Starting phenix.real_space_refine
on Wed Mar  4 05:55:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kyb_23074/03_2026/7kyb_23074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kyb_23074/03_2026/7kyb_23074.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kyb_23074/03_2026/7kyb_23074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kyb_23074/03_2026/7kyb_23074.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kyb_23074/03_2026/7kyb_23074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kyb_23074/03_2026/7kyb_23074.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       3      5.49       5
     Mg      2      5.21       5
     S      50      5.16       5
     C    6985      2.51       5
     N    1763      2.21       5
     O    2006      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 145 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: 10814
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 7646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 957, 7646
          Classifications: {'peptide': 957}
          Link IDs: {'PTRANS': 29, 'TRANS': 927}
          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: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          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: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 86
          Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1, 'POV': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.58, per 1000 atoms: 0.24
  Number of scatterers: 10814
  At special positions: 0
  Unit cell: (127.204, 113.988, 132.16, 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      50     16.00
     P       3     15.00
     Al      1     13.00
     Mg      2     11.99
     F       4      9.00
     O    2006      8.00
     N    1763      7.00
     C    6985      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=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    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 B1002 " - " ASN B 113 "
      " NAG C   1 " - " ASN B 240 "
      " NAG D   1 " - " ASN B 256 "
      " NAG E   1 " - " ASN B 332 "
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 397.5 milliseconds
  

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2478

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 7 sheets defined
      52.9% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 217 through 232
      removed outlier: 3.696A  pdb=" N   VAL A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 244 through 267
    Processing helix  chain 'A' and resid 543 through 577
      removed outlier: 3.778A  pdb=" N   ARG A 547 " --> pdb=" O   SER A 543 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LYS A 577 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 586
      removed outlier: 3.597A  pdb=" N   GLU A 586 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 609
      removed outlier: 3.818A  pdb=" N   ILE A 607 " --> pdb=" O   TRP A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 635
    Processing helix  chain 'A' and resid 694 through 705
    Processing helix  chain 'A' and resid 707 through 734
      removed outlier: 4.202A  pdb=" N   GLU A 711 " --> pdb=" O   ASP A 707 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ARG A 714 " --> pdb=" O   THR A 710 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   SER A 734 " --> pdb=" O   LEU A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 744
      removed outlier: 3.565A  pdb=" N   GLU A 743 " --> pdb=" O   TYR A 740 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL A 744 " --> pdb=" O   PRO A 741 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 740 through 744'
    Processing helix  chain 'A' and resid 748 through 757
      removed outlier: 4.031A  pdb=" N   VAL A 752 " --> pdb=" O   SER A 748 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLY A 757 " --> pdb=" O   ARG A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 777
    Processing helix  chain 'A' and resid 798 through 812
      removed outlier: 3.613A  pdb=" N   GLY A 812 " --> pdb=" O   ALA A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 880
    Processing helix  chain 'A' and resid 891 through 907
    Processing helix  chain 'A' and resid 919 through 935
    Processing helix  chain 'A' and resid 939 through 952
      removed outlier: 4.189A  pdb=" N   GLU A 943 " --> pdb=" O   ASN A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 981
    Processing helix  chain 'A' and resid 992 through 1003
    Processing helix  chain 'A' and resid 1018 through 1026
      removed outlier: 4.818A  pdb=" N   GLU A1024 " --> pdb=" O   ASP A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1045
    Processing helix  chain 'A' and resid 1050 through 1058
    Processing helix  chain 'A' and resid 1074 through 1083
