Starting phenix.real_space_refine
on Thu Jul 31 17:48:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cml_16730/07_2025/8cml_16730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cml_16730/07_2025/8cml_16730.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cml_16730/07_2025/8cml_16730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cml_16730/07_2025/8cml_16730.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cml_16730/07_2025/8cml_16730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cml_16730/07_2025/8cml_16730.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    8662      2.51       5
     N    2258      2.21       5
     O    2621      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13594
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 909
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "E"
      Number of atoms: 5141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 651, 5141
          Classifications: {'peptide': 651}
          Link IDs: {'PTRANS': 34, 'TRANS': 616}
    Chain: "B"
      Number of atoms: 6560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 829, 6560
          Classifications: {'peptide': 829}
          Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 796}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 956
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 4, 'TRANS': 123}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 8.65, per 1000 atoms: 0.64
  Number of scatterers: 13594
  At special positions: 0
  Unit cell: (100.88, 154.96, 140.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    2621      8.00
     N    2258      7.00
     C    8662      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 567 " - pdb=" SG  CYS B 810 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 634 " - pdb=" SG  CYS E 669 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 698 " - pdb=" SG  CYS B 724 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 699 " - pdb=" SG  CYS B 731 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 711 " - pdb=" SG  CYS B 732 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 856 " - pdb=" SG  CYS B 883 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 866 " - pdb=" SG  CYS B1527 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1101 " - pdb=" SG  CYS B1159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1375 " - pdb=" SG  CYS B1505 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1405 " - pdb=" SG  CYS B1474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN B 911 "
  Time building additional restraints: 3.36
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3228

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 32 sheets defined
      19.8% alpha, 31.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.89
  Creating SS restraints...
    Processing helix  chain 'E' and resid 88 through 92
      removed outlier: 3.804A  pdb=" N   LEU E  92 " --> pdb=" O   PRO E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 302 through 309
      removed outlier: 4.049A  pdb=" N   GLU E 309 " --> pdb=" O   THR E 305 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 443 through 447
    Processing helix  chain 'E' and resid 531 through 535
      removed outlier: 3.907A  pdb=" N   VAL E 535 " --> pdb=" O   GLN E 532 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 608 through 611
    Processing helix  chain 'E' and resid 618 through 628
      removed outlier: 5.030A  pdb=" N   PHE E 624 " --> pdb=" O   LEU E 620 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   GLN E 625 " --> pdb=" O   GLU E 621 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 629 through 631
      No H-bonds generated for 'chain 'E' and resid 629 through 631'
    Processing helix  chain 'E' and resid 641 through 649
    Processing helix  chain 'B' and resid 680 through 691
      removed outlier: 3.789A  pdb=" N   ILE B 686 " --> pdb=" O   LYS B 682 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS B 691 " --> pdb=" O   ALA B 687 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 692 through 703
      removed outlier: 3.855A  pdb=" N   LYS B 697 " --> pdb=" O   SER B 693 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 710 through 717
      removed outlier: 4.035A  pdb=" N   ARG B 717 " --> pdb=" O   GLN B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 739
      removed outlier: 3.553A  pdb=" N   ILE B 725 " --> pdb=" O   GLY B 721 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   ALA B 727 " --> pdb=" O   ARG B 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 745 through 755
      removed outlier: 3.542A  pdb=" N   LEU B 749 " --> pdb=" O   LYS B 745 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ARG B 751 " --> pdb=" O   MET B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 984 through 992
    Processing helix  chain 'B' and resid 1007 through 1014
      removed outlier: 3.668A  pdb=" N   SER B1014 " --> pdb=" O   ALA B1010 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1015 through 1029
    Processing helix  chain 'B' and resid 1030 through 1034
      removed outlier: 3.768A  pdb=" N   PHE B1034 " --> pdb=" O   TRP B1031 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1037 through 1056
      removed outlier: 3.675A  pdb=" N   GLU B1041 " --> pdb=" O   ASP B1037 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1057 through 1060
    Processing helix  chain 'B' and resid 1075 through 1090
    Processing helix  chain 'B' and resid 1096 through 1110
    Processing helix  chain 'B' and resid 1132 through 1155
    Processing helix  chain 'B' and resid 1161 through 1180
      removed outlier: 3.567A  pdb=" N   ASP B1165 " --> pdb=" O   LEU B1161 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   LEU B1180 " --> pdb=" O   LEU B1176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1184 through 1197
    Processing helix  chain 'B' and resid 1202 through 1215
      removed outlier: 3.634A  pdb=" N   GLU B1215 " --> pdb=" O   ALA B1211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1244 through 1261
    Processing helix  chain 'B' and resid 1267 through 1278
    Processing helix  chain 'B' and resid 1286 through 1304
      removed outlier: 3.631A  pdb=" N   ASN B1292 " --> pdb=" O   GLN B1288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1435 through 1444
      removed outlier: 3.981A  pdb=" N   LEU B1439 " --> pdb=" O   ASN B1435 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 31
    Processing helix  chain 'C' and resid 62 through 65
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12
      removed outlier: 3.555A  pdb=" N   THR A 113 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   VAL A 115 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLY A  92 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE A  95 " --> pdb=" O   PHE A  37 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   ARG A  38 " --> pdb=" O   PHE A  47 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   PHE A  47 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 23
    Processing sheet with id=AA3, first strand: chain 'E' and resid 80 through 85
      removed outlier: 8.322A  pdb=" N   ASN E  38 " --> pdb=" O   PRO E  28 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 31 through 32
      removed outlier: 6.286A  pdb=" N   PHE E  31 " --> pdb=" O   THR E 120 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   SER E  67 " --> pdb=" O   ILE E  56 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 125 through 130
    Processing sheet with id=AA6, first strand: chain 'E' and resid 134 through 135
      removed outlier: 4.232A  pdb=" N   ASP E 172 " --> pdb=" O   PHE E 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AA8, first strand: chain 'E' and resid 221 through 222
