Starting phenix.real_space_refine
on Wed Sep 17 11:56:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jjo_61534/09_2025/9jjo_61534.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jjo_61534/09_2025/9jjo_61534.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jjo_61534/09_2025/9jjo_61534.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jjo_61534/09_2025/9jjo_61534.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jjo_61534/09_2025/9jjo_61534.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jjo_61534/09_2025/9jjo_61534.cif"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      63      5.16       5
     C    5395      2.51       5
     N    1425      2.21       5
     O    1495      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8379
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1051, 8271
          Classifications: {'peptide': 1051}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 55, 'TRANS': 995}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.23, per 1000 atoms: 0.27
  Number of scatterers: 8379
  At special positions: 0
  Unit cell: (73.6912, 87.927, 164.13, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     P       1     15.00
     O    1495      8.00
     N    1425      7.00
     C    5395      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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 B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A1202 "
      " NAG C   1 " - " ASN A1205 "
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 331.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1996

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      54.9% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 44
    Processing helix  chain 'A' and resid 46 through 54
    Processing helix  chain 'A' and resid 66 through 82
    Processing helix  chain 'A' and resid 93 through 122
    Processing helix  chain 'A' and resid 123 through 139
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 249 through 260
      removed outlier: 4.359A  pdb=" N   ASN A 253 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 302
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 309 through 323
    Processing helix  chain 'A' and resid 329 through 348
    Processing helix  chain 'A' and resid 375 through 392
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 575 through 577
      No H-bonds generated for 'chain 'A' and resid 575 through 577'
    Processing helix  chain 'A' and resid 578 through 594
      removed outlier: 3.513A  pdb=" N   LEU A 582 " --> pdb=" O   HIS A 578 " (cutoff:3.500A)
      Proline residue:  A 584  - end of helix
      removed outlier: 3.562A  pdb=" N   VAL A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 616
      removed outlier: 3.716A  pdb=" N   ARG A 601 " --> pdb=" O   SER A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 638
      removed outlier: 3.592A  pdb=" N   ALA A 634 " --> pdb=" O   LEU A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 645
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 726 through 744
      removed outlier: 3.863A  pdb=" N   SER A 743 " --> pdb=" O   ARG A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 763
    Processing helix  chain 'A' and resid 814 through 819
      removed outlier: 3.627A  pdb=" N   LEU A 818 " --> pdb=" O   CYS A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 846
      removed outlier: 3.823A  pdb=" N   ASN A 846 " --> pdb=" O   ASP A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 869
      removed outlier: 3.621A  pdb=" N   LYS A 868 " --> pdb=" O   VAL A 864 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   MET A 869 " --> pdb=" O   PHE A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 957 through 965
    Processing helix  chain 'A' and resid 979 through 992
      removed outlier: 3.633A  pdb=" N   CYS A 984 " --> pdb=" O   PRO A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1015
      removed outlier: 4.297A  pdb=" N   LEU A1011 " --> pdb=" O   ARG A1007 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLN A1014 " --> pdb=" O   CYS A1010 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER A1015 " --> pdb=" O   LEU A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1050 through 1060
    Processing helix  chain 'A' and resid 1073 through 1113
      removed outlier: 4.412A  pdb=" N   ARG A1077 " --> pdb=" O   ILE A1073 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE A1095 " --> pdb=" O   LYS A1091 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A1096 " --> pdb=" O   CYS A1092 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU A1103 " --> pdb=" O   CYS A1099 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER A1110 " --> pdb=" O   ILE A1106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1130
    Processing helix  chain 'A' and resid 1130 through 1138
