Starting phenix.real_space_refine
on Sat Jul 26 10:17:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jjo_61534/07_2025/9jjo_61534.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jjo_61534/07_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_61534/07_2025/9jjo_61534.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jjo_61534/07_2025/9jjo_61534.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jjo_61534/07_2025/9jjo_61534.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jjo_61534/07_2025/9jjo_61534.cif"
  }
  resolution = 3.24
  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=   0.041
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.67, per 1000 atoms: 0.68
  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: 2.17
  Conformation dependent library (CDL) restraints added in 949.3 milliseconds
  

  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: 0.93
  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: 3.01

  Time building geometry restraints manager: 2.58 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:             2.870
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     23.050
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.510
-------------------------------------------------------------------------------
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 (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:  1.91 (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
 TRP   0.007   0.001   TRP A  67 
 HIS   0.006   0.000   HIS A1084 
 PHE   0.016   0.001   PHE A 434 
 TYR   0.008   0.001   TYR A 312 
 ARG   0.004   0.000   ARG A 129 

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

*********************** 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  : 0.966 
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: 0.2255
  time to fit residues: 32.4784
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  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 95 optimal weight:    0.8980
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 821 GLN
A1345 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.152761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.100831 restraints weight = 11001.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 2.14
r_work: 0.3044 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8570  Z= 0.191
  Angle     :  0.642   8.421  11644  Z= 0.318
  Chirality :  0.042   0.188   1371
  Planarity :  0.005   0.054   1445
  Dihedral  :  8.892  71.288   1242
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.77 %
    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 (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:  1.87 (0.27), residues: 1033
  helix:  2.49 (0.22), residues: 540
  sheet: -0.73 (0.52), residues: 97
  loop :  0.05 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 717 
 HIS   0.011   0.001   HIS A1084 
 PHE   0.014   0.002   PHE A1189 
 TYR   0.024   0.002   TYR A1132 
 ARG   0.005   0.000   ARG A 241 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00308 (    2)
  link_NAG-ASN         : angle       2.49372 (    6)
  link_BETA1-4         : bond        0.00085 (    2)
  link_BETA1-4         : angle       1.71712 (    6)
  hydrogen bonds       : bond        0.06630 (  453)
  hydrogen bonds       : angle       4.49576 ( 1335)
  covalent geometry    : bond        0.00453 ( 8566)
  covalent geometry    : angle       0.63889 (11632)

*********************** 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
  103 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 75
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ARG cc_start: 0.8389 (ptm160) cc_final: 0.8053 (ptm-80)
REVERT: A  240 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6501 (m-70)
REVERT: A  378 MET cc_start: 0.8749 (tpp) cc_final: 0.8510 (tpt)
REVERT: A  628 TRP cc_start: 0.5898 (m100) cc_final: 0.5344 (m100)
REVERT: A  824 MET cc_start: 0.7311 (mpp) cc_final: 0.6431 (ttp)
REVERT: A  967 ASN cc_start: 0.8958 (p0) cc_final: 0.8689 (p0)
REVERT: A 1068 ARG cc_start: 0.8173 (ptm160) cc_final: 0.7615 (ptm-80)
  outliers start: 28
  outliers final: 13
  residues processed: 98
  average time/residue: 0.1882
  time to fit residues: 26.5146
Evaluate side-chains
  82 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
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  240 HIS
Chi-restraints excluded: chain A residue  322 VAL
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  855 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1131 CYS
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 2 optimal weight:    0.7980
   chunk 97 optimal weight:    0.4980
   chunk 93 optimal weight:    0.5980
   chunk 53 optimal weight:    0.2980
   chunk 43 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3864 r_free = 0.3864 target = 0.155624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.103808 restraints weight = 11091.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.12
r_work: 0.3072 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8570  Z= 0.120
  Angle     :  0.547   6.885  11644  Z= 0.269
  Chirality :  0.038   0.134   1371
  Planarity :  0.004   0.051   1445
  Dihedral  :  7.168  71.420   1242
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.55 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.00 (0.27), residues: 1033
  helix:  2.60 (0.22), residues: 539
  sheet: -0.68 (0.58), residues: 87
  loop :  0.08 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  67 
 HIS   0.009   0.001   HIS A1084 
 PHE   0.011   0.001   PHE A 736 
 TYR   0.015   0.001   TYR A 737 
 ARG   0.005   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00071 (    2)
  link_NAG-ASN         : angle       2.37025 (    6)
  link_BETA1-4         : bond        0.00395 (    2)
  link_BETA1-4         : angle       1.82533 (    6)
  hydrogen bonds       : bond        0.05373 (  453)
  hydrogen bonds       : angle       4.16598 ( 1335)
  covalent geometry    : bond        0.00258 ( 8566)
  covalent geometry    : angle       0.54320 (11632)