      removed outlier: 5.773A  pdb=" N   GLU E 221 " --> pdb=" O   ILE B 765 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'E' and resid 228 through 233
    Processing sheet with id=AB1, first strand: chain 'E' and resid 237 through 238
    Processing sheet with id=AB2, first strand: chain 'E' and resid 281 through 282
    Processing sheet with id=AB3, first strand: chain 'E' and resid 281 through 282
    Processing sheet with id=AB4, first strand: chain 'E' and resid 353 through 356
      removed outlier: 3.912A  pdb=" N   VAL E 373 " --> pdb=" O   ALA E 418 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 401 through 403
    Processing sheet with id=AB6, first strand: chain 'E' and resid 401 through 403
    Processing sheet with id=AB7, first strand: chain 'E' and resid 466 through 469
    Processing sheet with id=AB8, first strand: chain 'E' and resid 508 through 516
      removed outlier: 5.508A  pdb=" N   ILE E 509 " --> pdb=" O   SER E 505 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   SER E 505 " --> pdb=" O   ILE E 509 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   HIS E 498 " --> pdb=" O   ILE E 545 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   ILE E 545 " --> pdb=" O   HIS E 498 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 572 through 575
    Processing sheet with id=AC1, first strand: chain 'E' and resid 581 through 582
    Processing sheet with id=AC2, first strand: chain 'E' and resid 581 through 582
    Processing sheet with id=AC3, first strand: chain 'B' and resid 823 through 827
      removed outlier: 3.652A  pdb=" N   LEU B 901 " --> pdb=" O   CYS B 866 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 823 through 827
    Processing sheet with id=AC5, first strand: chain 'B' and resid 832 through 834
      removed outlier: 6.045A  pdb=" N   VAL B 833 " --> pdb=" O   VAL B 930 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC5
    Processing sheet with id=AC6, first strand: chain 'B' and resid 886 through 888
    Processing sheet with id=AC7, first strand: chain 'B' and resid 934 through 944
      removed outlier: 4.509A  pdb=" N   ARG B 975 " --> pdb=" O   VAL B1340 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL B1338 " --> pdb=" O   LEU B 977 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 956 through 959
      removed outlier: 3.994A  pdb=" N   VAL B1315 " --> pdb=" O   HIS B1324 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   HIS B1324 " --> pdb=" O   VAL B1315 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   TYR B1317 " --> pdb=" O   ALA B1322 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   ALA B1322 " --> pdb=" O   TYR B1317 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 1217 through 1219
    Processing sheet with id=AD1, first strand: chain 'B' and resid 1377 through 1385
      removed outlier: 4.106A  pdb=" N   LYS B1400 " --> pdb=" O   ILE B1479 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 1452 through 1456
      removed outlier: 4.482A  pdb=" N   THR B1492 " --> pdb=" O   SER B1427 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.915A  pdb=" N   GLY C  16 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU C  18 " --> pdb=" O   ASN C  84 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   ASN C  84 " --> pdb=" O   LEU C  18 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   LEU C  20 " --> pdb=" O   GLN C  82 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   GLN C  82 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   CYS C  22 " --> pdb=" O   TYR C  80 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   TYR C  80 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ALA C  24 " --> pdb=" O   THR C  78 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   THR C  78 " --> pdb=" O   ALA C  24 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 13
      removed outlier: 5.920A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 124 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   SER C 126 " --> pdb=" O   GLY C  10 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL C  12 " --> pdb=" O   SER C 126 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD4
    Processing sheet with id=AD5, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.613A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   CYS C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ILE C  34 " --> pdb=" O   CYS C  50 " (cutoff:3.500A)

    562 hydrogen bonds defined for protein.
    1512 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: 7.39

  Time building geometry restraints manager: 3.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4356
        1.34 -     1.46: 3094
        1.46 -     1.58: 6354
        1.58 -     1.70: 0
        1.70 -     1.83: 79
  Bond restraints: 13883
  Sorted by residual:
  bond pdb=" N   ASP E  61 "
       pdb=" CA  ASP E  61 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.17e-02 7.31e+03 7.78e+00
  bond pdb=" N   ILE B1127 "
       pdb=" CA  ILE B1127 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.35e+00
  bond pdb=" N   ASP E 187 "
       pdb=" CA  ASP E 187 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.27e-02 6.20e+03 7.15e+00
  bond pdb=" N   PHE E 185 "
       pdb=" CA  PHE E 185 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.034 1.51e-02 4.39e+03 4.97e+00
  bond pdb=" N   TYR E  59 "
       pdb=" CA  TYR E  59 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.41e-02 5.03e+03 4.94e+00
  ... (remaining 13878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 18506
        2.15 -     4.30: 280
        4.30 -     6.46: 31
        6.46 -     8.61: 6
        8.61 -    10.76: 4
  Bond angle restraints: 18827
  Sorted by residual:
  angle pdb=" CB  MET C  83 "
        pdb=" CG  MET C  83 "
        pdb=" SD  MET C  83 "
      ideal   model   delta    sigma   weight residual
     112.70  122.68   -9.98 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" CA  ASP E 187 "
        pdb=" C   ASP E 187 "
        pdb=" O   ASP E 187 "
      ideal   model   delta    sigma   weight residual
     121.88  118.37    3.51 1.13e+00 7.83e-01 9.66e+00
  angle pdb=" C   VAL B1015 "
        pdb=" N   VAL B1016 "
        pdb=" CA  VAL B1016 "
      ideal   model   delta    sigma   weight residual
     120.33  122.69   -2.36 8.00e-01 1.56e+00 8.70e+00
  angle pdb=" C   THR B 756 "
        pdb=" N   LEU B 757 "
        pdb=" CA  LEU B 757 "
      ideal   model   delta    sigma   weight residual
     121.54  126.86   -5.32 1.91e+00 2.74e-01 7.76e+00
  angle pdb=" CA  GLU A  44 "
        pdb=" CB  GLU A  44 "
        pdb=" CG  GLU A  44 "
      ideal   model   delta    sigma   weight residual
     114.10  119.62   -5.52 2.00e+00 2.50e-01 7.61e+00
  ... (remaining 18822 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.34: 7527
       21.34 -    42.68: 724
       42.68 -    64.02: 104
       64.02 -    85.36: 16
       85.36 -   106.70: 13
  Dihedral angle restraints: 8384
    sinusoidal: 3352
      harmonic: 5032
  Sorted by residual:
  dihedral pdb=" CB  CYS E 634 "
           pdb=" SG  CYS E 634 "
           pdb=" SG  CYS E 669 "
           pdb=" CB  CYS E 669 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.53  -82.47     1      1.00e+01 1.00e-02 8.34e+01
  dihedral pdb=" CB  CYS B 698 "
           pdb=" SG  CYS B 698 "
           pdb=" SG  CYS B 724 "
           pdb=" CB  CYS B 724 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -15.91  -70.09     1      1.00e+01 1.00e-02 6.33e+01
  dihedral pdb=" CA  GLU A  99 "
           pdb=" C   GLU A  99 "
           pdb=" N   PHE A 100 "
           pdb=" CA  PHE A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.48  -23.52     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 8381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1606