    Processing helix  chain 'A' and resid 1161 through 1201
      removed outlier: 5.087A  pdb=" N   LEU A1178 " --> pdb=" O   LEU A1174 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   THR A1179 " --> pdb=" O   LYS A1175 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU A1184 " --> pdb=" O   ILE A1180 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER A1197 " --> pdb=" O   SER A1193 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASP A1200 " --> pdb=" O   ASP A1196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1225 through 1252
      removed outlier: 4.011A  pdb=" N   THR A1250 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1265
      removed outlier: 3.658A  pdb=" N   THR A1265 " --> pdb=" O   SER A1262 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1262 through 1265'
    Processing helix  chain 'A' and resid 1266 through 1289
      Proline residue:  A1274  - end of helix
    Processing helix  chain 'A' and resid 1301 through 1305
      removed outlier: 3.567A  pdb=" N   ASP A1304 " --> pdb=" O   GLY A1301 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL A1305 " --> pdb=" O   LEU A1302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1301 through 1305'
    Processing helix  chain 'A' and resid 1306 through 1348
      removed outlier: 3.834A  pdb=" N   TRP A1310 " --> pdb=" O   PRO A1306 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A1317 " --> pdb=" O   GLY A1313 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A1318 " --> pdb=" O   CYS A1314 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU A1344 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 178
      removed outlier: 4.225A  pdb=" N   TRP A 167 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   ILE A 187 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 878 through 880
      removed outlier: 6.349A  pdb=" N   ILE A 879 " --> pdb=" O   THR A 976 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   PHE A 975 " --> pdb=" O   PHE A 851 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   TYR A 853 " --> pdb=" O   PHE A 975 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   VAL A 412 " --> pdb=" O   CYS A 998 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   LEU A1000 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   CYS A 414 " --> pdb=" O   LEU A1000 " (cutoff:3.500A)
      removed outlier: 8.344A  pdb=" N   SER A1002 " --> pdb=" O   CYS A 414 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   THR A 997 " --> pdb=" O   ILE A1017 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   ILE A1019 " --> pdb=" O   THR A 997 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   CYS A 999 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   LEU A1021 " --> pdb=" O   CYS A 999 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLY A1001 " --> pdb=" O   LEU A1021 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   SER A1018 " --> pdb=" O   LEU A1065 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   PHE A1067 " --> pdb=" O   SER A1018 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1067 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 557
      removed outlier: 5.674A  pdb=" N   GLN A 821 " --> pdb=" O   CYS A 713 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   GLY A 825 " --> pdb=" O   TRP A 717 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 556 through 557
      removed outlier: 7.869A  pdb=" N   GLN A 821 " --> pdb=" O   PRO A 753 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   PHE A 823 " --> pdb=" O   TYR A 751 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   TYR A 751 " --> pdb=" O   PHE A 823 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   GLY A 825 " --> pdb=" O   PHE A 749 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   PHE A 749 " --> pdb=" O   GLY A 825 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LYS A 752 " --> pdb=" O   MET A 700 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   MET A 700 " --> pdb=" O   LYS A 752 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU A 688 " --> pdb=" O   LEU A 701 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   SER A 683 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   LYS A 691 " --> pdb=" O   GLN A 649 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   GLN A 649 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 10.399A  pdb=" N   LYS A 765 " --> pdb=" O   GLU A 650 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   HIS A 652 " --> pdb=" O   LYS A 765 " (cutoff:3.500A)
      removed outlier: 8.967A  pdb=" N   ILE A 767 " --> pdb=" O   HIS A 652 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ALA A 654 " --> pdb=" O   ILE A 767 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   LEU A 769 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   TYR A 656 " --> pdb=" O   LEU A 769 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 435 through 436
    Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 560
    Processing sheet with id=AA7, first strand: chain 'A' and resid 756 through 757

    459 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.62

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1603
        1.33 -     1.45: 2014
        1.45 -     1.58: 4862
        1.58 -     1.70: 2
        1.70 -     1.82: 85
  Bond restraints: 8566
  Sorted by residual:
  bond pdb=" C   LEU A1061 "
       pdb=" N   PRO A1062 "
    ideal  model  delta    sigma   weight residual
    1.331  1.350 -0.018 7.90e-03 1.60e+04 5.39e+00
  bond pdb=" C   PRO A1143 "
       pdb=" N   PRO A1144 "
    ideal  model  delta    sigma   weight residual
    1.329  1.356 -0.027 1.20e-02 6.94e+03 5.03e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.18e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.49e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.94e+00
  ... (remaining 8561 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.91: 11601
        4.91 -     9.81: 22
        9.81 -    14.72: 5
       14.72 -    19.63: 2
       19.63 -    24.54: 2
  Bond angle restraints: 11632
  Sorted by residual:
  angle pdb=" C   HIS A 240 "
        pdb=" CA  HIS A 240 "
        pdb=" CB  HIS A 240 "
      ideal   model   delta    sigma   weight residual
     110.42   85.88   24.54 1.99e+00 2.53e-01 1.52e+02
  angle pdb=" N   ARG A 241 "
        pdb=" CA  ARG A 241 "
        pdb=" CB  ARG A 241 "
      ideal   model   delta    sigma   weight residual
     110.49  129.56  -19.07 1.69e+00 3.50e-01 1.27e+02
  angle pdb=" N   ARG A 241 "
        pdb=" CA  ARG A 241 "
        pdb=" C   ARG A 241 "
      ideal   model   delta    sigma   weight residual
     110.80   88.88   21.92 2.13e+00 2.20e-01 1.06e+02
  angle pdb=" C   ARG A 241 "
        pdb=" CA  ARG A 241 "
        pdb=" CB  ARG A 241 "
      ideal   model   delta    sigma   weight residual
     110.42  126.05  -15.63 1.99e+00 2.53e-01 6.17e+01
  angle pdb=" C   GLN A 239 "
        pdb=" CA  GLN A 239 "
        pdb=" CB  GLN A 239 "
      ideal   model   delta    sigma   weight residual
     110.10  123.39  -13.29 1.90e+00 2.77e-01 4.90e+01
  ... (remaining 11627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.11: 4610
       21.11 -    42.22: 483
       42.22 -    63.33: 86
       63.33 -    84.44: 12
       84.44 -   105.54: 13
  Dihedral angle restraints: 5204
    sinusoidal: 2148
      harmonic: 3056
  Sorted by residual:
  dihedral pdb=" N   ARG A 241 "
           pdb=" C   ARG A 241 "
           pdb=" CA  ARG A 241 "
           pdb=" CB  ARG A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  140.68  -17.88     0      2.50e+00 1.60e-01 5.12e+01
  dihedral pdb=" C   HIS A 240 "
           pdb=" N   HIS A 240 "
           pdb=" CA  HIS A 240 "
           pdb=" CB  HIS A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -105.25  -17.35     0      2.50e+00 1.60e-01 4.82e+01
  dihedral pdb=" C   ARG A 241 "
           pdb=" N   ARG A 241 "
           pdb=" CA  ARG A 241 "
           pdb=" CB  ARG A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.36   15.76     0      2.50e+00 1.60e-01 3.97e+01
  ... (remaining 5201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.155: 1368
       0.155 -    0.309: 2
       0.309 -    0.464: 0
       0.464 -    0.619: 0
       0.619 -    0.773: 1
  Chirality restraints: 1371
  Sorted by residual:
  chirality pdb=" CA  ARG A 241 "
            pdb=" N   ARG A 241 "
            pdb=" C   ARG A 241 "
            pdb=" CB  ARG A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.74    0.77 2.00e-01 2.50e+01 1.50e+01
  chirality pdb=" CG  LEU A  79 "
            pdb=" CB  LEU A  79 "
            pdb=" CD1 LEU A  79 "
            pdb=" CD2 LEU A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  ASN A 876 "
            pdb=" N   ASN A 876 "
            pdb=" C   ASN A 876 "
            pdb=" CB  ASN A 876 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.20e-01
  ... (remaining 1368 not shown)

  Planarity restraints: 1447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A1142 "    0.042 5.00e-02 4.00e+02   6.38e-02 6.51e+00
        pdb=" N   PRO A1143 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A1143 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A1143 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 313 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.86e+00
        pdb=" C   THR A 313 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   THR A 313 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A 314 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 157 "   -0.036 5.00e-02 4.00e+02   5.41e-02 4.69e+00
