Starting phenix.real_space_refine
on Wed Mar  4 04:08:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ky9_23072/03_2026/7ky9_23072.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ky9_23072/03_2026/7ky9_23072.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ky9_23072/03_2026/7ky9_23072.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ky9_23072/03_2026/7ky9_23072.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ky9_23072/03_2026/7ky9_23072.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ky9_23072/03_2026/7ky9_23072.map"
  }
  resolution = 4.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       2      5.49       5
     Mg      2      5.21       5
     S      53      5.16       5
     C    6646      2.51       5
     N    1690      2.21       5
     O    1956      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10354
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 7229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 910, 7229
          Classifications: {'peptide': 910}
          Link IDs: {'PTRANS': 25, 'TRANS': 884}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2959
          Classifications: {'peptide': 365}
          Link IDs: {'PTRANS': 19, 'TRANS': 345}
    Chain: "C"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 51
          Unusual residues: {'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      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: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'MAN': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.41, per 1000 atoms: 0.23
  Number of scatterers: 10354
  At special positions: 0
  Unit cell: (129.682, 114.814, 130.508, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      53     16.00
     P       2     15.00
     Al      1     13.00
     Mg      2     11.99
     F       4      9.00
     O    1956      8.00
     N    1690      7.00
     C    6646      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 110 " - pdb=" SG  CYS B 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 216 " - pdb=" SG  CYS B 231 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Links applied
    ALPHA1-4
      " NAG C   2 " - " MAN C   3 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG B1001 " - " ASN B 298 "
      " NAG C   1 " - " ASN B 240 "
      " NAG D   1 " - " ASN B 256 "
      " NAG E   1 " - " ASN B 332 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 496.0 milliseconds
  

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2384

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 7 sheets defined
      51.5% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 282 through 301
      removed outlier: 3.600A  pdb=" N   SER A 301 " --> pdb=" O   GLY A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 619
      removed outlier: 3.682A  pdb=" N   ARG A 592 " --> pdb=" O   SER A 588 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   VAL A 615 " --> pdb=" O   THR A 611 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLY A 617 " --> pdb=" O   GLY A 613 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   TYR A 619 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 654
    Processing helix  chain 'A' and resid 661 through 679
      removed outlier: 5.005A  pdb=" N   GLU A 667 " --> pdb=" O   TYR A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 684
    Processing helix  chain 'A' and resid 700 through 705
      removed outlier: 3.694A  pdb=" N   GLY A 704 " --> pdb=" O   ASP A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 749
    Processing helix  chain 'A' and resid 754 through 779
      removed outlier: 3.511A  pdb=" N   SER A 779 " --> pdb=" O   LEU A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 799
      removed outlier: 3.873A  pdb=" N   VAL A 797 " --> pdb=" O   SER A 793 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU A 798 " --> pdb=" O   LYS A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 821
    Processing helix  chain 'A' and resid 843 through 857
    Processing helix  chain 'A' and resid 918 through 925
      removed outlier: 4.200A  pdb=" N   ARG A 925 " --> pdb=" O   VAL A 921 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 949
    Processing helix  chain 'A' and resid 962 through 977
    Processing helix  chain 'A' and resid 983 through 995
    Processing helix  chain 'A' and resid 1013 through 1024
      removed outlier: 3.796A  pdb=" N   SER A1017 " --> pdb=" O   GLY A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1046
    Processing helix  chain 'A' and resid 1063 through 1069
      removed outlier: 4.038A  pdb=" N   GLU A1067 " --> pdb=" O   GLU A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1087
      removed outlier: 3.930A  pdb=" N   VAL A1075 " --> pdb=" O   ASP A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1104
    Processing helix  chain 'A' and resid 1116 through 1124
      removed outlier: 3.782A  pdb=" N   LEU A1124 " --> pdb=" O   LEU A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1137
    Processing helix  chain 'A' and resid 1149 through 1163
    Processing helix  chain 'A' and resid 1177 through 1183
    Processing helix  chain 'A' and resid 1193 through 1200
      removed outlier: 3.792A  pdb=" N   GLN A1197 " --> pdb=" O   GLU A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1208 through 1210
      No H-bonds generated for 'chain 'A' and resid 1208 through 1210'
    Processing helix  chain 'A' and resid 1211 through 1218
      removed outlier: 3.505A  pdb=" N   LEU A1217 " --> pdb=" O   THR A1213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1218 through 1249
      Proline residue:  A1232  - end of helix
      removed outlier: 3.712A  pdb=" N   VAL A1239 " --> pdb=" O   PHE A1235 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ILE A1240 " --> pdb=" O   TYR A1236 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   PHE A1241 " --> pdb=" O   LYS A1237 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   THR A1242 " --> pdb=" O   ASN A1238 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU A1245 " --> pdb=" O   PHE A1241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1255