      removed outlier: 3.576A  pdb=" N   LEU A1079 " --> pdb=" O   ASP A1075 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   GLY A1083 " --> pdb=" O   LEU A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1096
      removed outlier: 4.117A  pdb=" N   ASN A1096 " --> pdb=" O   LEU A1092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1120
    Processing helix  chain 'A' and resid 1131 through 1140
      removed outlier: 4.002A  pdb=" N   ALA A1136 " --> pdb=" O   SER A1132 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1167 through 1207
      removed outlier: 4.266A  pdb=" N   ARG A1171 " --> pdb=" O   ARG A1167 " (cutoff:3.500A)
      Proline residue:  A1189  - end of helix
      removed outlier: 4.109A  pdb=" N   PHE A1198 " --> pdb=" O   LYS A1194 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU A1202 " --> pdb=" O   PHE A1198 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   PHE A1203 " --> pdb=" O   ALA A1199 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ILE A1207 " --> pdb=" O   PHE A1203 " (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 1218 through 1228
      removed outlier: 4.808A  pdb=" N   ASN A1226 " --> pdb=" O   MET A1222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1230 through 1241
      removed outlier: 4.198A  pdb=" N   VAL A1234 " --> pdb=" O   THR A1230 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASP A1241 " --> pdb=" O   LEU A1237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1245 through 1252
    Processing helix  chain 'A' and resid 1253 through 1255
      No H-bonds generated for 'chain 'A' and resid 1253 through 1255'
    Processing helix  chain 'A' and resid 1256 through 1262
    Processing helix  chain 'A' and resid 1267 through 1287
    Processing helix  chain 'A' and resid 1287 through 1293
    Processing helix  chain 'A' and resid 1307 through 1331
    Processing helix  chain 'A' and resid 1336 through 1358
      removed outlier: 3.890A  pdb=" N   SER A1358 " --> pdb=" O   GLY A1354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1367 through 1373
    Processing helix  chain 'A' and resid 1375 through 1404
      removed outlier: 3.714A  pdb=" N   TRP A1379 " --> pdb=" O   ALA A1375 " (cutoff:3.500A)
      Proline residue:  A1392  - end of helix
    Processing helix  chain 'A' and resid 1406 through 1418
      removed outlier: 3.654A  pdb=" N   HIS A1417 " --> pdb=" O   GLU A1413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 99
      Proline residue:  B  77  - end of helix
      removed outlier: 3.640A  pdb=" N   LYS B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 111
      removed outlier: 4.547A  pdb=" N   MET B 111 " --> pdb=" O   GLN B 108 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 108 through 111'
    Processing helix  chain 'B' and resid 188 through 192
      removed outlier: 3.530A  pdb=" N   LEU B 191 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 204 through 210
    Processing helix  chain 'B' and resid 231 through 237
      removed outlier: 4.489A  pdb=" N   ALA B 235 " --> pdb=" O   CYS B 231 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   SER B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 272
      removed outlier: 3.520A  pdb=" N   LYS B 270 " --> pdb=" O   GLU B 267 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS B 271 " --> pdb=" O   SER B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 315
    Processing helix  chain 'B' and resid 372 through 399
    Processing helix  chain 'B' and resid 409 through 414
      removed outlier: 3.987A  pdb=" N   LYS B 414 " --> pdb=" O   SER B 410 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1011 through 1014
      removed outlier: 3.588A  pdb=" N   VAL A1071 " --> pdb=" O   LEU A1013 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   TYR A1068 " --> pdb=" O   ALA A1099 " (cutoff:3.500A)
      removed outlier: 8.517A  pdb=" N   LEU A1101 " --> pdb=" O   TYR A1068 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ILE A1070 " --> pdb=" O   LEU A1101 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   CYS A1103 " --> pdb=" O   ILE A1070 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ILE A1072 " --> pdb=" O   CYS A1103 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL A1100 " --> pdb=" O   LEU A 985 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   ILE A 664 " --> pdb=" O   TRP A 986 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LEU A 988 " --> pdb=" O   ILE A 664 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   SER A 666 " --> pdb=" O   LEU A 988 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   THR A1125 " --> pdb=" O   VAL A1143 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   ILE A1145 " --> pdb=" O   THR A1125 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   ALA A1127 " --> pdb=" O   ILE A1145 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   ILE A1147 " --> pdb=" O   ALA A1127 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   GLY A1129 " --> pdb=" O   ILE A1147 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR A1161 " --> pdb=" O   GLY A1144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 689