       0.045 -    0.090: 353
       0.090 -    0.135: 167
       0.135 -    0.180: 6
       0.180 -    0.225: 1
  Chirality restraints: 2133
  Sorted by residual:
  chirality pdb=" CB  ILE B 725 "
            pdb=" CA  ILE B 725 "
            pdb=" CG1 ILE B 725 "
            pdb=" CG2 ILE B 725 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" C2  NAG D   2 "
            pdb=" C1  NAG D   2 "
            pdb=" C3  NAG D   2 "
            pdb=" N2  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.33   -0.16 2.00e-01 2.50e+01 6.72e-01
  chirality pdb=" CB  VAL C  93 "
            pdb=" CA  VAL C  93 "
            pdb=" CG1 VAL C  93 "
            pdb=" CG2 VAL C  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.25e-01
  ... (remaining 2130 not shown)

  Planarity restraints: 2406
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 237 "    0.013 2.00e-02 2.50e+03   1.58e-02 4.38e+00
        pdb=" CG  PHE E 237 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 237 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 237 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 237 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 237 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 237 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 490 "   -0.035 5.00e-02 4.00e+02   5.20e-02 4.33e+00
        pdb=" N   PRO E 491 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO E 491 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E 491 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 930 "    0.031 5.00e-02 4.00e+02   4.61e-02 3.41e+00
        pdb=" N   PRO B 931 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 931 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 931 "    0.025 5.00e-02 4.00e+02
  ... (remaining 2403 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 207
        2.67 -     3.23: 12314
        3.23 -     3.79: 19669
        3.79 -     4.34: 26256
        4.34 -     4.90: 44764
  Nonbonded interactions: 103210
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B1009 "
            pdb=" OG1 THR B1287 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" OG  SER C   7 "
            pdb=" OG  SER C  21 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" NH1 ARG A 101 "
            pdb=" O   LEU B1197 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OE1 GLU B 937 "
            pdb=" OH  TYR B 939 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OH  TYR E 196 "
            pdb=" OE2 GLU E 221 "
     model   vdw
     2.222 3.040
  ... (remaining 103205 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.100
  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:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     36.280
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
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      :  0.003   0.057  13897  Z= 0.148
  Angle     :  0.659  10.760  18857  Z= 0.349
  Chirality :  0.045   0.225   2133
  Planarity :  0.004   0.052   2405
  Dihedral  : 16.467 106.701   5120
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.25 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 23.61 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.20), residues: 1714
  helix:  0.92 (0.32), residues: 287
  sheet:  0.53 (0.22), residues: 586
  loop : -1.41 (0.21), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  36 
 HIS   0.005   0.001   HIS E 498 
 PHE   0.037   0.002   PHE E 237 
 TYR   0.015   0.001   TYR B1326 
 ARG   0.006   0.000   ARG B 928 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00103 (    1)
  link_NAG-ASN         : angle       1.58778 (    3)
  link_BETA1-4         : bond        0.00161 (    1)
  link_BETA1-4         : angle       0.79484 (    3)
  hydrogen bonds       : bond        0.12491 (  549)
  hydrogen bonds       : angle       5.93841 ( 1512)
  SS BOND              : bond        0.00328 (   12)
  SS BOND              : angle       0.84020 (   24)
  covalent geometry    : bond        0.00299 (13883)
  covalent geometry    : angle       0.65853 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 171
  time to evaluate  : 1.615 
Fit side-chains
REVERT: B 1326 TYR cc_start: 0.6372 (m-80) cc_final: 0.6143 (m-80)
  outliers start: 9
  outliers final: 5
  residues processed: 173
  average time/residue: 0.2589
  time to fit residues: 67.4096
Evaluate side-chains
  162 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 157
  time to evaluate  : 1.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain B residue 1107 LEU
Chi-restraints excluded: chain B residue 1311 MET
Chi-restraints excluded: chain C residue   20 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 129 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0670
   chunk 134 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 99 optimal weight:    0.9980
   chunk 155 optimal weight:    2.9990
   overall best weight:    1.1922

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
E  42 GLN
E 242 ASN
** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 656 ASN
B 706 ASN
B 753 HIS
B1360 HIS
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.203108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.174656 restraints weight = 16840.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.171860 restraints weight = 25180.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.173829 restraints weight = 24997.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.4010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  13897  Z= 0.176
  Angle     :  0.633  10.280  18857  Z= 0.322
  Chirality :  0.046   0.266   2133
  Planarity :  0.004   0.050   2405
  Dihedral  :  7.577  86.517   1919
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.83 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 23.74 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.20), residues: 1714
  helix:  0.81 (0.31), residues: 291
  sheet:  0.47 (0.22), residues: 584
  loop : -1.39 (0.21), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 469 
 HIS   0.004   0.001   HIS E 498 
 PHE   0.017   0.002   PHE E 237 
 TYR   0.016   0.001   TYR E 543 
 ARG   0.004   0.000   ARG B1153 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00383 (    1)
  link_NAG-ASN         : angle       2.38748 (    3)
  link_BETA1-4         : bond        0.00666 (    1)
  link_BETA1-4         : angle       2.48595 (    3)
  hydrogen bonds       : bond        0.03976 (  549)
  hydrogen bonds       : angle       5.24769 ( 1512)
  SS BOND              : bond        0.00316 (   12)
  SS BOND              : angle       1.18938 (   24)
  covalent geometry    : bond        0.00428 (13883)
  covalent geometry    : angle       0.63101 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 163
  time to evaluate  : 1.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6594 (m-10)
REVERT: B  955 ARG cc_start: 0.3985 (ptm160) cc_final: 0.3417 (mtp85)
  outliers start: 55
  outliers final: 34
  residues processed: 202
  average time/residue: 0.2249
  time to fit residues: 69.5639
Evaluate side-chains
  188 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 153
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain E residue  330 ILE
Chi-restraints excluded: chain E residue  410 VAL
Chi-restraints excluded: chain E residue  441 ASP
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  490 SER
Chi-restraints excluded: chain E residue  531 THR
Chi-restraints excluded: chain B residue  725 ILE
Chi-restraints excluded: chain B residue  747 MET
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  952 THR
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1107 LEU
Chi-restraints excluded: chain B residue 1209 VAL
Chi-restraints excluded: chain B residue 1212 LEU
Chi-restraints excluded: chain B residue 1264 ILE