      removed outlier: 4.622A  pdb=" N   ASN A1253 " --> pdb=" O   ILE A1250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1263 through 1271
      removed outlier: 3.775A  pdb=" N   PHE A1267 " --> pdb=" O   THR A1263 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   TYR A1268 " --> pdb=" O   TYR A1264 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   ASN A1269 " --> pdb=" O   LEU A1265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1274 through 1283
      removed outlier: 3.931A  pdb=" N   ILE A1278 " --> pdb=" O   SER A1274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1288 through 1295
    Processing helix  chain 'A' and resid 1296 through 1298
      No H-bonds generated for 'chain 'A' and resid 1296 through 1298'
    Processing helix  chain 'A' and resid 1299 through 1305
    Processing helix  chain 'A' and resid 1309 through 1334
      removed outlier: 3.502A  pdb=" N   PHE A1313 " --> pdb=" O   ASN A1309 " (cutoff:3.500A)
      Proline residue:  A1331  - end of helix
    Processing helix  chain 'A' and resid 1350 through 1374
    Processing helix  chain 'A' and resid 1380 through 1399
      removed outlier: 3.622A  pdb=" N   PHE A1384 " --> pdb=" O   PHE A1380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1402 through 1406
    Processing helix  chain 'A' and resid 1410 through 1416
    Processing helix  chain 'A' and resid 1418 through 1447
      removed outlier: 4.107A  pdb=" N   TRP A1422 " --> pdb=" O   GLN A1418 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL A1427 " --> pdb=" O   ALA A1423 " (cutoff:3.500A)
      Proline residue:  A1435  - end of helix
    Processing helix  chain 'A' and resid 1449 through 1461
      removed outlier: 3.733A  pdb=" N   GLY A1461 " --> pdb=" O   MET A1457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 61
    Processing helix  chain 'B' and resid 71 through 98
      Proline residue:  B  77  - end of helix
    Processing helix  chain 'B' and resid 186 through 191
    Processing helix  chain 'B' and resid 204 through 210
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 267 through 273
    Processing helix  chain 'B' and resid 286 through 290
      removed outlier: 3.879A  pdb=" N   GLU B 290 " --> pdb=" O   PRO B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 314
      removed outlier: 4.055A  pdb=" N   TRP B 314 " --> pdb=" O   GLU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 354
      removed outlier: 3.683A  pdb=" N   PHE B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 399
    Processing helix  chain 'B' and resid 405 through 409
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1055 through 1057
      removed outlier: 6.473A  pdb=" N   VAL A1113 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   VAL A1143 " --> pdb=" O   LEU A1028 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL A1030 " --> pdb=" O   VAL A1143 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   CYS A1145 " --> pdb=" O   VAL A1030 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   ILE A 709 " --> pdb=" O   TRP A1029 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   LEU A1031 " --> pdb=" O   ILE A 709 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   SER A 711 " --> pdb=" O   LEU A1031 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   TYR A 708 " --> pdb=" O   LEU A1169 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 732 through 734
      removed outlier: 5.520A  pdb=" N   VAL A 721 " --> pdb=" O   ARG A1009 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ARG A1009 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LYS A 725 " --> pdb=" O   ALA A1005 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   ALA A1005 " --> pdb=" O   LYS A 725 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   CYS A 727 " --> pdb=" O   GLY A1003 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   GLY A1003 " --> pdb=" O   CYS A 727 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ILE A 729 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
      removed outlier: 10.236A  pdb=" N   LEU A1001 " --> pdb=" O   ILE A 729 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU A 956 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   GLY A1003 " --> pdb=" O   LEU A 954 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LEU A 954 " --> pdb=" O   GLY A1003 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ALA A1005 " --> pdb=" O   ARG A 952 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ARG A 952 " --> pdb=" O   ALA A1005 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 858 through 860
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1188 through 1190
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1377 through 1378
    Processing sheet with id=AA6, first strand: chain 'B' and resid 126 through 129
      removed outlier: 6.897A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B 329 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ILE B 329 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU B 175 " --> pdb=" O   ILE B 327 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 119 through 120
      removed outlier: 4.035A  pdb=" N   GLN B 341 " --> pdb=" O   THR B 248 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   THR B 248 " --> pdb=" O   GLN B 341 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ASP B 343 " --> pdb=" O   GLN B 246 " (cutoff:3.500A)
      removed outlier: 8.570A  pdb=" N   GLN B 246 " --> pdb=" O   ASP B 343 " (cutoff:3.500A)

    493 hydrogen bonds defined for protein.
    1386 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3265
        1.34 -     1.46: 2385
        1.46 -     1.58: 4853
        1.58 -     1.69: 3
        1.69 -     1.81: 80
  Bond restraints: 10586
  Sorted by residual:
  bond pdb=" F1  ALF A1702 "
       pdb="AL   ALF A1702 "
    ideal  model  delta    sigma   weight residual
    1.684  1.785 -0.101 2.00e-02 2.50e+03 2.57e+01
  bond pdb=" F2  ALF A1702 "
       pdb="AL   ALF A1702 "
    ideal  model  delta    sigma   weight residual
    1.685  1.785 -0.100 2.00e-02 2.50e+03 2.51e+01
  bond pdb=" F4  ALF A1702 "