      removed outlier: 8.071A  pdb=" N   MET A 677 " --> pdb=" O   ARG A 966 " (cutoff:3.500A)
      removed outlier: 8.301A  pdb=" N   ARG A 966 " --> pdb=" O   MET A 677 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   PHE A 679 " --> pdb=" O   GLU A 964 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLU A 964 " --> pdb=" O   PHE A 679 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   LEU A 957 " --> pdb=" O   GLN A 915 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLN A 915 " --> pdb=" O   LEU A 957 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLY A 959 " --> pdb=" O   ILE A 913 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ARG A 848 " --> pdb=" O   GLU A 841 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   GLU A 841 " --> pdb=" O   ARG A 848 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   SER A 850 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   ILE A 839 " --> pdb=" O   SER A 850 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ILE A 852 " --> pdb=" O   LEU A 837 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 815 through 816
      removed outlier: 3.584A  pdb=" N   VAL A 816 " --> pdb=" O   ILE A 824 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ILE A 824 " --> pdb=" O   VAL A 816 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1334 through 1335
    Processing sheet with id=AA5, first strand: chain 'B' and resid 127 through 129
      removed outlier: 5.856A  pdb=" N   TYR B 177 " --> pdb=" O   LEU B 326 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   LEU B 326 " --> pdb=" O   TYR B 177 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   LEU B 179 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   THR B 324 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 120
      removed outlier: 5.622A  pdb=" N   ASP B 343 " --> pdb=" O   GLN B 246 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   GLN B 246 " --> pdb=" O   ASP B 343 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 227 through 228
      removed outlier: 6.090A  pdb=" N   ILE B 227 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    537 hydrogen bonds defined for protein.
    1563 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: 1.89

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1742
        1.30 -     1.43: 3076
        1.43 -     1.56: 6168
        1.56 -     1.69: 6
        1.69 -     1.81: 77
  Bond restraints: 11069
  Sorted by residual:
  bond pdb=" F2  ALF A1603 "
       pdb="AL   ALF A1603 "
    ideal  model  delta    sigma   weight residual
    1.685  1.784 -0.099 2.00e-02 2.50e+03 2.44e+01
  bond pdb=" F4  ALF A1603 "
       pdb="AL   ALF A1603 "
    ideal  model  delta    sigma   weight residual
    1.686  1.783 -0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" C31 POV A1601 "
       pdb=" O31 POV A1601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.421 -0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" F1  ALF A1603 "
       pdb="AL   ALF A1603 "
    ideal  model  delta    sigma   weight residual
    1.684  1.778 -0.094 2.00e-02 2.50e+03 2.20e+01
  bond pdb=" F3  ALF A1603 "
       pdb="AL   ALF A1603 "
    ideal  model  delta    sigma   weight residual
    1.685  1.776 -0.091 2.00e-02 2.50e+03 2.05e+01
  ... (remaining 11064 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.94: 14999
       13.94 -    27.88: 4
       27.88 -    41.82: 0
       41.82 -    55.75: 0
       55.75 -    69.69: 2
  Bond angle restraints: 15005
  Sorted by residual:
  angle pdb=" F1  ALF A1603 "
        pdb="AL   ALF A1603 "
        pdb=" F2  ALF A1603 "
      ideal   model   delta    sigma   weight residual
     108.68  178.37  -69.69 3.00e+00 1.11e-01 5.40e+02
  angle pdb=" F3  ALF A1603 "
        pdb="AL   ALF A1603 "
        pdb=" F4  ALF A1603 "
      ideal   model   delta    sigma   weight residual
     109.63  178.39  -68.76 3.00e+00 1.11e-01 5.25e+02
  angle pdb=" F1  ALF A1603 "
        pdb="AL   ALF A1603 "
        pdb=" F3  ALF A1603 "
      ideal   model   delta    sigma   weight residual
     109.69   88.61   21.08 3.00e+00 1.11e-01 4.94e+01
  angle pdb=" F2  ALF A1603 "
        pdb="AL   ALF A1603 "
        pdb=" F4  ALF A1603 "
      ideal   model   delta    sigma   weight residual
     110.21   90.24   19.97 3.00e+00 1.11e-01 4.43e+01
  angle pdb=" F1  ALF A1603 "
        pdb="AL   ALF A1603 "
        pdb=" F4  ALF A1603 "
      ideal   model   delta    sigma   weight residual
     109.02   90.13   18.89 3.00e+00 1.11e-01 3.96e+01