        pdb=" N   PRO A 158 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 158 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 158 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1444 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1035
        2.75 -     3.29: 8032
        3.29 -     3.83: 13825
        3.83 -     4.36: 15569
        4.36 -     4.90: 27750
  Nonbonded interactions: 66211
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 557 "
            pdb=" OD2 ASP A 571 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" N   ARG A 241 "
            pdb=" O   ARG A 241 "
     model   vdw
     2.229 2.496
  nonbonded pdb=" OD1 ASP A 550 "
            pdb=" N   TYR A 551 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OG  SER A1120 "
            pdb=" OD2 ASP A1123 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   PHE A1012 "
            pdb=" OG  SER A1018 "
     model   vdw
     2.263 3.040
  ... (remaining 66206 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.060
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.570
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
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      :  0.002   0.041   8570  Z= 0.122
  Angle     :  0.759  24.536  11644  Z= 0.369
  Chirality :  0.044   0.773   1371
  Planarity :  0.004   0.064   1445
  Dihedral  : 17.586 105.545   3208
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 23.11 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.30 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.27), residues: 1033
  helix:  2.52 (0.22), residues: 519
  sheet: -0.42 (0.48), residues: 97
  loop :  0.14 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 129 
 TYR   0.008   0.001   TYR A 312 
 PHE   0.016   0.001   PHE A 434 
 TRP   0.007   0.001   TRP A  67 
 HIS   0.006   0.000   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8566)
  covalent geometry    : angle       0.75484 (11632)
  hydrogen bonds       : bond        0.23424 (  453)
  hydrogen bonds       : angle       6.24026 ( 1335)
  link_BETA1-4         : bond        0.00372 (    2)
  link_BETA1-4         : angle       2.16808 (    6)
  link_NAG-ASN         : bond        0.00144 (    2)
  link_NAG-ASN         : angle       2.93210 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8186 (tpp80)
REVERT: A  143 ARG cc_start: 0.8536 (ptm160) cc_final: 0.7743 (ptm-80)
REVERT: A  247 GLU cc_start: 0.8102 (tp30) cc_final: 0.7369 (tp30)
REVERT: A  378 MET cc_start: 0.7361 (tpp) cc_final: 0.7158 (tpt)
REVERT: A  628 TRP cc_start: 0.4051 (m100) cc_final: 0.3432 (m100)
REVERT: A  824 MET cc_start: 0.7216 (mpp) cc_final: 0.6040 (ttp)
REVERT: A  967 ASN cc_start: 0.8384 (p0) cc_final: 0.8024 (p0)
REVERT: A 1068 ARG cc_start: 0.6439 (ptm160) cc_final: 0.5776 (ptm-80)
REVERT: A 1307 LEU cc_start: 0.7832 (pp) cc_final: 0.7447 (mt)
REVERT: A 1335 ARG cc_start: 0.7209 (ttm-80) cc_final: 0.7000 (ttm-80)
  outliers start: 2
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1077
  time to fit residues: 15.4451
Evaluate side-chains
  73 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.0980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
A 311 GLN
A 588 ASN
A 821 GLN
A1345 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.151162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.098699 restraints weight = 11123.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 2.11
r_work: 0.3000 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   8570  Z= 0.266
  Angle     :  0.704   8.332  11644  Z= 0.351
  Chirality :  0.045   0.191   1371
  Planarity :  0.005   0.055   1445
  Dihedral  :  9.037  68.496   1242
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.55 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.27), residues: 1033
  helix:  2.34 (0.22), residues: 540
  sheet: -0.80 (0.51), residues: 97
  loop :  0.01 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 241 
 TYR   0.029   0.002   TYR A1132 
 PHE   0.018   0.002   PHE A1189 
 TRP   0.010   0.001   TRP A 717 
 HIS   0.011   0.001   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 ( 8566)
  covalent geometry    : angle       0.70023 (11632)
  hydrogen bonds       : bond        0.07034 (  453)
  hydrogen bonds       : angle       4.57405 ( 1335)
  link_BETA1-4         : bond        0.00262 (    2)
  link_BETA1-4         : angle       1.87182 (    6)
  link_NAG-ASN         : bond        0.00409 (    2)
  link_NAG-ASN         : angle       2.72460 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 76
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 MET cc_start: 0.8705 (tpp) cc_final: 0.8471 (tpt)
REVERT: A  628 TRP cc_start: 0.6034 (m100) cc_final: 0.5467 (m100)
REVERT: A  700 MET cc_start: 0.5111 (ppp) cc_final: 0.4845 (ppp)
REVERT: A  824 MET cc_start: 0.7340 (mpp) cc_final: 0.6510 (ttp)
  outliers start: 30
  outliers final: 11
  residues processed: 102
  average time/residue: 0.0880