       pdb="AL   ALF A1702 "
    ideal  model  delta    sigma   weight residual
    1.686  1.785 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" F3  ALF A1702 "
       pdb="AL   ALF A1702 "
    ideal  model  delta    sigma   weight residual
    1.685  1.784 -0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" C5  MAN C   3 "
       pdb=" O5  MAN C   3 "
    ideal  model  delta    sigma   weight residual
    1.418  1.461 -0.043 2.00e-02 2.50e+03 4.61e+00
  ... (remaining 10581 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.24: 14356
       14.24 -    28.48: 5
       28.48 -    42.71: 0
       42.71 -    56.95: 0
       56.95 -    71.19: 2
  Bond angle restraints: 14363
  Sorted by residual:
  angle pdb=" F1  ALF A1702 "
        pdb="AL   ALF A1702 "
        pdb=" F2  ALF A1702 "
      ideal   model   delta    sigma   weight residual
     108.68  179.87  -71.19 3.00e+00 1.11e-01 5.63e+02
  angle pdb=" F3  ALF A1702 "
        pdb="AL   ALF A1702 "
        pdb=" F4  ALF A1702 "
      ideal   model   delta    sigma   weight residual
     109.63  179.94  -70.31 3.00e+00 1.11e-01 5.49e+02
  angle pdb=" F2  ALF A1702 "
        pdb="AL   ALF A1702 "
        pdb=" F4  ALF A1702 "
      ideal   model   delta    sigma   weight residual
     110.21   90.13   20.08 3.00e+00 1.11e-01 4.48e+01
  angle pdb=" F2  ALF A1702 "
        pdb="AL   ALF A1702 "
        pdb=" F3  ALF A1702 "
      ideal   model   delta    sigma   weight residual
     109.59   89.89   19.70 3.00e+00 1.11e-01 4.31e+01
  angle pdb=" F1  ALF A1702 "
        pdb="AL   ALF A1702 "
        pdb=" F3  ALF A1702 "
      ideal   model   delta    sigma   weight residual
     109.69   90.00   19.69 3.00e+00 1.11e-01 4.31e+01
  ... (remaining 14358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.79: 6163
       28.79 -    57.58: 208
       57.58 -    86.38: 18
       86.38 -   115.17: 5
      115.17 -   143.96: 2
  Dihedral angle restraints: 6396
    sinusoidal: 2679
      harmonic: 3717
  Sorted by residual:
  dihedral pdb=" CB  CYS B 110 "
           pdb=" SG  CYS B 110 "
           pdb=" SG  CYS B 159 "
           pdb=" CB  CYS B 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.60   71.60     1      1.00e+01 1.00e-02 6.57e+01
  dihedral pdb=" O1B ADP A1701 "
           pdb=" O3A ADP A1701 "
           pdb=" PB  ADP A1701 "
           pdb=" PA  ADP A1701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   83.96 -143.96     1      2.00e+01 2.50e-03 4.34e+01
  dihedral pdb=" O2A ADP A1701 "
           pdb=" O3A ADP A1701 "
           pdb=" PA  ADP A1701 "
           pdb=" PB  ADP A1701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -150.44   90.44     1      2.00e+01 2.50e-03 2.42e+01
  ... (remaining 6393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.165: 1622
       0.165 -    0.329: 2
       0.329 -    0.494: 0
       0.494 -    0.659: 0
       0.659 -    0.824: 1
  Chirality restraints: 1625
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN B 240 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.58   -0.82 2.00e-01 2.50e+01 1.70e+01
  chirality pdb=" C1  MAN C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  MAN C   3 "
            pdb=" O5  MAN C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.36    0.04 2.00e-02 2.50e+03 4.03e+00
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.37   -0.03 2.00e-02 2.50e+03 2.09e+00
  ... (remaining 1622 not shown)

  Planarity restraints: 1806
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 648 "    0.023 2.00e-02 2.50e+03   2.22e-02 1.23e+01
        pdb=" CG  TRP A 648 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 648 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 648 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 648 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 648 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 648 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 648 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 648 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 648 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 240 "   -0.002 2.00e-02 2.50e+03   2.93e-02 1.07e+01
        pdb=" CG  ASN B 240 "    0.029 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 240 "   -0.033 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 240 "    0.037 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 240 "    0.012 2.00e-02 2.50e+03   2.41e-02 5.80e+00
        pdb=" C   ASN B 240 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ASN B 240 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ASP B 241 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1803 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1142
        2.74 -     3.28: 11225
        3.28 -     3.82: 17779
        3.82 -     4.36: 20162
        4.36 -     4.90: 33082
  Nonbonded interactions: 83390
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 304 "
            pdb=" N   ILE B 305 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" OE1 GLU A1193 "
            pdb=" F3  ALF A1702 "
     model   vdw
     2.216 2.990
  nonbonded pdb=" OG1 THR A 718 "
            pdb=" O   ARG A1009 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ARG B 188 "
            pdb=" OG  SER B 192 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" CG2 THR A1342 "
            pdb=" O   LEU A1346 "
     model   vdw
     2.244 3.460
  ... (remaining 83385 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 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.230
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
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      :  0.004   0.101  10597  Z= 0.186
  Angle     :  1.150  71.188  14391  Z= 0.476
  Chirality :  0.049   0.824   1625
  Planarity :  0.003   0.042   1802
  Dihedral  : 14.166 143.959   4006
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.24), residues: 1267
  helix:  0.13 (0.22), residues: 568
  sheet: -0.22 (0.42), residues: 143
  loop : -2.01 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A1130 
 TYR   0.022   0.002   TYR B  79 
 PHE   0.027   0.002   PHE A1437 
 TRP   0.060   0.002   TRP A 648 