*********************** 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  : 0.890 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ARG cc_start: 0.8389 (ptm160) cc_final: 0.8075 (ptm-80)
REVERT: A  247 GLU cc_start: 0.8361 (tp30) cc_final: 0.7892 (tp30)
REVERT: A  378 MET cc_start: 0.8718 (tpp) cc_final: 0.8490 (tpt)
REVERT: A  628 TRP cc_start: 0.5860 (m100) cc_final: 0.5194 (m100)
REVERT: A  754 MET cc_start: 0.4457 (mtm) cc_final: 0.3840 (mtt)
REVERT: A  824 MET cc_start: 0.7300 (mpp) cc_final: 0.6954 (mpp)
REVERT: A  967 ASN cc_start: 0.8973 (p0) cc_final: 0.8730 (p0)
  outliers start: 22
  outliers final: 10
  residues processed: 90
  average time/residue: 0.1891
  time to fit residues: 24.4872
Evaluate side-chains
  78 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 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  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 7 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 88 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0000
   chunk 27 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.1188

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.152762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.101746 restraints weight = 11034.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.07
r_work: 0.3020 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.2195

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= 0.170
  Angle     :  0.566   7.381  11644  Z= 0.280
  Chirality :  0.040   0.149   1371
  Planarity :  0.004   0.049   1445
  Dihedral  :  6.906  68.842   1242
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.96 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.94 (0.27), residues: 1033
  helix:  2.63 (0.22), residues: 534
  sheet: -0.90 (0.55), residues: 99
  loop :  0.05 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 875 
 HIS   0.008   0.001   HIS A1084 
 PHE   0.013   0.001   PHE A1187 
 TYR   0.014   0.001   TYR A1132 
 ARG   0.004   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00306 (    2)
  link_NAG-ASN         : angle       2.57299 (    6)
  link_BETA1-4         : bond        0.00286 (    2)
  link_BETA1-4         : angle       1.95136 (    6)
  hydrogen bonds       : bond        0.05468 (  453)
  hydrogen bonds       : angle       4.14562 ( 1335)
  covalent geometry    : bond        0.00412 ( 8566)
  covalent geometry    : angle       0.56160 (11632)

*********************** 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
  102 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 71
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8403 (mtt90) cc_final: 0.7973 (mtt-85)
REVERT: A  628 TRP cc_start: 0.6070 (m100) cc_final: 0.5348 (m100)
REVERT: A  754 MET cc_start: 0.4545 (mtm) cc_final: 0.3636 (mtm)
REVERT: A  824 MET cc_start: 0.7413 (mpp) cc_final: 0.7074 (mpp)
REVERT: A  967 ASN cc_start: 0.8944 (p0) cc_final: 0.8654 (p0)
REVERT: A 1295 ASP cc_start: 0.8302 (t0) cc_final: 0.8033 (t0)
  outliers start: 31
  outliers final: 15
  residues processed: 100
  average time/residue: 0.2145
  time to fit residues: 30.1707
Evaluate side-chains
  84 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
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  333 LEU
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  747 SER
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 70 optimal weight:    0.0020
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 49 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.0994