  time to fit residues: 12.8965
Evaluate side-chains
  80 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  707 ASP
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1153 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 25 optimal weight:    0.0040
   chunk 76 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0060
   chunk 42 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    0.5210

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
A 240 HIS
A 588 ASN
** A 649 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 = 0.3855 r_free = 0.3855 target = 0.154708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.102943 restraints weight = 11016.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.12
r_work: 0.3062 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8570  Z= 0.118
  Angle     :  0.548   6.968  11644  Z= 0.270
  Chirality :  0.039   0.134   1371
  Planarity :  0.004   0.051   1445
  Dihedral  :  7.214  69.593   1242
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.02 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.27), residues: 1033
  helix:  2.50 (0.22), residues: 540
  sheet: -0.71 (0.57), residues: 87
  loop :  0.08 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 140 
 TYR   0.017   0.001   TYR A 737 
 PHE   0.011   0.001   PHE A 736 
 TRP   0.007   0.001   TRP A  67 
 HIS   0.010   0.001   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8566)
  covalent geometry    : angle       0.54423 (11632)
  hydrogen bonds       : bond        0.05357 (  453)
  hydrogen bonds       : angle       4.19668 ( 1335)
  link_BETA1-4         : bond        0.00425 (    2)
  link_BETA1-4         : angle       1.84327 (    6)
  link_NAG-ASN         : bond        0.00055 (    2)
  link_NAG-ASN         : angle       2.41069 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 GLU cc_start: 0.8361 (tp30) cc_final: 0.7913 (tp30)
REVERT: A  628 TRP cc_start: 0.5958 (m100) cc_final: 0.5432 (m100)
  outliers start: 22
  outliers final: 11
  residues processed: 90
  average time/residue: 0.0920
  time to fit residues: 11.9277
Evaluate side-chains
  75 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  707 ASP
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1340 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 42 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0970
   chunk 88 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
A 588 ASN
** A 649 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 = 0.3859 r_free = 0.3859 target = 0.154944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.103975 restraints weight = 11197.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.10
r_work: 0.3066 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8570  Z= 0.111
  Angle     :  0.520   6.083  11644  Z= 0.255
  Chirality :  0.038   0.133   1371
  Planarity :  0.004   0.051   1445
  Dihedral  :  6.680  70.817   1242
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.38 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.27), residues: 1033
  helix:  2.62 (0.22), residues: 540
  sheet: -0.84 (0.58), residues: 90
  loop :  0.08 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 140 
 TYR   0.013   0.001   TYR A 737 
 PHE   0.011   0.001   PHE A 736 
 TRP   0.009   0.001   TRP A 875 
 HIS   0.008   0.001   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8566)
  covalent geometry    : angle       0.51567 (11632)
  hydrogen bonds       : bond        0.04715 (  453)
  hydrogen bonds       : angle       4.02796 ( 1335)
  link_BETA1-4         : bond        0.00392 (    2)
  link_BETA1-4         : angle       2.00451 (    6)
  link_NAG-ASN         : bond        0.00150 (    2)
  link_NAG-ASN         : angle       2.33382 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.8420 (tp30) cc_final: 0.8136 (tp30)
REVERT: A  628 TRP cc_start: 0.5972 (m100) cc_final: 0.5255 (m100)
REVERT: A  824 MET cc_start: 0.7383 (mpp) cc_final: 0.7058 (mpp)
REVERT: A 1068 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7390 (ptm-80)
  outliers start: 30
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0927
  time to fit residues: 13.1280
Evaluate side-chains
  80 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  707 ASP
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1195 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0470
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 91 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
A 588 ASN
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1253 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.154427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.103312 restraints weight = 11004.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.08
r_work: 0.3059 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8570  Z= 0.119
  Angle     :  0.528   8.659  11644  Z= 0.258