 HIS   0.008   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (10586)
  covalent geometry    : angle       1.14022 (14363)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.95191 (    4)
  hydrogen bonds       : bond        0.14355 (  493)
  hydrogen bonds       : angle       6.30171 ( 1386)
  Misc. bond           : bond        0.00031 (    1)
  link_ALPHA1-4        : bond        0.00110 (    1)
  link_ALPHA1-4        : angle       1.91195 (    3)
  link_BETA1-4         : bond        0.00176 (    3)
  link_BETA1-4         : angle       1.15013 (    9)
  link_NAG-ASN         : bond        0.00409 (    4)
  link_NAG-ASN         : angle       5.27647 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: -0.0507 (tmm) cc_final: -0.0782 (tmm)
REVERT: A  784 PHE cc_start: 0.8947 (p90) cc_final: 0.8497 (t80)
REVERT: A 1130 ARG cc_start: 0.9604 (ptp90) cc_final: 0.9308 (ptp90)
REVERT: A 1200 MET cc_start: 0.9229 (mpp) cc_final: 0.8903 (mpp)
REVERT: A 1213 THR cc_start: 0.8914 (m) cc_final: 0.8662 (t)
REVERT: A 1421 TYR cc_start: 0.7916 (t80) cc_final: 0.7499 (t80)
REVERT: A 1457 MET cc_start: 0.9097 (ppp) cc_final: 0.8592 (ppp)
REVERT: B  179 LEU cc_start: 0.8636 (mp) cc_final: 0.8370 (mp)
REVERT: B  182 PHE cc_start: 0.8496 (t80) cc_final: 0.7809 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.0886
  time to fit residues: 27.6431
Evaluate side-chains
  171 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:   30.0000
   chunk 123 optimal weight:    8.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1041 ASN
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 113 ASN
** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** 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 = 0.3944 r_free = 0.3944 target = 0.099943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.076047 restraints weight = 43833.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.078635 restraints weight = 26418.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.080302 restraints weight = 18474.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.081644 restraints weight = 14333.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.082381 restraints weight = 11830.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  10597  Z= 0.280
  Angle     :  0.781  14.111  14391  Z= 0.395
  Chirality :  0.047   0.190   1625
  Planarity :  0.005   0.049   1802
  Dihedral  :  8.606 126.796   1606
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 21.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  9.52 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.23), residues: 1267
  helix: -0.17 (0.21), residues: 585
  sheet: -0.62 (0.41), residues: 146
  loop : -2.01 (0.28), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 162 
 TYR   0.022   0.003   TYR A1332 
 PHE   0.026   0.003   PHE A1330 
 TRP   0.026   0.003   TRP A 648 
 HIS   0.007   0.002   HIS A1350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 (10586)
  covalent geometry    : angle       0.76969 (14363)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       0.90888 (    4)
  hydrogen bonds       : bond        0.04433 (  493)
  hydrogen bonds       : angle       5.43667 ( 1386)
  Misc. bond           : bond        0.00006 (    1)
  link_ALPHA1-4        : bond        0.01335 (    1)
  link_ALPHA1-4        : angle       2.27467 (    3)
  link_BETA1-4         : bond        0.00340 (    3)
  link_BETA1-4         : angle       1.67158 (    9)
  link_NAG-ASN         : bond        0.00491 (    4)
  link_NAG-ASN         : angle       4.22839 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  784 PHE cc_start: 0.9017 (p90) cc_final: 0.8512 (t80)
REVERT: A 1141 LYS cc_start: 0.7420 (mmtt) cc_final: 0.7206 (pttt)
REVERT: A 1213 THR cc_start: 0.9148 (m) cc_final: 0.8901 (t)
REVERT: A 1238 ASN cc_start: 0.8568 (t0) cc_final: 0.8367 (t0)
REVERT: A 1303 ILE cc_start: 0.9371 (mm) cc_final: 0.9131 (mt)
REVERT: A 1341 VAL cc_start: 0.8000 (m) cc_final: 0.7723 (p)
REVERT: A 1457 MET cc_start: 0.9117 (ppp) cc_final: 0.8825 (ppp)
REVERT: B  182 PHE cc_start: 0.8818 (t80) cc_final: 0.8184 (t80)
REVERT: B  199 ARG cc_start: 0.8669 (mpp-170) cc_final: 0.8095 (mmt180)
REVERT: B  304 ASP cc_start: 0.7382 (t0) cc_final: 0.7093 (t0)
REVERT: B  333 ASP cc_start: 0.8689 (m-30) cc_final: 0.8405 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 198
  average time/residue: 0.0907
  time to fit residues: 26.5330
Evaluate side-chains
  163 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   chunk 42 optimal weight:    9.9990
   chunk 114 optimal weight:    0.0010
   chunk 34 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.3590

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

Flipped N/Q/H residues before XYZ refinement:
A 942 HIS
** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 HIS
B 176 ASN
B 347 HIS
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.104100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.079799 restraints weight = 41931.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.082634 restraints weight = 24579.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.084614 restraints weight = 16848.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.086020 restraints weight = 12777.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.086870 restraints weight = 10423.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10597  Z= 0.131
  Angle     :  0.652   9.746  14391  Z= 0.327
  Chirality :  0.044   0.157   1625
  Planarity :  0.004   0.047   1802
  Dihedral  :  7.903 121.833   1606
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.24), residues: 1267
  helix: -0.03 (0.22), residues: 581
  sheet: -0.37 (0.42), residues: 142
  loop : -1.88 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1300 
 TYR   0.019   0.002   TYR A 678 
 PHE   0.029   0.002   PHE A1426 
 TRP   0.018   0.001   TRP A1308 
 HIS   0.008   0.001   HIS A 942 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10586)
  covalent geometry    : angle       0.64332 (14363)
  SS BOND              : bond        0.00359 (    2)
  SS BOND              : angle       1.12471 (    4)