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.151062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.100316 restraints weight = 11032.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.65
r_work: 0.2992 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8570  Z= 0.158
  Angle     :  0.554   8.695  11644  Z= 0.274
  Chirality :  0.040   0.143   1371
  Planarity :  0.004   0.050   1445
  Dihedral  :  6.793  67.774   1242
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.34 %
    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 (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:  1.97 (0.27), residues: 1033
  helix:  2.67 (0.22), residues: 533
  sheet: -0.93 (0.54), residues: 99
  loop :  0.07 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 875 
 HIS   0.008   0.001   HIS A1084 
 PHE   0.011   0.001   PHE A1187 
 TYR   0.010   0.001   TYR A 312 
 ARG   0.004   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00263 (    2)
  link_NAG-ASN         : angle       2.61383 (    6)
  link_BETA1-4         : bond        0.00249 (    2)
  link_BETA1-4         : angle       1.93331 (    6)
  hydrogen bonds       : bond        0.05245 (  453)
  hydrogen bonds       : angle       4.10111 ( 1335)
  covalent geometry    : bond        0.00383 ( 8566)
  covalent geometry    : angle       0.54942 (11632)

*********************** 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
  101 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 70
  time to evaluate  : 1.467 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8341 (mtt90) cc_final: 0.7791 (mtt-85)
REVERT: A  247 GLU cc_start: 0.8649 (tp30) cc_final: 0.8411 (tp30)
REVERT: A  581 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7190 (p)
REVERT: A  628 TRP cc_start: 0.5958 (m100) cc_final: 0.5199 (m100)
REVERT: A  700 MET cc_start: 0.4622 (ppp) cc_final: 0.4193 (ppp)
REVERT: A  754 MET cc_start: 0.4669 (mtm) cc_final: 0.3442 (mtt)
REVERT: A  824 MET cc_start: 0.7521 (mpp) cc_final: 0.6591 (ttp)
REVERT: A  963 GLN cc_start: 0.8742 (mm110) cc_final: 0.8448 (mt0)
REVERT: A  967 ASN cc_start: 0.9061 (p0) cc_final: 0.8785 (p0)
REVERT: A 1068 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7518 (ptm-80)
REVERT: A 1295 ASP cc_start: 0.8339 (t0) cc_final: 0.8049 (t0)
  outliers start: 31
  outliers final: 15
  residues processed: 97
  average time/residue: 0.1922
  time to fit residues: 26.7600
Evaluate side-chains
  85 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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  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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 97 optimal weight:    0.0870
   chunk 60 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 93 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0050
   chunk 88 optimal weight:    1.9990
   chunk 69 optimal weight:    0.2980
   overall best weight:    0.3772

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3846 r_free = 0.3846 target = 0.153916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.102896 restraints weight = 11053.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.66
r_work: 0.3033 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8570  Z= 0.105
  Angle     :  0.519  10.310  11644  Z= 0.253
  Chirality :  0.038   0.136   1371
  Planarity :  0.004   0.050   1445
  Dihedral  :  6.508  68.748   1242
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 21.19 %
    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 (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:  2.10 (0.27), residues: 1033
  helix:  2.78 (0.22), residues: 534
  sheet: -0.95 (0.57), residues: 89
  loop :  0.11 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 875 
 HIS   0.007   0.000   HIS A1084 
 PHE   0.011   0.001   PHE A 736 
 TYR   0.010   0.001   TYR A 312 
 ARG   0.003   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00055 (    2)
  link_NAG-ASN         : angle       2.37324 (    6)
  link_BETA1-4         : bond        0.00329 (    2)
  link_BETA1-4         : angle       1.96110 (    6)
  hydrogen bonds       : bond        0.04411 (  453)
  hydrogen bonds       : angle       3.95602 ( 1335)
  covalent geometry    : bond        0.00225 ( 8566)
  covalent geometry    : angle       0.51413 (11632)