Chi-restraints excluded: chain B residue 1267 VAL
Chi-restraints excluded: chain B residue 1298 THR
Chi-restraints excluded: chain B residue 1328 MET
Chi-restraints excluded: chain B residue 1457 ASP
Chi-restraints excluded: chain B residue 1492 THR
Chi-restraints excluded: chain B residue 1506 THR
Chi-restraints excluded: chain B residue 1507 MET
Chi-restraints excluded: chain C residue   20 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 135 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 147 optimal weight:    0.3980
   chunk 52 optimal weight:    0.0980
   chunk 133 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0670
   chunk 50 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 104 optimal weight:    0.0970
   overall best weight:    0.2516

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
B 706 ASN
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.208956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.181574 restraints weight = 16940.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.179599 restraints weight = 23931.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.180642 restraints weight = 23440.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13897  Z= 0.102
  Angle     :  0.563   9.730  18857  Z= 0.282
  Chirality :  0.044   0.248   2133
  Planarity :  0.004   0.045   2405
  Dihedral  :  6.893  77.939   1913
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.84 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 24.34 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.21), residues: 1714
  helix:  1.13 (0.31), residues: 290
  sheet:  0.60 (0.22), residues: 589
  loop : -1.29 (0.21), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  36 
 HIS   0.003   0.000   HIS E 498 
 PHE   0.017   0.001   PHE B1019 
 TYR   0.019   0.001   TYR E 196 
 ARG   0.003   0.000   ARG B1153 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00057 (    1)
  link_NAG-ASN         : angle       1.81217 (    3)
  link_BETA1-4         : bond        0.00073 (    1)
  link_BETA1-4         : angle       2.03198 (    3)
  hydrogen bonds       : bond        0.03318 (  549)
  hydrogen bonds       : angle       4.90831 ( 1512)
  SS BOND              : bond        0.00213 (   12)
  SS BOND              : angle       0.84494 (   24)
  covalent geometry    : bond        0.00232 (13883)
  covalent geometry    : angle       0.56206 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 170
  time to evaluate  : 1.568 
Fit side-chains
REVERT: B  923 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7042 (tm)
REVERT: B  955 ARG cc_start: 0.3975 (ptm160) cc_final: 0.3446 (mtp85)
REVERT: B 1104 LEU cc_start: 0.7156 (tt) cc_final: 0.6862 (tt)
REVERT: B 1259 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8354 (mt)
REVERT: C  104 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7049 (mm)
  outliers start: 52
  outliers final: 28
  residues processed: 207
  average time/residue: 0.2232
  time to fit residues: 72.8697
Evaluate side-chains
  183 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 THR
Chi-restraints excluded: chain E residue  257 ASN
Chi-restraints excluded: chain E residue  375 VAL
Chi-restraints excluded: chain E residue  430 VAL
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  490 SER
Chi-restraints excluded: chain E residue  531 THR
Chi-restraints excluded: chain E residue  551 THR
Chi-restraints excluded: chain B residue  725 ILE
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  776 GLU
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  841 LEU
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  923 LEU
Chi-restraints excluded: chain B residue  952 THR
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1259 LEU
Chi-restraints excluded: chain B residue 1271 ILE
Chi-restraints excluded: chain B residue 1328 MET
Chi-restraints excluded: chain B residue 1506 THR
Chi-restraints excluded: chain B residue 1507 MET
Chi-restraints excluded: chain B residue 1527 CYS
Chi-restraints excluded: chain C residue   50 CYS
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  125 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 121 optimal weight:    0.0070
   chunk 19 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 122 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    0.8600

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
E  80 GLN
** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 753 HIS
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.205677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.176325 restraints weight = 16917.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.173654 restraints weight = 22913.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.175943 restraints weight = 22834.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13897  Z= 0.139
  Angle     :  0.591   9.515  18857  Z= 0.297
  Chirality :  0.045   0.264   2133
  Planarity :  0.004   0.043   2405
  Dihedral  :  6.295  66.809   1909
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.48 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.34 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.20), residues: 1714
  helix:  1.18 (0.31), residues: 291
  sheet:  0.61 (0.22), residues: 571
  loop : -1.24 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  36 
 HIS   0.005   0.001   HIS B 753 
 PHE   0.020   0.002   PHE E 237 
 TYR   0.021   0.001   TYR B1300 
 ARG   0.003   0.000   ARG C  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00228 (    1)
  link_NAG-ASN         : angle       2.14950 (    3)
  link_BETA1-4         : bond        0.00007 (    1)
  link_BETA1-4         : angle       2.16622 (    3)
  hydrogen bonds       : bond        0.03508 (  549)
  hydrogen bonds       : angle       4.84465 ( 1512)
  SS BOND              : bond        0.00245 (   12)
  SS BOND              : angle       0.81858 (   24)
  covalent geometry    : bond        0.00335 (13883)
  covalent geometry    : angle       0.58930 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 171
  time to evaluate  : 1.552 
Fit side-chains
REVERT: E  282 MET cc_start: 0.6395 (mmt) cc_final: 0.6156 (mmm)
REVERT: B  923 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6851 (tm)
REVERT: B  955 ARG cc_start: 0.4350 (ptm160) cc_final: 0.3920 (mtp-110)
REVERT: C   19 ARG cc_start: 0.7302 (tpp80) cc_final: 0.6959 (tpp80)
REVERT: C   82 GLN cc_start: 0.5659 (tp40) cc_final: 0.5401 (tm-30)
REVERT: C  104 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6983 (mm)
  outliers start: 63
  outliers final: 42
  residues processed: 219
  average time/residue: 0.2412
  time to fit residues: 80.3765
Evaluate side-chains
  204 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 160
  time to evaluate  : 1.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain E residue   54 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 THR
Chi-restraints excluded: chain E residue  257 ASN
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain E residue  330 ILE
Chi-restraints excluded: chain E residue  375 VAL
Chi-restraints excluded: chain E residue  417 VAL
Chi-restraints excluded: chain E residue  430 VAL
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  478 VAL
Chi-restraints excluded: chain E residue  490 SER
Chi-restraints excluded: chain E residue  531 THR
Chi-restraints excluded: chain E residue  551 THR
Chi-restraints excluded: chain E residue  571 LEU
Chi-restraints excluded: chain B residue  725 ILE
Chi-restraints excluded: chain B residue  747 MET
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  799 ILE
Chi-restraints excluded: chain B residue  841 LEU
Chi-restraints excluded: chain B residue  923 LEU
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1149 VAL
Chi-restraints excluded: chain B residue 1184 SER
