.03638 (  362)
  hydrogen bonds       : angle       4.57042 ( 1005)
  Misc. bond           : bond        0.00087 (    1)
  link_ALPHA1-4        : bond        0.01582 (    1)
  link_ALPHA1-4        : angle       5.07344 (    3)
  link_NAG-ASN         : bond        0.00612 (    3)
  link_NAG-ASN         : angle       2.31619 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 121
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A  124 THR cc_start: 0.8576 (m) cc_final: 0.8279 (t)
REVERT: A  135 ARG cc_start: 0.7881 (ptm-80) cc_final: 0.7552 (tmt-80)
REVERT: A  191 ARG cc_start: 0.7367 (mmm160) cc_final: 0.6485 (mmm160)
REVERT: A  256 LYS cc_start: 0.8699 (ptmm) cc_final: 0.8425 (pttp)
REVERT: A  329 GLN cc_start: 0.8107 (tp40) cc_final: 0.7692 (mm-40)
REVERT: A  339 LYS cc_start: 0.7770 (tptp) cc_final: 0.7121 (ttpt)
REVERT: A  359 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8961 (ttm)
REVERT: A  717 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6770 (tm-30)
REVERT: A  721 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5946 (mp0)
REVERT: A  774 ILE cc_start: 0.8120 (mt) cc_final: 0.7838 (mp)
REVERT: A  926 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8328 (pp)
REVERT: A  928 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7085 (mp10)
REVERT: C  152 ASN cc_start: 0.8076 (t0) cc_final: 0.7861 (m-40)
REVERT: C  155 LYS cc_start: 0.8224 (mttp) cc_final: 0.7606 (pttm)
REVERT: C  238 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7756 (pttp)
REVERT: C  270 ARG cc_start: 0.8719 (mtt180) cc_final: 0.8170 (mtm-85)
REVERT: C  290 ARG cc_start: 0.7827 (mtp180) cc_final: 0.7485 (mtm110)
  outliers start: 43
  outliers final: 14
  residues processed: 156
  average time/residue: 0.5105
  time to fit residues: 85.6324
Evaluate side-chains
  134 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  928 GLN
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1065 SER
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain C residue  228 LYS
Chi-restraints excluded: chain C residue  339 LEU
Chi-restraints excluded: chain C residue  343 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0000
   chunk 82 optimal weight:    0.1980
   chunk 70 optimal weight:    4.9990
   chunk 20 optimal weight:   20.0000
   chunk 13 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.0188

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
A 769 ASN
C 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.149855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.107550 restraints weight = 10081.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.90
r_work: 0.2955 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9572  Z= 0.141
  Angle     :  0.852  30.672  12986  Z= 0.369
  Chirality :  0.044   0.230   1465
  Planarity :  0.004   0.064   1612
  Dihedral  :  8.729 101.370   1393
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 26.65 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.25), residues: 1129
  helix:  0.31 (0.23), residues: 505
  sheet: -0.13 (0.42), residues: 163
  loop : -2.04 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 723 
 TYR   0.012   0.001   TYR A 324 
 PHE   0.015   0.001   PHE C 108 
 TRP   0.014   0.001   TRP A 323 
 HIS   0.005   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9564)
  covalent geometry    : angle       0.84513 (12968)
  SS BOND              : bond        0.00299 (    3)
  SS BOND              : angle       2.66991 (    6)
  hydrogen bonds       : bond        0.03742 (  362)
  hydrogen bonds       : angle       4.54883 ( 1005)
  Misc. bond           : bond        0.00097 (    1)
  link_ALPHA1-4        : bond        0.01346 (    1)
  link_ALPHA1-4        : angle       5.17275 (    3)
  link_NAG-ASN         : bond        0.00628 (    3)
  link_NAG-ASN         : angle       2.23453 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 THR cc_start: 0.8553 (m) cc_final: 0.8299 (t)
REVERT: A  135 ARG cc_start: 0.7906 (ptm-80) cc_final: 0.7527 (tmt-80)
REVERT: A  191 ARG cc_start: 0.7351 (mmm160) cc_final: 0.6431 (mmm160)
REVERT: A  329 GLN cc_start: 0.8159 (tp40) cc_final: 0.7767 (mm-40)
REVERT: A  339 LYS cc_start: 0.7827 (tptp) cc_final: 0.7171 (ttpt)
REVERT: A  717 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6873 (tm-30)
REVERT: A  774 ILE cc_start: 0.8261 (mt) cc_final: 0.7977 (mp)
REVERT: A  926 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8402 (pp)
REVERT: A  928 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7094 (mp10)
REVERT: C  152 ASN cc_start: 0.8133 (t0) cc_final: 0.7867 (m-40)
REVERT: C  155 LYS cc_start: 0.8281 (mttp) cc_final: 0.7647 (pttm)
REVERT: C  184 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6313 (pm20)