  Chirality :  0.038   0.139   1371
  Planarity :  0.004   0.051   1445
  Dihedral  :  6.588  70.202   1242
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.81 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.27), residues: 1033
  helix:  2.68 (0.22), residues: 541
  sheet: -0.83 (0.58), residues: 90
  loop :  0.12 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 143 
 TYR   0.009   0.001   TYR A 312 
 PHE   0.009   0.001   PHE A1093 
 TRP   0.013   0.001   TRP A 875 
 HIS   0.007   0.001   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8566)
  covalent geometry    : angle       0.52350 (11632)
  hydrogen bonds       : bond        0.04684 (  453)
  hydrogen bonds       : angle       4.01964 ( 1335)
  link_BETA1-4         : bond        0.00320 (    2)
  link_BETA1-4         : angle       2.05085 (    6)
  link_NAG-ASN         : bond        0.00158 (    2)
  link_NAG-ASN         : angle       2.41609 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.8479 (tp30) cc_final: 0.8207 (tp30)
REVERT: A  628 TRP cc_start: 0.6012 (m100) cc_final: 0.5274 (m100)
REVERT: A  824 MET cc_start: 0.7424 (mpp) cc_final: 0.7082 (mpp)
REVERT: A 1068 ARG cc_start: 0.8171 (ptm160) cc_final: 0.7362 (ptm-80)
  outliers start: 26
  outliers final: 20
  residues processed: 94
  average time/residue: 0.0855
  time to fit residues: 11.8563
Evaluate side-chains
  89 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  707 ASP
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  875 TRP
Chi-restraints excluded: chain A residue 1050 SER
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1340 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:   30.0000
   chunk 43 optimal weight:    9.9990
   chunk 79 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 11 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 41 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
A 588 ASN
** A 649 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 = 0.3816 r_free = 0.3816 target = 0.151244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.100672 restraints weight = 11132.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.64
r_work: 0.2999 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8570  Z= 0.163
  Angle     :  0.551   9.493  11644  Z= 0.269
  Chirality :  0.039   0.147   1371
  Planarity :  0.004   0.050   1445
  Dihedral  :  6.600  68.872   1242
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.55 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.27), residues: 1033
  helix:  2.67 (0.22), residues: 540
  sheet: -0.81 (0.58), residues: 89
  loop :  0.11 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 140 
 TYR   0.009   0.001   TYR A 312 
 PHE   0.013   0.001   PHE A1187 
 TRP   0.013   0.001   TRP A 875 
 HIS   0.014   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8566)
  covalent geometry    : angle       0.54651 (11632)
  hydrogen bonds       : bond        0.05040 (  453)
  hydrogen bonds       : angle       4.07188 ( 1335)
  link_BETA1-4         : bond        0.00268 (    2)
  link_BETA1-4         : angle       1.93365 (    6)
  link_NAG-ASN         : bond        0.00283 (    2)
  link_NAG-ASN         : angle       2.59922 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  581 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7203 (p)
REVERT: A  628 TRP cc_start: 0.5972 (m100) cc_final: 0.5224 (m100)
REVERT: A  824 MET cc_start: 0.7544 (mpp) cc_final: 0.6602 (ttp)
REVERT: A 1068 ARG cc_start: 0.8114 (ptm160) cc_final: 0.7554 (ptm-80)
REVERT: A 1295 ASP cc_start: 0.8384 (t0) cc_final: 0.8074 (t0)
  outliers start: 28
  outliers final: 18
  residues processed: 92
  average time/residue: 0.0840
  time to fit residues: 11.4563
Evaluate side-chains
  87 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  875 TRP
Chi-restraints excluded: chain A residue 1050 SER
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1320 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
A 588 ASN
** A 649 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 = 0.3800 r_free = 0.3800 target = 0.149921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.098155 restraints weight = 11258.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 2.45
r_work: 0.2977 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8570  Z= 0.180
  Angle     :  0.571  10.345  11644  Z= 0.279
  Chirality :  0.040   0.150   1371
  Planarity :  0.004   0.048   1445
  Dihedral  :  6.798  70.383   1242
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.66 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.27), residues: 1033
  helix:  2.65 (0.22), residues: 534
  sheet: -0.85 (0.58), residues: 89
  loop :  0.04 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1254 
 TYR   0.009   0.001   TYR A 312 
 PHE   0.015   0.001   PHE A1187 
 TRP   0.013   0.001   TRP A 875 