Chi-restraints excluded: chain B residue 1212 LEU
Chi-restraints excluded: chain B residue 1264 ILE
Chi-restraints excluded: chain B residue 1267 VAL
Chi-restraints excluded: chain B residue 1328 MET
Chi-restraints excluded: chain B residue 1448 GLN
Chi-restraints excluded: chain B residue 1506 THR
Chi-restraints excluded: chain B residue 1507 MET
Chi-restraints excluded: chain B residue 1527 CYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   50 CYS
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  125 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 141 optimal weight:    4.9990
   chunk 114 optimal weight:    0.0270
   chunk 16 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 50 optimal weight:    0.4980
   chunk 159 optimal weight:   20.0000
   chunk 41 optimal weight:    0.0170
   chunk 84 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 105 optimal weight:    6.9990
   overall best weight:    0.9078

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.204558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.177770 restraints weight = 16975.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.175076 restraints weight = 27078.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.177018 restraints weight = 25668.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13897  Z= 0.143
  Angle     :  0.601  11.181  18857  Z= 0.300
  Chirality :  0.045   0.271   2133
  Planarity :  0.004   0.043   2405
  Dihedral  :  5.873  55.890   1909
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.78 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 23.74 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.21), residues: 1714
  helix:  1.19 (0.31), residues: 290
  sheet:  0.58 (0.22), residues: 577
  loop : -1.24 (0.21), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C  36 
 HIS   0.005   0.001   HIS B 908 
 PHE   0.021   0.001   PHE B1019 
 TYR   0.021   0.001   TYR E 196 
 ARG   0.002   0.000   ARG A  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00208 (    1)
  link_NAG-ASN         : angle       2.09404 (    3)
  link_BETA1-4         : bond        0.00039 (    1)
  link_BETA1-4         : angle       2.21257 (    3)
  hydrogen bonds       : bond        0.03432 (  549)
  hydrogen bonds       : angle       4.79730 ( 1512)
  SS BOND              : bond        0.00286 (   12)
  SS BOND              : angle       0.74407 (   24)
  covalent geometry    : bond        0.00343 (13883)
  covalent geometry    : angle       0.59928 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 175
  time to evaluate  : 1.626 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6894 (m-10)
REVERT: E  282 MET cc_start: 0.6321 (mmt) cc_final: 0.6116 (mmm)
REVERT: E  618 LYS cc_start: 0.5433 (mptt) cc_final: 0.5153 (mttt)
REVERT: B  820 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6137 (t80)
REVERT: B  923 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6983 (tm)
REVERT: B  955 ARG cc_start: 0.4253 (ptm160) cc_final: 0.3945 (mtp-110)
REVERT: B 1104 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7251 (tt)
REVERT: B 1259 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8559 (mt)
REVERT: C   19 ARG cc_start: 0.7228 (tpp80) cc_final: 0.6890 (tpp80)
REVERT: C  104 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7047 (mm)
  outliers start: 72
  outliers final: 54
  residues processed: 231
  average time/residue: 0.2492
  time to fit residues: 87.5035
Evaluate side-chains
  226 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 166
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  162 THR
Chi-restraints excluded: chain E residue  257 ASN
Chi-restraints excluded: chain E residue  267 ILE
Chi-restraints excluded: chain E residue  292 LEU
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain E residue  330 ILE
Chi-restraints excluded: chain E residue  375 VAL
Chi-restraints excluded: chain E residue  404 LEU
Chi-restraints excluded: chain E residue  417 VAL
Chi-restraints excluded: chain E residue  430 VAL
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  478 VAL
Chi-restraints excluded: chain E residue  490 SER
Chi-restraints excluded: chain E residue  531 THR
Chi-restraints excluded: chain E residue  551 THR
Chi-restraints excluded: chain E residue  571 LEU
Chi-restraints excluded: chain B residue  725 ILE
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  799 ILE
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  820 PHE
Chi-restraints excluded: chain B residue  841 LEU
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  923 LEU
Chi-restraints excluded: chain B residue  952 THR
Chi-restraints excluded: chain B residue  987 ILE
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1076 THR
Chi-restraints excluded: chain B residue 1104 LEU
Chi-restraints excluded: chain B residue 1149 VAL
Chi-restraints excluded: chain B residue 1161 LEU
Chi-restraints excluded: chain B residue 1184 SER
Chi-restraints excluded: chain B residue 1212 LEU
Chi-restraints excluded: chain B residue 1259 LEU
Chi-restraints excluded: chain B residue 1264 ILE
Chi-restraints excluded: chain B residue 1267 VAL
Chi-restraints excluded: chain B residue 1328 MET
Chi-restraints excluded: chain B residue 1448 GLN
Chi-restraints excluded: chain B residue 1492 THR
Chi-restraints excluded: chain B residue 1506 THR
Chi-restraints excluded: chain B residue 1507 MET
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  125 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9990
   chunk 123 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0770
   chunk 115 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 152 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0970
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** B 706 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 = 0.4333 r_free = 0.4333 target = 0.205069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.178063 restraints weight = 16972.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.176817 restraints weight = 25473.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.178175 restraints weight = 21943.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13897  Z= 0.116
  Angle     :  0.581   9.525  18857  Z= 0.290
  Chirality :  0.045   0.245   2133
  Planarity :  0.004   0.041   2405
  Dihedral  :  5.437  55.545   1909
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.25 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 25.13 %
    Favored  : 70.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.20), residues: 1714
  helix:  1.30 (0.31), residues: 291
  sheet:  0.60 (0.22), residues: 585
  loop : -1.23 (0.21), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  36 
 HIS   0.002   0.000   HIS E 498 
 PHE   0.027   0.001   PHE E 237 
 TYR   0.031   0.001   TYR E 196 
 ARG   0.003   0.000   ARG C  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00103 (    1)
  link_NAG-ASN         : angle       2.20527 (    3)
  link_BETA1-4         : bond        0.00472 (    1)
  link_BETA1-4         : angle       1.96839 (    3)
  hydrogen bonds       : bond        0.03163 (  549)
  hydrogen bonds       : angle       4.73301 ( 1512)
  SS BOND              : bond        0.00227 (   12)
  SS BOND              : angle       0.81181 (   24)
  covalent geometry    : bond        0.00276 (13883)
  covalent geometry    : angle       0.57904 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 167
  time to evaluate  : 1.541 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6847 (m-10)
REVERT: E  618 LYS cc_start: 0.5389 (mptt) cc_final: 0.5108 (mttt)
REVERT: E  627 LEU cc_start: 0.9030 (tp) cc_final: 0.8827 (tt)
REVERT: B  820 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6168 (t80)
REVERT: B  923 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6927 (tm)