  hydrogen bonds       : bond        0.03851 (  493)
  hydrogen bonds       : angle       5.09470 ( 1386)
  Misc. bond           : bond        0.00010 (    1)
  link_ALPHA1-4        : bond        0.01372 (    1)
  link_ALPHA1-4        : angle       2.40818 (    3)
  link_BETA1-4         : bond        0.00303 (    3)
  link_BETA1-4         : angle       1.14387 (    9)
  link_NAG-ASN         : bond        0.00236 (    4)
  link_NAG-ASN         : angle       3.51466 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  784 PHE cc_start: 0.8995 (p90) cc_final: 0.8464 (t80)
REVERT: A 1199 VAL cc_start: 0.8803 (m) cc_final: 0.8497 (m)
REVERT: A 1301 VAL cc_start: 0.8742 (p) cc_final: 0.8533 (m)
REVERT: A 1457 MET cc_start: 0.9024 (ppp) cc_final: 0.8463 (ppp)
REVERT: B  180 GLU cc_start: 0.8219 (tp30) cc_final: 0.7517 (tm-30)
REVERT: B  181 LYS cc_start: 0.8854 (tmmt) cc_final: 0.8380 (tmtt)
REVERT: B  182 PHE cc_start: 0.8669 (t80) cc_final: 0.8113 (t80)
REVERT: B  304 ASP cc_start: 0.7432 (t0) cc_final: 0.7083 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0872
  time to fit residues: 26.7424
Evaluate side-chains
  167 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 113 optimal weight:    0.5980
   chunk 36 optimal weight:   20.0000
   chunk 68 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 117 optimal weight:    0.0070
   chunk 87 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0010
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    0.4604

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

Flipped N/Q/H residues before XYZ refinement:
** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS
B 412 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.105730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.081213 restraints weight = 41531.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.084110 restraints weight = 24432.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.086038 restraints weight = 16802.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.087503 restraints weight = 12837.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.088413 restraints weight = 10503.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10597  Z= 0.111
  Angle     :  0.617  10.014  14391  Z= 0.306
  Chirality :  0.043   0.151   1625
  Planarity :  0.004   0.037   1802
  Dihedral  :  7.224 115.175   1606
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.24), residues: 1267
  helix:  0.07 (0.22), residues: 584
  sheet: -0.31 (0.41), residues: 142
  loop : -1.86 (0.28), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 401 
 TYR   0.020   0.001   TYR A1299 
 PHE   0.014   0.001   PHE A1408 
 TRP   0.015   0.001   TRP A1458 
 HIS   0.004   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10586)
  covalent geometry    : angle       0.60956 (14363)
  SS BOND              : bond        0.00403 (    2)
  SS BOND              : angle       1.09849 (    4)
  hydrogen bonds       : bond        0.03412 (  493)
  hydrogen bonds       : angle       4.85832 ( 1386)
  Misc. bond           : bond        0.00015 (    1)
  link_ALPHA1-4        : bond        0.01564 (    1)
  link_ALPHA1-4        : angle       2.72145 (    3)
  link_BETA1-4         : bond        0.00387 (    3)
  link_BETA1-4         : angle       1.08783 (    9)
  link_NAG-ASN         : bond        0.00347 (    4)
  link_NAG-ASN         : angle       2.95577 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  610 PHE cc_start: 0.7403 (t80) cc_final: 0.7165 (t80)
REVERT: A  784 PHE cc_start: 0.9003 (p90) cc_final: 0.8472 (t80)
REVERT: A 1136 LEU cc_start: 0.9494 (pp) cc_final: 0.9199 (tp)
REVERT: A 1199 VAL cc_start: 0.8712 (m) cc_final: 0.8390 (m)
REVERT: A 1301 VAL cc_start: 0.8661 (p) cc_final: 0.8435 (m)
REVERT: A 1303 ILE cc_start: 0.9324 (mm) cc_final: 0.9089 (mt)
REVERT: A 1317 MET cc_start: 0.8159 (ttt) cc_final: 0.7863 (tmm)
REVERT: A 1372 MET cc_start: 0.8736 (ttm) cc_final: 0.8522 (ttm)
REVERT: A 1457 MET cc_start: 0.9019 (ppp) cc_final: 0.8796 (ppp)
REVERT: B  180 GLU cc_start: 0.8181 (tp30) cc_final: 0.7468 (tm-30)
REVERT: B  181 LYS cc_start: 0.8790 (tmmt) cc_final: 0.8188 (tmmt)
REVERT: B  182 PHE cc_start: 0.8642 (t80) cc_final: 0.8006 (t80)
REVERT: B  333 ASP cc_start: 0.8262 (m-30) cc_final: 0.8026 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0848
  time to fit residues: 25.9382
Evaluate side-chains
  172 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0970
   chunk 19 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 125 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 62 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1233 GLN
B 155 GLN
B 347 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.106053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.081553 restraints weight = 40982.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.084437 restraints weight = 24147.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.086287 restraints weight = 16620.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.087803 restraints weight = 12759.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.088752 restraints weight = 10408.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10597  Z= 0.117
  Angle     :  0.642  11.421  14391  Z= 0.312
  Chirality :  0.044   0.280   1625
  Planarity :  0.004   0.038   1802
  Dihedral  :  6.943 108.019   1606
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.24), residues: 1267
  helix:  0.12 (0.22), residues: 582
  sheet: -0.29 (0.41), residues: 142
  loop : -1.89 (0.28), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 156 
 TYR   0.019   0.001   TYR A 678 
 PHE   0.015   0.001   PHE B 239 
 TRP   0.020   0.001   TRP B 308 
 HIS   0.006   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10586)
  covalent geometry    : angle       0.62915 (14363)
  SS BOND              : bond        0.00321 (    2)
  SS BOND              : angle       1.02412 (    4)
  hydrogen bonds       : bond        0.03333 (  493)
  hydrogen bonds       : angle       4.81792 ( 1386)
  Misc. bond           : bond        0.00003 (    1)
  link_ALPHA1-4        : bond        0.01646 (    1)