 HIS   0.007   0.001   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 8566)
  covalent geometry    : angle       0.56592 (11632)
  hydrogen bonds       : bond        0.05332 (  453)
  hydrogen bonds       : angle       4.06862 ( 1335)
  link_BETA1-4         : bond        0.00154 (    2)
  link_BETA1-4         : angle       1.84272 (    6)
  link_NAG-ASN         : bond        0.00326 (    2)
  link_NAG-ASN         : angle       2.77807 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  581 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.7412 (p)
REVERT: A  628 TRP cc_start: 0.6067 (m100) cc_final: 0.5265 (m100)
REVERT: A  824 MET cc_start: 0.7586 (mpp) cc_final: 0.6650 (ttp)
REVERT: A 1295 ASP cc_start: 0.8428 (t0) cc_final: 0.8126 (t0)
  outliers start: 28
  outliers final: 17
  residues processed: 96
  average time/residue: 0.0785
  time to fit residues: 11.3309
Evaluate side-chains
  89 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  588 ASN
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  875 TRP
Chi-restraints excluded: chain A residue 1050 SER
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1320 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 102 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 30 optimal weight:    0.5980
   chunk 65 optimal weight:    0.3980
   chunk 93 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 588 ASN
** A 649 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 = 0.3822 r_free = 0.3822 target = 0.151823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.100350 restraints weight = 11070.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.62
r_work: 0.3007 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8570  Z= 0.120
  Angle     :  0.542  12.478  11644  Z= 0.262
  Chirality :  0.039   0.158   1371
  Planarity :  0.004   0.048   1445
  Dihedral  :  6.704  70.724   1242
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 21.51 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.27), residues: 1033
  helix:  2.73 (0.22), residues: 534
  sheet: -0.88 (0.58), residues: 89
  loop :  0.05 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1068 
 TYR   0.010   0.001   TYR A 312 
 PHE   0.010   0.001   PHE A1187 
 TRP   0.012   0.001   TRP A 875 
 HIS   0.007   0.001   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8566)
  covalent geometry    : angle       0.53758 (11632)
  hydrogen bonds       : bond        0.04818 (  453)
  hydrogen bonds       : angle       3.99342 ( 1335)
  link_BETA1-4         : bond        0.00220 (    2)
  link_BETA1-4         : angle       1.92746 (    6)
  link_NAG-ASN         : bond        0.00106 (    2)
  link_NAG-ASN         : angle       2.59364 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  581 SER cc_start: 0.7809 (OUTLIER) cc_final: 0.7401 (p)
REVERT: A  628 TRP cc_start: 0.6041 (m100) cc_final: 0.5263 (m100)
REVERT: A  705 THR cc_start: 0.6603 (m) cc_final: 0.6355 (m)
REVERT: A  824 MET cc_start: 0.7601 (mpp) cc_final: 0.6588 (ttp)
REVERT: A 1068 ARG cc_start: 0.7852 (ptm-80) cc_final: 0.6777 (ptm-80)
REVERT: A 1295 ASP cc_start: 0.8377 (t0) cc_final: 0.8077 (t0)
  outliers start: 23
  outliers final: 19
  residues processed: 91
  average time/residue: 0.0808
  time to fit residues: 11.0008
Evaluate side-chains
  91 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  875 TRP
Chi-restraints excluded: chain A residue 1050 SER
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1151 MET
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1320 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 69 optimal weight:    0.4980
   chunk 55 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
A 588 ASN
** A 649 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 = 0.3817 r_free = 0.3817 target = 0.151304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.099146 restraints weight = 11127.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.16
r_work: 0.3004 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8570  Z= 0.136
  Angle     :  0.561  11.301  11644  Z= 0.269
  Chirality :  0.039   0.200   1371
  Planarity :  0.004   0.049   1445
  Dihedral  :  6.706  70.213   1242
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.73 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.27), residues: 1033
  helix:  2.72 (0.22), residues: 534
  sheet: -0.93 (0.57), residues: 91
  loop :  0.06 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1068 
 TYR   0.019   0.001   TYR A 737 
 PHE   0.013   0.001   PHE A1187 
 TRP   0.013   0.001   TRP A 875 
 HIS   0.007   0.001   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8566)
  covalent geometry    : angle       0.55625 (11632)
  hydrogen bonds       : bond        0.04817 (  453)
  hydrogen bonds       : angle       3.96822 ( 1335)
  link_BETA1-4         : bond        0.00248 (    2)