  ... (remaining 15000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.11: 6406
       35.11 -    70.22: 235
       70.22 -   105.33: 14
      105.33 -   140.45: 5
      140.45 -   175.56: 1
  Dihedral angle restraints: 6661
    sinusoidal: 2798
      harmonic: 3863
  Sorted by residual:
  dihedral pdb=" C5' ADP A1602 "
           pdb=" O5' ADP A1602 "
           pdb=" PA  ADP A1602 "
           pdb=" O2A ADP A1602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  115.56 -175.56     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" CA  LYS B 170 "
           pdb=" C   LYS B 170 "
           pdb=" N   ASN B 171 "
           pdb=" CA  ASN B 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.60   31.40     0      5.00e+00 4.00e-02 3.94e+01
  dihedral pdb=" CA  PHE A1365 "
           pdb=" C   PHE A1365 "
           pdb=" N   PHE A1366 "
           pdb=" CA  PHE A1366 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.95  -25.05     0      5.00e+00 4.00e-02 2.51e+01
  ... (remaining 6658 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1066
       0.046 -    0.093: 469
       0.093 -    0.139: 119
       0.139 -    0.185: 13
       0.185 -    0.232: 5
  Chirality restraints: 1672
  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   -2.63    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CB  VAL B 190 "
            pdb=" CA  VAL B 190 "
            pdb=" CG1 VAL B 190 "
            pdb=" CG2 VAL B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 332 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.29e-01
  ... (remaining 1669 not shown)

  Planarity restraints: 1887
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1173 "    0.013 2.00e-02 2.50e+03   2.54e-02 6.44e+00
        pdb=" C   VAL A1173 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL A1173 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A1174 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A1225 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.31e+00
        pdb=" C   TYR A1225 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   TYR A1225 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN A1226 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1174 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.17e+00
        pdb=" C   LEU A1174 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   LEU A1174 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL A1175 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1884 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 85
        2.51 -     3.11: 8306
        3.11 -     3.71: 16323
        3.71 -     4.30: 24528
        4.30 -     4.90: 41949
  Nonbonded interactions: 91191
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 667 "
            pdb=" F2  ALF A1603 "
     model   vdw
     1.917 2.990
  nonbonded pdb=" OD2 ASP A 667 "
            pdb=" F3  ALF A1603 "
     model   vdw
     1.942 2.990
  nonbonded pdb=" O1B ADP A1602 "
            pdb=" F2  ALF A1603 "
     model   vdw
     2.159 2.990
  nonbonded pdb=" O   VAL A 237 "
            pdb=" OG1 THR A 238 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" O   SER B 237 "
            pdb=" OG  SER B 237 "
     model   vdw
     2.164 3.040
  ... (remaining 91186 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.850
  Find NCS groups from input model:        0.170
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
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      :  0.012   0.099  11080  Z= 0.515
  Angle     :  1.243  69.693  15036  Z= 0.552
  Chirality :  0.053   0.232   1672
  Planarity :  0.005   0.047   1882
  Dihedral  : 17.754 175.557   4177
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.91 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  8.04 %
    Allowed  : 13.99 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (0.20), residues: 1314
  helix: -0.96 (0.19), residues: 616
  sheet: -1.61 (0.36), residues: 158
  loop : -2.89 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1167 
 TYR   0.024   0.003   TYR A1326 
 PHE   0.022   0.002   PHE A1365 
 TRP   0.017   0.002   TRP A 603 
 HIS   0.008   0.002   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.01214 (11069)
  covalent geometry    : angle       1.23295 (15005)
  SS BOND              : bond        0.00607 (    2)
  SS BOND              : angle       1.41971 (    4)
  hydrogen bonds       : bond        0.12621 (  537)
  hydrogen bonds       : angle       5.74176 ( 1563)
  link_ALPHA1-4        : bond        0.00569 (    1)
  link_ALPHA1-4        : angle       4.34358 (    3)
  link_BETA1-4         : bond        0.00947 (    3)
  link_BETA1-4         : angle       2.88019 (    9)
  link_NAG-ASN         : bond        0.01388 (    5)
  link_NAG-ASN         : angle       4.37192 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 114