  link_ALPHA1-4        : angle       2.70986 (    3)
  link_BETA1-4         : bond        0.00299 (    3)
  link_BETA1-4         : angle       1.10594 (    9)
  link_NAG-ASN         : bond        0.00319 (    4)
  link_NAG-ASN         : angle       4.22362 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  610 PHE cc_start: 0.7370 (t80) cc_final: 0.7139 (t80)
REVERT: A  669 ILE cc_start: 0.8880 (pt) cc_final: 0.8566 (tt)
REVERT: A  784 PHE cc_start: 0.8993 (p90) cc_final: 0.8450 (t80)
REVERT: A 1136 LEU cc_start: 0.9508 (pp) cc_final: 0.9279 (tp)
REVERT: A 1199 VAL cc_start: 0.8690 (m) cc_final: 0.8372 (m)
REVERT: A 1301 VAL cc_start: 0.8687 (p) cc_final: 0.8443 (m)
REVERT: A 1303 ILE cc_start: 0.9314 (mm) cc_final: 0.9017 (mt)
REVERT: A 1317 MET cc_start: 0.8173 (ttt) cc_final: 0.7908 (tmm)
REVERT: A 1457 MET cc_start: 0.9011 (ppp) cc_final: 0.8798 (ppp)
REVERT: B  180 GLU cc_start: 0.8187 (tp30) cc_final: 0.7421 (tm-30)
REVERT: B  181 LYS cc_start: 0.8827 (tmmt) cc_final: 0.8240 (tmtt)
REVERT: B  182 PHE cc_start: 0.8650 (t80) cc_final: 0.8019 (t80)
REVERT: B  333 ASP cc_start: 0.8268 (m-30) cc_final: 0.8016 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.0877
  time to fit residues: 26.6151
Evaluate side-chains
  167 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0870
   chunk 26 optimal weight:    8.9990
   chunk 97 optimal weight:    0.1980
   chunk 85 optimal weight:    1.9990
   chunk 99 optimal weight:    0.1980
   chunk 33 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    0.6962

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

Flipped N/Q/H residues before XYZ refinement:
** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.106582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.082132 restraints weight = 41431.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.084981 restraints weight = 24428.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.086971 restraints weight = 16844.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.088366 restraints weight = 12822.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.089240 restraints weight = 10506.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
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      :  0.002   0.028  10597  Z= 0.110
  Angle     :  0.632  10.889  14391  Z= 0.307
  Chirality :  0.043   0.157   1625
  Planarity :  0.003   0.037   1802
  Dihedral  :  6.544  97.340   1606
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.24), residues: 1267
  helix:  0.17 (0.22), residues: 583
  sheet: -0.26 (0.42), residues: 142
  loop : -1.86 (0.28), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 925 
 TYR   0.021   0.001   TYR A1299 
 PHE   0.020   0.001   PHE A1368 
 TRP   0.024   0.001   TRP A1308 
 HIS   0.003   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (10586)
  covalent geometry    : angle       0.62161 (14363)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       0.98521 (    4)
  hydrogen bonds       : bond        0.03269 (  493)
  hydrogen bonds       : angle       4.74490 ( 1386)
  Misc. bond           : bond        0.00008 (    1)
  link_ALPHA1-4        : bond        0.01759 (    1)
  link_ALPHA1-4        : angle       2.90640 (    3)
  link_BETA1-4         : bond        0.00323 (    3)
  link_BETA1-4         : angle       1.04843 (    9)
  link_NAG-ASN         : bond        0.00290 (    4)
  link_NAG-ASN         : angle       3.64949 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  610 PHE cc_start: 0.7378 (t80) cc_final: 0.7147 (t80)
REVERT: A  695 LYS cc_start: 0.8460 (tptt) cc_final: 0.8241 (tptp)
REVERT: A  784 PHE cc_start: 0.8947 (p90) cc_final: 0.8411 (t80)
REVERT: A 1136 LEU cc_start: 0.9483 (pp) cc_final: 0.9216 (tp)
REVERT: A 1199 VAL cc_start: 0.8639 (m) cc_final: 0.8312 (m)
REVERT: A 1301 VAL cc_start: 0.8581 (p) cc_final: 0.8323 (m)
REVERT: A 1303 ILE cc_start: 0.9298 (mm) cc_final: 0.9070 (mt)
REVERT: A 1317 MET cc_start: 0.8150 (ttt) cc_final: 0.7898 (tmm)
REVERT: B  180 GLU cc_start: 0.8160 (tp30) cc_final: 0.7389 (tm-30)
REVERT: B  181 LYS cc_start: 0.8762 (tmmt) cc_final: 0.8118 (tmmt)
REVERT: B  182 PHE cc_start: 0.8650 (t80) cc_final: 0.7984 (t80)
REVERT: B  333 ASP cc_start: 0.8235 (m-30) cc_final: 0.7997 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.0859
  time to fit residues: 26.5005
Evaluate side-chains
  173 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 83 optimal weight:    5.9990
   chunk 126 optimal weight:    7.9990
   chunk 108 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    8.9990
   chunk 124 optimal weight:    8.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1041 ASN
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.102838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.078899 restraints weight = 42227.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.081636 restraints weight = 24747.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.083520 restraints weight = 17042.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.084738 restraints weight = 13013.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.085719 restraints weight = 10752.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10597  Z= 0.165
  Angle     :  0.671  10.512  14391  Z= 0.334
  Chirality :  0.045   0.168   1625
  Planarity :  0.004   0.044   1802
  Dihedral  :  6.495  85.809   1606
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.24), residues: 1267
  helix:  0.20 (0.22), residues: 585
  sheet: -0.27 (0.42), residues: 142
  loop : -1.78 (0.29), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 162 
 TYR   0.027   0.002   TYR B 278 
 PHE   0.022   0.002   PHE A1313 
 TRP   0.032   0.002   TRP A1308 
 HIS   0.006   0.001   HIS A1350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (10586)
  covalent geometry    : angle       0.66186 (14363)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       0.87524 (    4)
  hydrogen bonds       : bond        0.03535 (  493)
  hydrogen bonds       : angle       4.85829 ( 1386)
  Misc. bond           : bond        0.00055 (    1)
  link_ALPHA1-4        : bond        0.01586 (    1)