REVERT: C  238 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7778 (pttp)
REVERT: C  270 ARG cc_start: 0.8777 (mtt180) cc_final: 0.8332 (mtm-85)
  outliers start: 30
  outliers final: 14
  residues processed: 145
  average time/residue: 0.5088
  time to fit residues: 79.4569
Evaluate side-chains
  135 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  928 GLN
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1065 SER
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain C residue  184 GLU
Chi-restraints excluded: chain C residue  228 LYS
Chi-restraints excluded: chain C residue  339 LEU
Chi-restraints excluded: chain C residue  343 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 74 optimal weight:    0.2980
   chunk 65 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 107 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.150259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.107651 restraints weight = 10020.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.91
r_work: 0.2965 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9572  Z= 0.139
  Angle     :  0.850  30.611  12986  Z= 0.366
  Chirality :  0.045   0.231   1465
  Planarity :  0.004   0.067   1612
  Dihedral  :  8.552  96.692   1393
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 25.96 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.25), residues: 1129
  helix:  0.40 (0.23), residues: 505
  sheet: -0.11 (0.42), residues: 160
  loop : -1.99 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 723 
 TYR   0.012   0.001   TYR A 324 
 PHE   0.015   0.001   PHE C 108 
 TRP   0.015   0.001   TRP A 323 
 HIS   0.005   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9564)
  covalent geometry    : angle       0.84349 (12968)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       2.46196 (    6)
  hydrogen bonds       : bond        0.03730 (  362)
  hydrogen bonds       : angle       4.49648 ( 1005)
  Misc. bond           : bond        0.00096 (    1)
  link_ALPHA1-4        : bond        0.01146 (    1)
  link_ALPHA1-4        : angle       5.21164 (    3)
  link_NAG-ASN         : bond        0.00638 (    3)
  link_NAG-ASN         : angle       2.25857 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  124 THR cc_start: 0.8549 (m) cc_final: 0.8313 (t)
REVERT: A  135 ARG cc_start: 0.7854 (ptm-80) cc_final: 0.7493 (tmt-80)
REVERT: A  191 ARG cc_start: 0.7353 (mmm160) cc_final: 0.6442 (mmm160)
REVERT: A  224 ARG cc_start: 0.7138 (ttm170) cc_final: 0.6547 (ttt90)
REVERT: A  329 GLN cc_start: 0.8167 (tp40) cc_final: 0.7777 (mm-40)
REVERT: A  339 LYS cc_start: 0.7899 (tptp) cc_final: 0.7238 (ttpt)
REVERT: A  717 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7175 (tm-30)
REVERT: A  774 ILE cc_start: 0.8222 (mt) cc_final: 0.7933 (mp)
REVERT: A  926 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8397 (pp)
REVERT: A  928 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7121 (mp10)
REVERT: C  152 ASN cc_start: 0.8126 (t0) cc_final: 0.7843 (m-40)
REVERT: C  155 LYS cc_start: 0.8283 (mttp) cc_final: 0.7640 (pttm)
REVERT: C  184 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6312 (pm20)
REVERT: C  238 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7750 (pttp)
REVERT: C  270 ARG cc_start: 0.8774 (mtt180) cc_final: 0.8320 (mtm-85)
REVERT: C  290 ARG cc_start: 0.7848 (mtp180) cc_final: 0.7538 (mtm110)
  outliers start: 38
  outliers final: 20
  residues processed: 148
  average time/residue: 0.5111
  time to fit residues: 81.3948
Evaluate side-chains
  141 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  814 ILE
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  928 GLN
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1065 SER
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain C residue  184 GLU
Chi-restraints excluded: chain C residue  228 LYS
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  339 LEU
Chi-restraints excluded: chain C residue  343 LEU
Chi-restraints excluded: chain C residue  344 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 95 optimal weight:    0.0060
   chunk 100 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0370
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.5476

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
** A 273 ASN ** 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 = 0.3657 r_free = 0.3657 target = 0.151613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.109184 restraints weight = 10039.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.86
r_work: 0.3007 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9572  Z= 0.112
  Angle     :  0.831  30.055  12986  Z= 0.353