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  795 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8010 (mmtp)
REVERT: A  849 MET cc_start: 0.8053 (ttm) cc_final: 0.7773 (ttt)
REVERT: A 1006 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7985 (mt)
REVERT: A 1150 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7028 (tp30)
REVERT: A 1190 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.6856 (mt-10)
REVERT: A 1196 MET cc_start: 0.8255 (ttt) cc_final: 0.7862 (ttt)
REVERT: A 1264 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7283 (mm-30)
REVERT: B  188 ARG cc_start: 0.8112 (tpm170) cc_final: 0.7739 (ttp-170)
REVERT: B  236 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8684 (t0)
  outliers start: 92
  outliers final: 71
  residues processed: 197
  average time/residue: 0.0947
  time to fit residues: 27.6344
Evaluate side-chains
  171 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 97
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  574 TYR
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  651 SER
Chi-restraints excluded: chain A residue  747 VAL
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  920 TRP
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1024 GLU
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1243 ASP
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1291 VAL
Chi-restraints excluded: chain A residue 1295 ASN
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1300 SER
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1377 SER
Chi-restraints excluded: chain A residue 1387 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1400 GLN
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  155 GLN
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  195 GLU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  216 CYS
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  282 GLN
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
A 220 ASN
A 550 ASN
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 640 ASN
A 685 ASN
A 738 GLN
A 763 GLN
A 797 GLN
A 902 GLN
A 939 ASN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1139 GLN
A1195 ASN
A1293 HIS
A1295 ASN
A1331 GLN
A1417 HIS
B  60 GLN
B  97 ASN
B 131 HIS
B 155 GLN
B 186 HIS
B 246 GLN
B 341 GLN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.169051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.130725 restraints weight = 11414.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.77
r_work: 0.2897 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11080  Z= 0.145
  Angle     :  0.626  14.618  15036  Z= 0.318
  Chirality :  0.042   0.170   1672
  Planarity :  0.004   0.040   1882
  Dihedral  : 13.857 173.814   1811
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 18.18 %
    Favored  : 76.66 %
  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: -1.55 (0.22), residues: 1314
  helix: -0.02 (0.20), residues: 640
  sheet: -1.05 (0.37), residues: 164
  loop : -2.31 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1178 
 TYR   0.022   0.002   TYR B 280 
 PHE   0.015   0.001   PHE A1285 
 TRP   0.015   0.001   TRP A 926 
 HIS   0.003   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (11069)
  covalent geometry    : angle       0.61922 (15005)
  SS BOND              : bond        0.00359 (    2)
  SS BOND              : angle       1.39503 (    4)
  hydrogen bonds       : bond        0.05105 (  537)
  hydrogen bonds       : angle       4.86987 ( 1563)
  link_ALPHA1-4        : bond        0.01501 (    1)
  link_ALPHA1-4        : angle       3.12303 (    3)
  link_BETA1-4         : bond        0.00184 (    3)
  link_BETA1-4         : angle       1.45140 (    9)
  link_NAG-ASN         : bond        0.00216 (    5)
  link_NAG-ASN         : angle       2.34944 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 111
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  585 TYR cc_start: 0.8870 (m-80) cc_final: 0.8417 (m-80)
REVERT: A  726 MET cc_start: 0.7685 (ttt) cc_final: 0.7072 (ttt)
REVERT: A  729 GLU cc_start: 0.7009 (mt-10) cc_final: 0.5936 (mp0)
REVERT: A  795 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7556 (mmtp)
REVERT: A  849 MET cc_start: 0.8448 (ttm) cc_final: 0.8119 (ttt)
REVERT: A 1024 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.4547 (pm20)
REVERT: A 1087 ARG cc_start: 0.7783 (mtm180) cc_final: 0.7189 (mtp-110)
REVERT: A 1153 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7637 (mtt90)
REVERT: A 1196 MET cc_start: 0.8403 (ttt) cc_final: 0.8143 (ttt)
REVERT: A 1258 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8776 (m)
REVERT: A 1409 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6995 (mt-10)
REVERT: B  181 LYS cc_start: 0.8749 (mttt) cc_final: 0.8456 (mttm)
REVERT: B  188 ARG cc_start: 0.8444 (tpm170) cc_final: 0.7728 (ttp-170)