REVERT: B  955 ARG cc_start: 0.4351 (ptm160) cc_final: 0.4041 (mtp-110)
REVERT: B 1104 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6996 (tt)
REVERT: B 1259 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8494 (mt)
REVERT: C   32 TYR cc_start: 0.6739 (t80) cc_final: 0.6506 (t80)
REVERT: C  104 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.7019 (mm)
  outliers start: 64
  outliers final: 46
  residues processed: 215
  average time/residue: 0.2432
  time to fit residues: 79.6729
Evaluate side-chains
  211 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 159
  time to evaluate  : 1.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain E residue   54 ILE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 THR
Chi-restraints excluded: chain E residue  257 ASN
Chi-restraints excluded: chain E residue  330 ILE
Chi-restraints excluded: chain E residue  430 VAL
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  476 LEU
Chi-restraints excluded: chain E residue  490 SER
Chi-restraints excluded: chain E residue  531 THR
Chi-restraints excluded: chain E residue  551 THR
Chi-restraints excluded: chain E residue  571 LEU
Chi-restraints excluded: chain B residue  725 ILE
Chi-restraints excluded: chain B residue  747 MET
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  776 GLU
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  799 ILE
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  820 PHE
Chi-restraints excluded: chain B residue  841 LEU
Chi-restraints excluded: chain B residue  923 LEU
Chi-restraints excluded: chain B residue  952 THR
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1076 THR
Chi-restraints excluded: chain B residue 1104 LEU
Chi-restraints excluded: chain B residue 1149 VAL
Chi-restraints excluded: chain B residue 1161 LEU
Chi-restraints excluded: chain B residue 1184 SER
Chi-restraints excluded: chain B residue 1209 VAL
Chi-restraints excluded: chain B residue 1212 LEU
Chi-restraints excluded: chain B residue 1259 LEU
Chi-restraints excluded: chain B residue 1328 MET
Chi-restraints excluded: chain B residue 1448 GLN
Chi-restraints excluded: chain B residue 1506 THR
Chi-restraints excluded: chain B residue 1507 MET
Chi-restraints excluded: chain B residue 1527 CYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   50 CYS
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  125 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 145 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   chunk 34 optimal weight:    0.5980
   chunk 140 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0970
   chunk 83 optimal weight:    6.9990
   chunk 86 optimal weight:    0.7980
   chunk 113 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   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  32 ASN
** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1465 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.203404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.176761 restraints weight = 17167.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.174023 restraints weight = 28054.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.175879 restraints weight = 26594.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13897  Z= 0.143
  Angle     :  0.604  12.228  18857  Z= 0.302
  Chirality :  0.045   0.261   2133
  Planarity :  0.004   0.044   2405
  Dihedral  :  5.196  55.933   1909
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.89 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 25.07 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.20), residues: 1714
  helix:  1.35 (0.32), residues: 290
  sheet:  0.51 (0.22), residues: 573
  loop : -1.26 (0.21), residues: 851

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 469 
 HIS   0.003   0.001   HIS B1023 
 PHE   0.020   0.002   PHE B1019 
 TYR   0.023   0.001   TYR B1024 
 ARG   0.002   0.000   ARG B1153 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00308 (    1)
  link_NAG-ASN         : angle       2.30730 (    3)
  link_BETA1-4         : bond        0.00189 (    1)
  link_BETA1-4         : angle       2.04388 (    3)
  hydrogen bonds       : bond        0.03440 (  549)
  hydrogen bonds       : angle       4.76792 ( 1512)
  SS BOND              : bond        0.00396 (   12)
  SS BOND              : angle       1.06860 (   24)
  covalent geometry    : bond        0.00347 (13883)
  covalent geometry    : angle       0.60190 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 164
  time to evaluate  : 1.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6947 (m-10)
REVERT: E  618 LYS cc_start: 0.5622 (mptt) cc_final: 0.5385 (mttt)
REVERT: B  820 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.6200 (t80)
REVERT: B  923 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6996 (tm)
REVERT: B  955 ARG cc_start: 0.4364 (ptm160) cc_final: 0.4159 (ttm-80)
REVERT: B 1104 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7171 (tt)
REVERT: B 1259 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8571 (mt)
REVERT: C   32 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6470 (t80)
REVERT: C  104 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6940 (mm)
  outliers start: 71
  outliers final: 52
  residues processed: 221
  average time/residue: 0.2327
  time to fit residues: 79.3035
Evaluate side-chains
  218 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 159
  time to evaluate  : 1.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   54 ILE
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 THR
Chi-restraints excluded: chain E residue  257 ASN
Chi-restraints excluded: chain E residue  292 LEU
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain E residue  430 VAL
Chi-restraints excluded: chain E residue  441 ASP
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  476 LEU
Chi-restraints excluded: chain E residue  478 VAL
Chi-restraints excluded: chain E residue  490 SER
Chi-restraints excluded: chain E residue  531 THR
Chi-restraints excluded: chain E residue  534 MET
Chi-restraints excluded: chain E residue  551 THR
Chi-restraints excluded: chain E residue  571 LEU
Chi-restraints excluded: chain B residue  747 MET
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  776 GLU
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  799 ILE
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  820 PHE
Chi-restraints excluded: chain B residue  858 LYS
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  923 LEU
Chi-restraints excluded: chain B residue  952 THR
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1056 ILE
Chi-restraints excluded: chain B residue 1076 THR
Chi-restraints excluded: chain B residue 1104 LEU
Chi-restraints excluded: chain B residue 1149 VAL
Chi-restraints excluded: chain B residue 1161 LEU
Chi-restraints excluded: chain B residue 1184 SER
Chi-restraints excluded: chain B residue 1209 VAL
Chi-restraints excluded: chain B residue 1212 LEU
Chi-restraints excluded: chain B residue 1259 LEU
Chi-restraints excluded: chain B residue 1264 ILE
Chi-restraints excluded: chain B residue 1267 VAL
Chi-restraints excluded: chain B residue 1448 GLN
Chi-restraints excluded: chain B residue 1506 THR
Chi-restraints excluded: chain B residue 1527 CYS
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   50 CYS
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  125 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 133 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 47 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0970
   chunk 88 optimal weight:    0.2980
   chunk 70 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1030 HIS