  link_ALPHA1-4        : angle       2.89552 (    3)
  link_BETA1-4         : bond        0.00110 (    3)
  link_BETA1-4         : angle       1.22557 (    9)
  link_NAG-ASN         : bond        0.00226 (    4)
  link_NAG-ASN         : angle       3.37637 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  610 PHE cc_start: 0.7389 (t80) cc_final: 0.7148 (t80)
REVERT: A  784 PHE cc_start: 0.8974 (p90) cc_final: 0.8414 (t80)
REVERT: A 1199 VAL cc_start: 0.8751 (m) cc_final: 0.8437 (m)
REVERT: A 1301 VAL cc_start: 0.8794 (p) cc_final: 0.8527 (m)
REVERT: A 1303 ILE cc_start: 0.9329 (mm) cc_final: 0.9050 (mt)
REVERT: A 1317 MET cc_start: 0.8845 (ttt) cc_final: 0.8554 (tmm)
REVERT: A 1457 MET cc_start: 0.9048 (ppp) cc_final: 0.8695 (ppp)
REVERT: B  111 MET cc_start: 0.8816 (ppp) cc_final: 0.8368 (ppp)
REVERT: B  180 GLU cc_start: 0.8284 (tp30) cc_final: 0.7462 (tm-30)
REVERT: B  181 LYS cc_start: 0.8743 (tmmt) cc_final: 0.8240 (tmtt)
REVERT: B  182 PHE cc_start: 0.8741 (t80) cc_final: 0.8077 (t80)
REVERT: B  333 ASP cc_start: 0.8462 (m-30) cc_final: 0.8164 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0863
  time to fit residues: 25.6249
Evaluate side-chains
  161 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 100 optimal weight:   10.0000
   chunk 96 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 124 optimal weight:    9.9990
   chunk 93 optimal weight:    5.9990
   chunk 80 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 125 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1233 GLN
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.098835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.075558 restraints weight = 43482.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.078135 restraints weight = 25744.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.079926 restraints weight = 17867.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.081044 restraints weight = 13663.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.081994 restraints weight = 11386.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  10597  Z= 0.228
  Angle     :  0.763  13.146  14391  Z= 0.382
  Chirality :  0.048   0.181   1625
  Planarity :  0.005   0.052   1802
  Dihedral  :  6.723  80.524   1606
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 19.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.24), residues: 1267
  helix: -0.10 (0.21), residues: 593
  sheet: -0.40 (0.42), residues: 143
  loop : -1.85 (0.29), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A1414 
 TYR   0.030   0.002   TYR B 378 
 PHE   0.024   0.002   PHE A1437 
 TRP   0.028   0.003   TRP B 266 
 HIS   0.014   0.002   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (10586)
  covalent geometry    : angle       0.75480 (14363)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       0.96138 (    4)
  hydrogen bonds       : bond        0.03940 (  493)
  hydrogen bonds       : angle       5.16705 ( 1386)
  Misc. bond           : bond        0.00099 (    1)
  link_ALPHA1-4        : bond        0.01515 (    1)
  link_ALPHA1-4        : angle       2.85079 (    3)
  link_BETA1-4         : bond        0.00310 (    3)
  link_BETA1-4         : angle       1.54626 (    9)
  link_NAG-ASN         : bond        0.00285 (    4)
  link_NAG-ASN         : angle       3.59128 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  610 PHE cc_start: 0.7375 (t80) cc_final: 0.7133 (t80)
REVERT: A  784 PHE cc_start: 0.8951 (p90) cc_final: 0.8383 (t80)
REVERT: A 1158 LYS cc_start: 0.9139 (pptt) cc_final: 0.8809 (pptt)
REVERT: A 1200 MET cc_start: 0.9211 (mmp) cc_final: 0.9000 (mmm)
REVERT: A 1229 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8284 (tm-30)
REVERT: A 1317 MET cc_start: 0.8790 (ttt) cc_final: 0.8486 (tmm)
REVERT: A 1457 MET cc_start: 0.9064 (ppp) cc_final: 0.8634 (ppp)
REVERT: B  169 MET cc_start: 0.8527 (tpt) cc_final: 0.7927 (mmm)
REVERT: B  182 PHE cc_start: 0.8862 (t80) cc_final: 0.8249 (t80)
REVERT: B  333 ASP cc_start: 0.8526 (m-30) cc_final: 0.8283 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0837
  time to fit residues: 24.2297
Evaluate side-chains
  150 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 91 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 126 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 113 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 115 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   overall best weight:    1.5382

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

Flipped N/Q/H residues before XYZ refinement:
** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.101794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.078086 restraints weight = 42337.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.080822 restraints weight = 24795.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.082713 restraints weight = 17051.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.084042 restraints weight = 13000.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.084789 restraints weight = 10646.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10597  Z= 0.142
  Angle     :  0.710  14.376  14391  Z= 0.347
  Chirality :  0.046   0.160   1625
  Planarity :  0.004   0.047   1802
  Dihedral  :  6.139  68.518   1606
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.24), residues: 1267
  helix:  0.00 (0.22), residues: 581
  sheet: -0.43 (0.41), residues: 149
  loop : -1.74 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1130 
 TYR   0.021   0.002   TYR A 678 
 PHE   0.022   0.002   PHE A1437 
 TRP   0.034   0.002   TRP A1308 
 HIS   0.012   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10586)
  covalent geometry    : angle       0.70263 (14363)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       1.12699 (    4)
  hydrogen bonds       : bond        0.03686 (  493)
  hydrogen bonds       : angle       4.98972 ( 1386)
  Misc. bond           : bond        0.00058 (    1)
  link_ALPHA1-4        : bond        0.02080 (    1)
  link_ALPHA1-4        : angle       3.08415 (    3)
  link_BETA1-4         : bond        0.00164 (    3)