REVERT: B  190 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8557 (m)
REVERT: B  236 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8799 (t0)
  outliers start: 59
  outliers final: 37
  residues processed: 164
  average time/residue: 0.1013
  time to fit residues: 24.1387
Evaluate side-chains
  145 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 102
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  574 TYR
Chi-restraints excluded: chain A residue  747 VAL
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue  920 TRP
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue 1024 GLU
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1193 TYR
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1266 ASN
Chi-restraints excluded: chain A residue 1291 VAL
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1409 GLU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   chunk 126 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 763 GLN
A 998 ASN
** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1417 HIS
B  97 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.167941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.128828 restraints weight = 11467.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.81
r_work: 0.2880 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  11080  Z= 0.193
  Angle     :  0.618  13.927  15036  Z= 0.311
  Chirality :  0.044   0.164   1672
  Planarity :  0.004   0.043   1882
  Dihedral  : 12.798 174.342   1747
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 20.02 %
    Favored  : 74.83 %
  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: -1.07 (0.22), residues: 1314
  helix:  0.38 (0.20), residues: 639
  sheet: -0.80 (0.37), residues: 163
  loop : -2.08 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 880 
 TYR   0.020   0.002   TYR B 280 
 PHE   0.016   0.001   PHE A1365 
 TRP   0.014   0.001   TRP A 926 
 HIS   0.003   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (11069)
  covalent geometry    : angle       0.60852 (15005)
  SS BOND              : bond        0.00386 (    2)
  SS BOND              : angle       1.13222 (    4)
  hydrogen bonds       : bond        0.05139 (  537)
  hydrogen bonds       : angle       4.76850 ( 1563)
  link_ALPHA1-4        : bond        0.01289 (    1)
  link_ALPHA1-4        : angle       3.72399 (    3)
  link_BETA1-4         : bond        0.00310 (    3)
  link_BETA1-4         : angle       1.70631 (    9)
  link_NAG-ASN         : bond        0.00659 (    5)
  link_NAG-ASN         : angle       2.66747 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 108
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  726 MET cc_start: 0.7782 (ttt) cc_final: 0.7135 (ttt)
REVERT: A  729 GLU cc_start: 0.7042 (mt-10) cc_final: 0.5982 (mp0)
REVERT: A  795 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7591 (mmtp)
REVERT: A  849 MET cc_start: 0.8490 (ttm) cc_final: 0.8154 (ttt)
REVERT: A  954 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6110 (tp30)
REVERT: A 1087 ARG cc_start: 0.7855 (mtm180) cc_final: 0.7270 (mtm-85)
REVERT: A 1153 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7706 (mtt90)
REVERT: A 1196 MET cc_start: 0.8455 (ttt) cc_final: 0.8200 (ttt)
REVERT: A 1227 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7869 (mp)
REVERT: A 1391 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7912 (tp)
REVERT: A 1409 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7012 (mt-10)
REVERT: B  181 LYS cc_start: 0.8775 (mttt) cc_final: 0.8508 (mttm)
REVERT: B  188 ARG cc_start: 0.8510 (tpm170) cc_final: 0.7776 (ttp-170)
REVERT: B  190 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8498 (m)
REVERT: B  236 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8734 (t0)
  outliers start: 59
  outliers final: 40
  residues processed: 158
  average time/residue: 0.0909
  time to fit residues: 20.9334
Evaluate side-chains
  146 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 99
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  574 TYR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  747 VAL
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue  920 TRP
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue 1024 GLU
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1193 TYR
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1227 LEU
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1266 ASN
Chi-restraints excluded: chain A residue 1274 MET
Chi-restraints excluded: chain A residue 1291 VAL
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1409 GLU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  352 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 108 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0670
   chunk 103 optimal weight:    5.9990
   overall best weight:    1.0520