*********************** 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
  97 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: A  247 GLU cc_start: 0.8644 (tp30) cc_final: 0.8291 (tp30)
REVERT: A  581 SER cc_start: 0.7813 (OUTLIER) cc_final: 0.7405 (p)
REVERT: A  628 TRP cc_start: 0.5948 (m100) cc_final: 0.5176 (m100)
REVERT: A  700 MET cc_start: 0.4985 (ppp) cc_final: 0.4748 (ppp)
REVERT: A  754 MET cc_start: 0.4792 (mtm) cc_final: 0.3822 (mtt)
REVERT: A  824 MET cc_start: 0.7457 (mpp) cc_final: 0.6596 (ttm)
REVERT: A  963 GLN cc_start: 0.8735 (mm110) cc_final: 0.8470 (mt0)
REVERT: A  967 ASN cc_start: 0.9061 (p0) cc_final: 0.8808 (p0)
REVERT: A 1068 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7181 (ptm-80)
REVERT: A 1125 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8823 (mm)
REVERT: A 1295 ASP cc_start: 0.8351 (t0) cc_final: 0.8059 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 93
  average time/residue: 0.2381
  time to fit residues: 33.2244
Evaluate side-chains
  84 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
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  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 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1125 LEU
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1195 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 48 optimal weight:   20.0000
   overall best weight:    0.6980

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

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

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 = 0.152547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.101777 restraints weight = 11153.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.70
r_work: 0.3023 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2546

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= 0.123
  Angle     :  0.534  11.521  11644  Z= 0.258
  Chirality :  0.038   0.139   1371
  Planarity :  0.004   0.049   1445
  Dihedral  :  6.460  68.594   1242
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 21.30 %
    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 (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:  2.13 (0.27), residues: 1033
  helix:  2.80 (0.22), residues: 534
  sheet: -0.90 (0.58), residues: 89
  loop :  0.13 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 875 
 HIS   0.006   0.001   HIS A1084 
 PHE   0.010   0.001   PHE A1187 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.006   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00148 (    2)
  link_NAG-ASN         : angle       2.49419 (    6)
  link_BETA1-4         : bond        0.00287 (    2)
  link_BETA1-4         : angle       1.95026 (    6)
  hydrogen bonds       : bond        0.04575 (  453)
  hydrogen bonds       : angle       3.94401 ( 1335)
  covalent geometry    : bond        0.00287 ( 8566)
  covalent geometry    : angle       0.52961 (11632)

*********************** 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
  95 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
REVERT: A  430 GLU cc_start: 0.7727 (tt0) cc_final: 0.7503 (tt0)
REVERT: A  581 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7403 (p)
REVERT: A  628 TRP cc_start: 0.5935 (m100) cc_final: 0.5160 (m100)
REVERT: A  754 MET cc_start: 0.4765 (mtm) cc_final: 0.3941 (mtt)
REVERT: A  824 MET cc_start: 0.7540 (mpp) cc_final: 0.6651 (ttm)
REVERT: A  963 GLN cc_start: 0.8718 (mm110) cc_final: 0.8454 (mt0)
REVERT: A  967 ASN cc_start: 0.9065 (p0) cc_final: 0.8815 (p0)
REVERT: A 1068 ARG cc_start: 0.8068 (ptm160) cc_final: 0.7529 (ptm-80)
REVERT: A 1295 ASP cc_start: 0.8373 (t0) cc_final: 0.8074 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 90
  average time/residue: 0.2204
  time to fit residues: 29.4635
Evaluate side-chains
  88 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
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  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  588 ASN
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  875 TRP
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 46 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 41 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3828 r_free = 0.3828 target = 0.152187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.099722 restraints weight = 11123.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.22
r_work: 0.3017 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8570  Z= 0.134
  Angle     :  0.547  12.362  11644  Z= 0.264
  Chirality :  0.039   0.164   1371
  Planarity :  0.004   0.048   1445
  Dihedral  :  6.486  70.141   1242
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.19 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.13 (0.27), residues: 1033
  helix:  2.81 (0.22), residues: 534
  sheet: -0.91 (0.58), residues: 89
  loop :  0.11 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 875 
 HIS   0.006   0.001   HIS A1084 
 PHE   0.011   0.001   PHE A1187 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.006   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00145 (    2)
  link_NAG-ASN         : angle       2.52660 (    6)
  link_BETA1-4         : bond        0.00218 (    2)
  link_BETA1-4         : angle       1.89565 (    6)
  hydrogen bonds       : bond        0.04664 (  453)
  hydrogen bonds       : angle       3.95166 ( 1335)
  covalent geometry    : bond        0.00319 ( 8566)
  covalent geometry    : angle       0.54298 (11632)