  link_BETA1-4         : angle       1.15367 (    9)
  link_NAG-ASN         : bond        0.00146 (    4)
  link_NAG-ASN         : angle       3.21456 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  610 PHE cc_start: 0.7339 (t80) cc_final: 0.7100 (t80)
REVERT: A  784 PHE cc_start: 0.8927 (p90) cc_final: 0.8366 (t80)
REVERT: A 1129 MET cc_start: 0.9163 (tpt) cc_final: 0.8909 (tpp)
REVERT: A 1136 LEU cc_start: 0.9535 (pp) cc_final: 0.9228 (tp)
REVERT: A 1200 MET cc_start: 0.9153 (mmp) cc_final: 0.8928 (mmm)
REVERT: A 1229 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: A 1317 MET cc_start: 0.8727 (ttt) cc_final: 0.8426 (tmm)
REVERT: A 1457 MET cc_start: 0.9056 (ppp) cc_final: 0.8611 (ppp)
REVERT: B  169 MET cc_start: 0.8393 (tpt) cc_final: 0.7899 (mmm)
REVERT: B  182 PHE cc_start: 0.8736 (t80) cc_final: 0.8113 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0841
  time to fit residues: 24.2494
Evaluate side-chains
  162 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 125 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 93 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0370
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 109 optimal weight:    6.9990
   overall best weight:    1.5662

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

Flipped N/Q/H residues before XYZ refinement:
** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.102132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.078399 restraints weight = 41572.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.081092 restraints weight = 24653.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.082908 restraints weight = 17076.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.084242 restraints weight = 13107.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.084962 restraints weight = 10760.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10597  Z= 0.140
  Angle     :  0.695  11.056  14391  Z= 0.342
  Chirality :  0.046   0.158   1625
  Planarity :  0.004   0.044   1802
  Dihedral  :  5.719  64.772   1606
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.24), residues: 1267
  helix:  0.02 (0.22), residues: 582
  sheet: -0.40 (0.41), residues: 149
  loop : -1.73 (0.29), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1414 
 TYR   0.021   0.002   TYR A 678 
 PHE   0.015   0.002   PHE A1313 
 TRP   0.045   0.002   TRP A1308 
 HIS   0.010   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10586)
  covalent geometry    : angle       0.68693 (14363)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       0.98321 (    4)
  hydrogen bonds       : bond        0.03581 (  493)
  hydrogen bonds       : angle       4.95774 ( 1386)
  Misc. bond           : bond        0.00063 (    1)
  link_ALPHA1-4        : bond        0.02312 (    1)
  link_ALPHA1-4        : angle       3.49233 (    3)
  link_BETA1-4         : bond        0.00167 (    3)
  link_BETA1-4         : angle       1.15228 (    9)
  link_NAG-ASN         : bond        0.00139 (    4)
  link_NAG-ASN         : angle       3.13429 (   12)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  610 PHE cc_start: 0.7348 (t80) cc_final: 0.7119 (t80)
REVERT: A  669 ILE cc_start: 0.8898 (pt) cc_final: 0.8551 (tt)
REVERT: A  784 PHE cc_start: 0.8950 (p90) cc_final: 0.8379 (t80)
REVERT: A 1129 MET cc_start: 0.9174 (tpt) cc_final: 0.8921 (tpp)
REVERT: A 1136 LEU cc_start: 0.9532 (pp) cc_final: 0.9235 (tp)
REVERT: A 1158 LYS cc_start: 0.9034 (pptt) cc_final: 0.8698 (pptt)
REVERT: A 1200 MET cc_start: 0.9137 (mmp) cc_final: 0.8894 (mmm)
REVERT: A 1317 MET cc_start: 0.8683 (ttt) cc_final: 0.8406 (tmm)
REVERT: A 1457 MET cc_start: 0.9046 (ppp) cc_final: 0.8598 (ppp)
REVERT: B  169 MET cc_start: 0.8263 (tpt) cc_final: 0.7809 (mmm)
REVERT: B  180 GLU cc_start: 0.8419 (tp30) cc_final: 0.8202 (tp30)
REVERT: B  182 PHE cc_start: 0.8715 (t80) cc_final: 0.8084 (t80)
REVERT: B  333 ASP cc_start: 0.8369 (m-30) cc_final: 0.8131 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0838
  time to fit residues: 23.8917
Evaluate side-chains
  163 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 78 optimal weight:    7.9990
   chunk 111 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 20 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   chunk 80 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.102422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.078578 restraints weight = 42306.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.081325 restraints weight = 24903.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.083214 restraints weight = 17133.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.084417 restraints weight = 13052.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.085444 restraints weight = 10775.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10597  Z= 0.138
  Angle     :  0.689  11.115  14391  Z= 0.340
  Chirality :  0.045   0.185   1625
  Planarity :  0.004   0.043   1802
  Dihedral  :  5.373  65.223   1606
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.25), residues: 1267
  helix:  0.07 (0.22), residues: 582
  sheet: -0.39 (0.42), residues: 149
  loop : -1.71 (0.29), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  62 
 TYR   0.022   0.002   TYR A 678 
 PHE   0.027   0.002   PHE A1437 
 TRP   0.038   0.002   TRP A1308 
 HIS   0.010   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10586)
  covalent geometry    : angle       0.68093 (14363)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       0.96101 (    4)
  hydrogen bonds       : bond        0.03577 (  493)
  hydrogen bonds       : angle       4.93667 ( 1386)
  Misc. bond           : bond        0.00061 (    1)
  link_ALPHA1-4        : bond        0.02521 (    1)
  link_ALPHA1-4        : angle       3.77713 (    3)
  link_BETA1-4         : bond        0.00236 (    3)
  link_BETA1-4         : angle       1.12140 (    9)
  link_NAG-ASN         : bond        0.00148 (    4)
  link_NAG-ASN         : angle       3.06030 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2069.39 seconds
wall clock time: 36 minutes 32.97 seconds (2192.97 seconds total)