B1306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.206171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.179918 restraints weight = 17063.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.177622 restraints weight = 25544.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.179583 restraints weight = 25156.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13897  Z= 0.114
  Angle     :  0.585  10.272  18857  Z= 0.290
  Chirality :  0.044   0.254   2133
  Planarity :  0.004   0.042   2405
  Dihedral  :  4.928  56.094   1909
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.37 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 25.53 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.20), residues: 1714
  helix:  1.44 (0.32), residues: 290
  sheet:  0.54 (0.21), residues: 587
  loop : -1.21 (0.21), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1077 
 HIS   0.002   0.000   HIS B1421 
 PHE   0.021   0.001   PHE B1019 
 TYR   0.027   0.001   TYR B1024 
 ARG   0.002   0.000   ARG A  45 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    1)
  link_NAG-ASN         : angle       2.02823 (    3)
  link_BETA1-4         : bond        0.00285 (    1)
  link_BETA1-4         : angle       1.83371 (    3)
  hydrogen bonds       : bond        0.03189 (  549)
  hydrogen bonds       : angle       4.63423 ( 1512)
  SS BOND              : bond        0.00363 (   12)
  SS BOND              : angle       1.19294 (   24)
  covalent geometry    : bond        0.00267 (13883)
  covalent geometry    : angle       0.58252 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 172
  time to evaluate  : 1.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6820 (m-10)
REVERT: B  753 HIS cc_start: 0.4930 (t-90) cc_final: 0.4688 (t-170)
REVERT: B  859 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5863 (mtp)
REVERT: B 1104 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7135 (tt)
REVERT: B 1259 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8545 (mt)
REVERT: C  104 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6918 (mm)
  outliers start: 66
  outliers final: 54
  residues processed: 225
  average time/residue: 0.2369
  time to fit residues: 82.2822
Evaluate side-chains
  216 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 157
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain E residue   54 ILE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 THR
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain E residue  330 ILE
Chi-restraints excluded: chain E residue  375 VAL
Chi-restraints excluded: chain E residue  430 VAL
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  476 LEU
Chi-restraints excluded: chain E residue  478 VAL
Chi-restraints excluded: chain E residue  490 SER
Chi-restraints excluded: chain E residue  531 THR
Chi-restraints excluded: chain E residue  534 MET
Chi-restraints excluded: chain E residue  551 THR
Chi-restraints excluded: chain E residue  571 LEU
Chi-restraints excluded: chain B residue  725 ILE
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  776 GLU
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  799 ILE
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  841 LEU
Chi-restraints excluded: chain B residue  844 THR
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  952 THR
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1076 THR
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain B residue 1104 LEU
Chi-restraints excluded: chain B residue 1149 VAL
Chi-restraints excluded: chain B residue 1161 LEU
Chi-restraints excluded: chain B residue 1184 SER
Chi-restraints excluded: chain B residue 1209 VAL
Chi-restraints excluded: chain B residue 1259 LEU
Chi-restraints excluded: chain B residue 1264 ILE
Chi-restraints excluded: chain B residue 1267 VAL
Chi-restraints excluded: chain B residue 1315 VAL
Chi-restraints excluded: chain B residue 1448 GLN
Chi-restraints excluded: chain B residue 1506 THR
Chi-restraints excluded: chain B residue 1507 MET
Chi-restraints excluded: chain B residue 1527 CYS
Chi-restraints excluded: chain B residue 1528 VAL
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   50 CYS
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  125 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 153 optimal weight:    0.9980
   chunk 125 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0670
   chunk 44 optimal weight:    0.8980
   chunk 139 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 142 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 130 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0770
   overall best weight:    0.6076

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.204731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.175405 restraints weight = 16916.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.172240 restraints weight = 22719.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.173518 restraints weight = 21307.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13897  Z= 0.122
  Angle     :  0.601  10.077  18857  Z= 0.298
  Chirality :  0.045   0.258   2133
  Planarity :  0.004   0.042   2405
  Dihedral  :  4.838  56.410   1909
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.72 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 25.66 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.21), residues: 1714
  helix:  1.46 (0.31), residues: 289
  sheet:  0.51 (0.21), residues: 618
  loop : -1.23 (0.22), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  36 
 HIS   0.003   0.001   HIS B1023 
 PHE   0.024   0.001   PHE B1019 
 TYR   0.026   0.001   TYR B1024 
 ARG   0.005   0.000   ARG B 962 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00276 (    1)
  link_NAG-ASN         : angle       1.92258 (    3)
  link_BETA1-4         : bond        0.00180 (    1)
  link_BETA1-4         : angle       1.68186 (    3)
  hydrogen bonds       : bond        0.03215 (  549)
  hydrogen bonds       : angle       4.58435 ( 1512)
  SS BOND              : bond        0.00295 (   12)
  SS BOND              : angle       1.08753 (   24)
  covalent geometry    : bond        0.00289 (13883)
  covalent geometry    : angle       0.59955 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 161
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6715 (m-10)
REVERT: B  753 HIS cc_start: 0.5072 (t-90) cc_final: 0.4817 (t-170)
REVERT: B  820 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.6203 (t80)
REVERT: B  859 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5844 (mtp)
REVERT: B 1104 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7029 (tt)
REVERT: B 1114 ASP cc_start: 0.6571 (p0) cc_final: 0.6368 (p0)
REVERT: B 1259 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8610 (mt)
REVERT: C  104 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6999 (mm)
  outliers start: 66
  outliers final: 53
  residues processed: 211
  average time/residue: 0.2180
  time to fit residues: 70.8882
Evaluate side-chains
  219 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 160
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain E residue   54 ILE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 THR
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain E residue  330 ILE
Chi-restraints excluded: chain E residue  375 VAL
Chi-restraints excluded: chain E residue  430 VAL
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  476 LEU
Chi-restraints excluded: chain E residue  478 VAL
Chi-restraints excluded: chain E residue  490 SER
Chi-restraints excluded: chain E residue  531 THR
Chi-restraints excluded: chain E residue  534 MET
Chi-restraints excluded: chain E residue  551 THR
Chi-restraints excluded: chain E residue  571 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  799 ILE
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  820 PHE
Chi-restraints excluded: chain B residue  841 LEU
Chi-restraints excluded: chain B residue  844 THR