  Chirality :  0.044   0.308   1465
  Planarity :  0.004   0.064   1612
  Dihedral  :  8.093  81.922   1393
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 27.73 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.26), residues: 1129
  helix:  0.71 (0.24), residues: 496
  sheet: -0.01 (0.43), residues: 154
  loop : -1.78 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 723 
 TYR   0.015   0.001   TYR A 324 
 PHE   0.014   0.001   PHE C 108 
 TRP   0.017   0.001   TRP A 323 
 HIS   0.004   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9564)
  covalent geometry    : angle       0.82514 (12968)
  SS BOND              : bond        0.00254 (    3)
  SS BOND              : angle       2.20845 (    6)
  hydrogen bonds       : bond        0.03368 (  362)
  hydrogen bonds       : angle       4.38240 ( 1005)
  Misc. bond           : bond        0.00052 (    1)
  link_ALPHA1-4        : bond        0.01226 (    1)
  link_ALPHA1-4        : angle       4.89985 (    3)
  link_NAG-ASN         : bond        0.00599 (    3)
  link_NAG-ASN         : angle       2.18754 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 THR cc_start: 0.8397 (m) cc_final: 0.8176 (t)
REVERT: A  135 ARG cc_start: 0.7875 (ptm-80) cc_final: 0.7553 (tmt-80)
REVERT: A  191 ARG cc_start: 0.7392 (mmm160) cc_final: 0.6491 (mmm160)
REVERT: A  215 GLN cc_start: 0.8480 (pt0) cc_final: 0.8183 (pm20)
REVERT: A  224 ARG cc_start: 0.7268 (ttm170) cc_final: 0.6605 (ttt90)
REVERT: A  329 GLN cc_start: 0.8118 (tp40) cc_final: 0.7703 (mm-40)
REVERT: A  339 LYS cc_start: 0.7842 (tptp) cc_final: 0.7210 (ttmt)
REVERT: A  680 THR cc_start: 0.6424 (OUTLIER) cc_final: 0.6173 (m)
REVERT: A  717 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7075 (tm-30)
REVERT: A  723 ARG cc_start: 0.6883 (ttp80) cc_final: 0.6644 (ttp80)
REVERT: A  774 ILE cc_start: 0.8140 (mt) cc_final: 0.7843 (mp)
REVERT: A  926 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8661 (pt)
REVERT: A  928 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7090 (mp10)
REVERT: C  152 ASN cc_start: 0.8161 (t0) cc_final: 0.7857 (m-40)
REVERT: C  155 LYS cc_start: 0.8228 (mttp) cc_final: 0.7625 (pttm)
REVERT: C  184 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6750 (mp0)
REVERT: C  238 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7644 (ptpp)
REVERT: C  270 ARG cc_start: 0.8652 (mtt180) cc_final: 0.8342 (mtm-85)
REVERT: C  290 ARG cc_start: 0.7792 (mtp180) cc_final: 0.7519 (mtm110)
  outliers start: 21
  outliers final: 11
  residues processed: 139
  average time/residue: 0.5167
  time to fit residues: 77.2456
Evaluate side-chains
  134 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  928 GLN
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1065 SER
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  184 GLU
Chi-restraints excluded: chain C residue  228 LYS
Chi-restraints excluded: chain C residue  234 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 22 optimal weight:    0.3980
   chunk 19 optimal weight:    0.0670
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    0.8720

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
A 777 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.149790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.107118 restraints weight = 9955.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.85
r_work: 0.2982 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9572  Z= 0.127
  Angle     :  0.835  30.296  12986  Z= 0.357
  Chirality :  0.044   0.323   1465
  Planarity :  0.004   0.065   1612
  Dihedral  :  8.140  83.178   1393
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 27.63 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.25), residues: 1129
  helix:  0.66 (0.23), residues: 505
  sheet: -0.11 (0.42), residues: 163
  loop : -1.89 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 723 
 TYR   0.012   0.001   TYR A 324 
 PHE   0.014   0.001   PHE C 108 
 TRP   0.014   0.001   TRP A 323 
 HIS   0.004   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9564)
  covalent geometry    : angle       0.82909 (12968)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       2.16419 (    6)
  hydrogen bonds       : bond        0.03555 (  362)
  hydrogen bonds       : angle       4.34931 ( 1005)
  Misc. bond           : bond        0.00084 (    1)
  link_ALPHA1-4        : bond        0.01187 (    1)
  link_ALPHA1-4        : angle       4.98525 (    3)
  link_NAG-ASN         : bond        0.00614 (    3)
  link_NAG-ASN         : angle       2.18306 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3207.68 seconds
wall clock time: 55 minutes 28.91 seconds (3328.91 seconds total)