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.169968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.130690 restraints weight = 11429.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.87
r_work: 0.2947 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11080  Z= 0.146
  Angle     :  0.580  14.036  15036  Z= 0.291
  Chirality :  0.042   0.169   1672
  Planarity :  0.004   0.041   1882
  Dihedral  : 12.159 174.155   1741
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 20.02 %
    Favored  : 74.56 %
  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: -0.66 (0.23), residues: 1314
  helix:  0.77 (0.21), residues: 629
  sheet: -0.61 (0.37), residues: 163
  loop : -1.88 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 880 
 TYR   0.020   0.001   TYR B 280 
 PHE   0.015   0.001   PHE A1285 
 TRP   0.013   0.001   TRP A 926 
 HIS   0.002   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (11069)
  covalent geometry    : angle       0.57233 (15005)
  SS BOND              : bond        0.00308 (    2)
  SS BOND              : angle       0.78908 (    4)
  hydrogen bonds       : bond        0.04613 (  537)
  hydrogen bonds       : angle       4.59596 ( 1563)
  link_ALPHA1-4        : bond        0.01350 (    1)
  link_ALPHA1-4        : angle       3.55451 (    3)
  link_BETA1-4         : bond        0.00143 (    3)
  link_BETA1-4         : angle       1.46103 (    9)
  link_NAG-ASN         : bond        0.00455 (    5)
  link_NAG-ASN         : angle       2.31759 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 108
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  726 MET cc_start: 0.7643 (ttt) cc_final: 0.6996 (ttt)
REVERT: A  729 GLU cc_start: 0.6943 (mt-10) cc_final: 0.5931 (mp0)
REVERT: A  795 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7615 (mmtp)
REVERT: A  849 MET cc_start: 0.8472 (ttm) cc_final: 0.8118 (ttt)
REVERT: A  954 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6128 (tp30)
REVERT: A 1087 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7283 (mtm-85)
REVERT: A 1098 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7552 (mtt180)
REVERT: A 1153 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7658 (mtt90)
REVERT: A 1196 MET cc_start: 0.8438 (ttt) cc_final: 0.8181 (ttt)
REVERT: A 1208 TYR cc_start: 0.9153 (m-80) cc_final: 0.8538 (m-80)
REVERT: A 1227 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7763 (mt)
REVERT: A 1391 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7715 (tp)
REVERT: A 1409 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6999 (mt-10)
REVERT: B  181 LYS cc_start: 0.8734 (mttt) cc_final: 0.8464 (mttm)
REVERT: B  188 ARG cc_start: 0.8487 (tpm170) cc_final: 0.7763 (ttp-170)
REVERT: B  190 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8546 (m)
REVERT: B  236 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8709 (t0)
  outliers start: 62
  outliers final: 43
  residues processed: 163
  average time/residue: 0.0999
  time to fit residues: 23.5101
Evaluate side-chains
  153 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 102
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  574 TYR
Chi-restraints excluded: chain A residue  747 VAL
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue  920 TRP
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1098 ARG
Chi-restraints excluded: chain A residue 1133 ASN
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1193 TYR
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1227 LEU
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1266 ASN
Chi-restraints excluded: chain A residue 1274 MET
Chi-restraints excluded: chain A residue 1291 VAL
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1387 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain A residue 1409 GLU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  172 ASN
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  352 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0980
   chunk 89 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1226 ASN
B  97 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.175025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.135613 restraints weight = 11323.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.71
r_work: 0.3025 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11080  Z= 0.112
  Angle     :  0.544  13.007  15036  Z= 0.272
  Chirality :  0.041   0.171   1672
  Planarity :  0.003   0.039   1882
  Dihedral  : 11.400 172.658   1734
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 21.07 %
    Favored  : 74.39 %
  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: -0.36 (0.23), residues: 1314
  helix:  1.00 (0.21), residues: 638
  sheet: -0.47 (0.38), residues: 153
  loop : -1.75 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 723 
 TYR   0.020   0.001   TYR B 280 