  link_BETA1-4         : angle       1.89078 (    6)
  link_NAG-ASN         : bond        0.00137 (    2)
  link_NAG-ASN         : angle       2.54234 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  581 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7559 (p)
REVERT: A  628 TRP cc_start: 0.6059 (m100) cc_final: 0.5343 (m100)
REVERT: A  824 MET cc_start: 0.7622 (mpp) cc_final: 0.6628 (ttp)
REVERT: A 1295 ASP cc_start: 0.8413 (t0) cc_final: 0.8124 (t0)
REVERT: A 1345 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8545 (tm-30)
  outliers start: 24
  outliers final: 18
  residues processed: 94
  average time/residue: 0.0815
  time to fit residues: 10.9979
Evaluate side-chains
  90 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  875 TRP
Chi-restraints excluded: chain A residue 1050 SER
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1320 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 70 optimal weight:    0.0980
   chunk 48 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0670
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
A 588 ASN
** A 649 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 = 0.3834 r_free = 0.3834 target = 0.152876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.100599 restraints weight = 11129.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.17
r_work: 0.3028 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8570  Z= 0.118
  Angle     :  0.563  11.616  11644  Z= 0.271
  Chirality :  0.039   0.202   1371
  Planarity :  0.004   0.048   1445
  Dihedral  :  6.578  70.980   1242
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.83 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.27), residues: 1033
  helix:  2.80 (0.22), residues: 533
  sheet: -0.96 (0.57), residues: 91
  loop :  0.06 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 140 
 TYR   0.018   0.001   TYR A 737 
 PHE   0.010   0.001   PHE A 736 
 TRP   0.012   0.001   TRP A 875 
 HIS   0.007   0.000   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8566)
  covalent geometry    : angle       0.55878 (11632)
  hydrogen bonds       : bond        0.04515 (  453)
  hydrogen bonds       : angle       3.91563 ( 1335)
  link_BETA1-4         : bond        0.00211 (    2)
  link_BETA1-4         : angle       1.92945 (    6)
  link_NAG-ASN         : bond        0.00032 (    2)
  link_NAG-ASN         : angle       2.45420 (    6)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A  581 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7526 (p)
REVERT: A  628 TRP cc_start: 0.5956 (m100) cc_final: 0.5199 (m100)
REVERT: A  824 MET cc_start: 0.7654 (mpp) cc_final: 0.6625 (ttp)
REVERT: A 1068 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7773 (ptm-80)
REVERT: A 1295 ASP cc_start: 0.8372 (t0) cc_final: 0.8073 (t0)
REVERT: A 1345 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8499 (tm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 92
  average time/residue: 0.0828
  time to fit residues: 11.3582
Evaluate side-chains
  90 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  588 ASN
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  875 TRP
Chi-restraints excluded: chain A residue 1050 SER
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1195 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 92 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 102 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
A 588 ASN
** A 649 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 = 0.3831 r_free = 0.3831 target = 0.152614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.101089 restraints weight = 11107.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.50
r_work: 0.3032 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8570  Z= 0.126
  Angle     :  0.568  10.987  11644  Z= 0.272
  Chirality :  0.039   0.206   1371
  Planarity :  0.004   0.048   1445
  Dihedral  :  6.564  70.914   1242
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.83 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.27), residues: 1033
  helix:  2.76 (0.22), residues: 534
  sheet: -0.96 (0.57), residues: 91
  loop :  0.08 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 140 
 TYR   0.016   0.001   TYR A 737 
 PHE   0.011   0.001   PHE A1187 
 TRP   0.013   0.001   TRP A 875 
 HIS   0.006   0.001   HIS A1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8566)
  covalent geometry    : angle       0.56369 (11632)
  hydrogen bonds       : bond        0.04565 (  453)
  hydrogen bonds       : angle       3.91136 ( 1335)
  link_BETA1-4         : bond        0.00264 (    2)
  link_BETA1-4         : angle       1.91212 (    6)
  link_NAG-ASN         : bond        0.00076 (    2)
  link_NAG-ASN         : angle       2.46157 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2669.44 seconds
wall clock time: 46 minutes 30.37 seconds (2790.37 seconds total)