*********************** 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
  94 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 1.385 
Fit side-chains
   revert: symmetry clash
REVERT: A  581 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7399 (p)
REVERT: A  628 TRP cc_start: 0.5916 (m100) cc_final: 0.5131 (m100)
REVERT: A  824 MET cc_start: 0.7559 (mpp) cc_final: 0.6661 (ttm)
REVERT: A  963 GLN cc_start: 0.8732 (mm110) cc_final: 0.8423 (mt0)
REVERT: A  967 ASN cc_start: 0.9076 (p0) cc_final: 0.8836 (p0)
REVERT: A 1068 ARG cc_start: 0.8023 (ptm160) cc_final: 0.7474 (ptm-80)
REVERT: A 1295 ASP cc_start: 0.8389 (t0) cc_final: 0.8081 (t0)
REVERT: A 1345 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8464 (tm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 89
  average time/residue: 0.2978
  time to fit residues: 38.4328
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  : 1.033 
-------------------------------------------------------------------------------
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  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  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 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1151 MET
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1195 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 73 optimal weight:    0.1980
   chunk 39 optimal weight:    0.0470
   chunk 99 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0770
   chunk 77 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3851 r_free = 0.3851 target = 0.154227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.101720 restraints weight = 11181.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.23
r_work: 0.3046 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8570  Z= 0.103
  Angle     :  0.530  11.776  11644  Z= 0.253
  Chirality :  0.038   0.214   1371
  Planarity :  0.004   0.049   1445
  Dihedral  :  6.364  72.656   1242
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.51 %
    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 (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:  2.20 (0.27), residues: 1033
  helix:  2.88 (0.22), residues: 534
  sheet: -0.93 (0.57), residues: 91
  loop :  0.14 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 875 
 HIS   0.007   0.000   HIS A1084 
 PHE   0.009   0.001   PHE A 736 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.006   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00029 (    2)
  link_NAG-ASN         : angle       2.37393 (    6)
  link_BETA1-4         : bond        0.00467 (    2)
  link_BETA1-4         : angle       1.97376 (    6)
  hydrogen bonds       : bond        0.04187 (  453)
  hydrogen bonds       : angle       3.88030 ( 1335)
  covalent geometry    : bond        0.00225 ( 8566)
  covalent geometry    : angle       0.52555 (11632)

*********************** 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
  92 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: A  581 SER cc_start: 0.7769 (OUTLIER) cc_final: 0.7344 (p)
REVERT: A  628 TRP cc_start: 0.5857 (m100) cc_final: 0.5134 (m100)
REVERT: A  824 MET cc_start: 0.7581 (mpp) cc_final: 0.6549 (ttp)
REVERT: A  967 ASN cc_start: 0.9073 (p0) cc_final: 0.8857 (p0)
REVERT: A 1068 ARG cc_start: 0.8058 (ptm160) cc_final: 0.7515 (ptm-80)
REVERT: A 1295 ASP cc_start: 0.8344 (t0) cc_final: 0.8041 (t0)
REVERT: A 1345 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8509 (tm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 88
  average time/residue: 0.2391
  time to fit residues: 30.5976
Evaluate side-chains
  88 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
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  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  588 ASN
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 1073 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1151 MET
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 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 104 optimal weight:    5.9990
   chunk 99 optimal weight:    0.0470
   chunk 86 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 12 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0070
   chunk 55 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0050
   overall best weight:    0.1988