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  952 THR
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1056 ILE
Chi-restraints excluded: chain B residue 1076 THR
Chi-restraints excluded: chain B residue 1104 LEU
Chi-restraints excluded: chain B residue 1149 VAL
Chi-restraints excluded: chain B residue 1161 LEU
Chi-restraints excluded: chain B residue 1184 SER
Chi-restraints excluded: chain B residue 1209 VAL
Chi-restraints excluded: chain B residue 1259 LEU
Chi-restraints excluded: chain B residue 1264 ILE
Chi-restraints excluded: chain B residue 1267 VAL
Chi-restraints excluded: chain B residue 1315 VAL
Chi-restraints excluded: chain B residue 1448 GLN
Chi-restraints excluded: chain B residue 1492 THR
Chi-restraints excluded: chain B residue 1506 THR
Chi-restraints excluded: chain B residue 1527 CYS
Chi-restraints excluded: chain B residue 1528 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   50 CYS
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  125 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 149 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   chunk 113 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 840 GLN
B1095 GLN
** B1306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1463 GLN
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.183204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.147655 restraints weight = 17535.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.145791 restraints weight = 21299.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.147570 restraints weight = 20474.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.081  13897  Z= 0.375
  Angle     :  0.864  11.313  18857  Z= 0.444
  Chirality :  0.055   0.300   2133
  Planarity :  0.006   0.058   2405
  Dihedral  :  5.888  57.628   1909
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.12 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 25.53 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.20), residues: 1714
  helix:  0.32 (0.30), residues: 283
  sheet:  0.09 (0.21), residues: 590
  loop : -1.76 (0.20), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 109 
 HIS   0.010   0.002   HIS B1421 
 PHE   0.028   0.003   PHE B1483 
 TYR   0.030   0.003   TYR E 544 
 ARG   0.004   0.001   ARG A 101 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01158 (    1)
  link_NAG-ASN         : angle       2.84423 (    3)
  link_BETA1-4         : bond        0.00624 (    1)
  link_BETA1-4         : angle       1.80628 (    3)
  hydrogen bonds       : bond        0.05355 (  549)
  hydrogen bonds       : angle       5.53607 ( 1512)
  SS BOND              : bond        0.00433 (   12)
  SS BOND              : angle       1.39296 (   24)
  covalent geometry    : bond        0.00917 (13883)
  covalent geometry    : angle       0.86191 (18827)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 166
  time to evaluate  : 1.699 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6624 (m-10)
REVERT: B  820 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.6916 (t80)
REVERT: B  859 MET cc_start: 0.6738 (mtp) cc_final: 0.6103 (mtp)
REVERT: B  905 ILE cc_start: 0.6699 (mm) cc_final: 0.6448 (mp)
REVERT: B  915 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6987 (tt0)
REVERT: B  955 ARG cc_start: 0.4435 (ttm-80) cc_final: 0.4233 (mtp-110)
REVERT: B 1259 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8351 (mt)
REVERT: C   32 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6991 (t80)
REVERT: C  104 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7339 (mm)
  outliers start: 71
  outliers final: 53
  residues processed: 221
  average time/residue: 0.2373
  time to fit residues: 80.9884
Evaluate side-chains
  217 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 158
  time to evaluate  : 1.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 THR
Chi-restraints excluded: chain E residue  259 VAL
Chi-restraints excluded: chain E residue  267 ILE
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain E residue  330 ILE
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  375 VAL
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  476 LEU
Chi-restraints excluded: chain E residue  478 VAL
Chi-restraints excluded: chain E residue  490 SER
Chi-restraints excluded: chain E residue  531 THR
Chi-restraints excluded: chain E residue  534 MET
Chi-restraints excluded: chain E residue  551 THR
Chi-restraints excluded: chain E residue  571 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  799 ILE
Chi-restraints excluded: chain B residue  820 PHE
Chi-restraints excluded: chain B residue  840 GLN
Chi-restraints excluded: chain B residue  844 THR
Chi-restraints excluded: chain B residue  915 GLU
Chi-restraints excluded: chain B residue  952 THR
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1076 THR
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain B residue 1104 LEU
Chi-restraints excluded: chain B residue 1161 LEU
Chi-restraints excluded: chain B residue 1184 SER
Chi-restraints excluded: chain B residue 1209 VAL
Chi-restraints excluded: chain B residue 1259 LEU
Chi-restraints excluded: chain B residue 1264 ILE
Chi-restraints excluded: chain B residue 1267 VAL
Chi-restraints excluded: chain B residue 1315 VAL
Chi-restraints excluded: chain B residue 1446 VAL
Chi-restraints excluded: chain B residue 1448 GLN
Chi-restraints excluded: chain B residue 1492 THR
Chi-restraints excluded: chain B residue 1506 THR
Chi-restraints excluded: chain B residue 1507 MET
Chi-restraints excluded: chain B residue 1527 CYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   50 CYS
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  125 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 145 optimal weight:    9.9990
   chunk 162 optimal weight:    6.9990
   chunk 66 optimal weight:    0.3980
   chunk 111 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 170 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 140 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 143 optimal weight:    7.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 753 HIS
** B1306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.183580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.146661 restraints weight = 17585.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145079 restraints weight = 17814.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.146963 restraints weight = 19406.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.126  13897  Z= 0.333
  Angle     :  1.015  59.192  18857  Z= 0.550
  Chirality :  0.055   0.833   2133
  Planarity :  0.005   0.058   2405
  Dihedral  :  5.905  57.232   1909
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.00 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 26.52 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.20), residues: 1714
  helix:  0.28 (0.30), residues: 283
  sheet:  0.03 (0.21), residues: 590
  loop : -1.80 (0.20), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 469 
 HIS   0.008   0.002   HIS E  72 
 PHE   0.025   0.003   PHE B1483 
 TYR   0.028   0.003   TYR E 544 
 ARG   0.004   0.001   ARG B1153 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01073 (    1)
  link_NAG-ASN         : angle       2.78956 (    3)
  link_BETA1-4         : bond        0.01846 (    1)
  link_BETA1-4         : angle       2.02932 (    3)
  hydrogen bonds       : bond        0.05173 (  549)
  hydrogen bonds       : angle       5.51941 ( 1512)
  SS BOND              : bond        0.00322 (   12)
  SS BOND              : angle       1.35133 (   24)
  covalent geometry    : bond        0.00810 (13883)
  covalent geometry    : angle       1.01323 (18827)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4362.53 seconds
wall clock time: 76 minutes 35.80 seconds (4595.80 seconds total)