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3856 r_free = 0.3856 target = 0.154953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.102568 restraints weight = 11032.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.22
r_work: 0.3060 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8570  Z= 0.100
  Angle     :  0.533  11.465  11644  Z= 0.253
  Chirality :  0.038   0.257   1371
  Planarity :  0.004   0.049   1445
  Dihedral  :  6.393  73.376   1242
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 21.62 %
    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 (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:  2.17 (0.27), residues: 1033
  helix:  2.83 (0.22), residues: 537
  sheet: -0.92 (0.56), residues: 94
  loop :  0.14 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 875 
 HIS   0.006   0.000   HIS A1084 
 PHE   0.009   0.001   PHE A 736 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.005   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00026 (    2)
  link_NAG-ASN         : angle       2.33768 (    6)
  link_BETA1-4         : bond        0.00371 (    2)
  link_BETA1-4         : angle       1.91614 (    6)
  hydrogen bonds       : bond        0.04064 (  453)
  hydrogen bonds       : angle       3.86085 ( 1335)
  covalent geometry    : bond        0.00208 ( 8566)
  covalent geometry    : angle       0.52863 (11632)

********************** 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
  90 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  581 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7322 (p)
REVERT: A  628 TRP cc_start: 0.5831 (m100) cc_final: 0.5121 (m100)
REVERT: A  824 MET cc_start: 0.7578 (mpp) cc_final: 0.6536 (ttp)
REVERT: A  967 ASN cc_start: 0.9064 (p0) cc_final: 0.8857 (p0)
REVERT: A 1068 ARG cc_start: 0.8035 (ptm160) cc_final: 0.7121 (ptm-80)
REVERT: A 1295 ASP cc_start: 0.8329 (t0) cc_final: 0.8026 (t0)
REVERT: A 1345 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8516 (tm-30)
  outliers start: 20
  outliers final: 17
  residues processed: 86
  average time/residue: 0.3164
  time to fit residues: 39.9929
Evaluate side-chains
  88 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
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  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  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 1073 ILE
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1151 MET
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 82 optimal weight:    0.0470
   chunk 90 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 75 optimal weight:    0.1980
   chunk 104 optimal weight:    0.9980
   chunk 6 optimal weight:    0.3980
   chunk 51 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3849 r_free = 0.3849 target = 0.154291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.101849 restraints weight = 11121.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.22
r_work: 0.3045 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8570  Z= 0.106
  Angle     :  0.543  13.948  11644  Z= 0.256
  Chirality :  0.038   0.232   1371
  Planarity :  0.004   0.049   1445
  Dihedral  :  6.313  73.747   1242
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 21.62 %
    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 (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:  2.18 (0.27), residues: 1033
  helix:  2.83 (0.22), residues: 537
  sheet: -0.89 (0.56), residues: 94
  loop :  0.15 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 875 
 HIS   0.006   0.000   HIS A1084 
 PHE   0.010   0.001   PHE A1187 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.005   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00060 (    2)
  link_NAG-ASN         : angle       2.34274 (    6)
  link_BETA1-4         : bond        0.00346 (    2)
  link_BETA1-4         : angle       1.88589 (    6)
  hydrogen bonds       : bond        0.04141 (  453)
  hydrogen bonds       : angle       3.84021 ( 1335)
  covalent geometry    : bond        0.00237 ( 8566)
  covalent geometry    : angle       0.53906 (11632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6974.64 seconds
wall clock time: 126 minutes 51.51 seconds (7611.51 seconds total)