 PHE   0.013   0.001   PHE A1285 
 TRP   0.012   0.001   TRP A 926 
 HIS   0.001   0.000   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (11069)
  covalent geometry    : angle       0.53756 (15005)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.73916 (    4)
  hydrogen bonds       : bond        0.04147 (  537)
  hydrogen bonds       : angle       4.41815 ( 1563)
  link_ALPHA1-4        : bond        0.01458 (    1)
  link_ALPHA1-4        : angle       3.44828 (    3)
  link_BETA1-4         : bond        0.00199 (    3)
  link_BETA1-4         : angle       1.30497 (    9)
  link_NAG-ASN         : bond        0.00764 (    5)
  link_NAG-ASN         : angle       1.99044 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 115
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 HIS cc_start: 0.4186 (OUTLIER) cc_final: 0.3011 (p-80)
REVERT: A  576 ASP cc_start: 0.7722 (t70) cc_final: 0.7370 (t70)
REVERT: A  695 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5906 (tm-30)
REVERT: A  795 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7663 (mmtp)
REVERT: A  849 MET cc_start: 0.8408 (ttm) cc_final: 0.8077 (ttt)
REVERT: A  954 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6046 (tp30)
REVERT: A 1087 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7377 (mtm-85)
REVERT: A 1098 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7460 (mtt180)
REVERT: A 1153 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7705 (mtp85)
REVERT: A 1196 MET cc_start: 0.8370 (ttt) cc_final: 0.8133 (ttt)
REVERT: A 1208 TYR cc_start: 0.9099 (m-80) cc_final: 0.8666 (m-80)
REVERT: A 1391 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7669 (tp)
REVERT: A 1409 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6957 (mt-10)
REVERT: B  181 LYS cc_start: 0.8697 (mttt) cc_final: 0.8416 (mttm)
REVERT: B  188 ARG cc_start: 0.8507 (tpm170) cc_final: 0.7830 (ttp-170)
REVERT: B  190 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8595 (m)
  outliers start: 52
  outliers final: 35
  residues processed: 160
  average time/residue: 0.1010
  time to fit residues: 23.2815
Evaluate side-chains
  148 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 105
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  747 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue  920 TRP
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1098 ARG
Chi-restraints excluded: chain A residue 1133 ASN
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1193 TYR
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1274 MET
Chi-restraints excluded: chain A residue 1291 VAL
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1387 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1409 GLU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   97 ASN
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  172 ASN
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 125 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0030
   chunk 101 optimal weight:    0.0010
   chunk 44 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.4002

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1226 ASN
A1417 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.172858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.135469 restraints weight = 11463.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.87
r_work: 0.2899 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11080  Z= 0.170
  Angle     :  0.585  13.869  15036  Z= 0.292
  Chirality :  0.043   0.167   1672
  Planarity :  0.004   0.041   1882
  Dihedral  : 11.243 174.027   1722
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 21.07 %
    Favored  : 74.13 %
  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: -0.34 (0.23), residues: 1314
  helix:  0.99 (0.21), residues: 635
  sheet: -0.43 (0.38), residues: 153
  loop : -1.69 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 723 
 TYR   0.019   0.002   TYR B 280 
 PHE   0.016   0.001   PHE A1285 
 TRP   0.013   0.001   TRP A 926 
 HIS   0.003   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (11069)
  covalent geometry    : angle       0.57675 (15005)
  SS BOND              : bond        0.00373 (    2)
  SS BOND              : angle       0.86188 (    4)
  hydrogen bonds       : bond        0.04568 (  537)
  hydrogen bonds       : angle       4.50707 ( 1563)
  link_ALPHA1-4        : bond        0.01216 (    1)
  link_ALPHA1-4        : angle       3.69219 (    3)
  link_BETA1-4         : bond        0.00199 (    3)
  link_BETA1-4         : angle       1.53404 (    9)
  link_NAG-ASN         : bond        0.00618 (    5)
  link_NAG-ASN         : angle       2.45992 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 112
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 HIS cc_start: 0.4198 (OUTLIER) cc_final: 0.3035 (p-80)
REVERT: A  576 ASP cc_start: 0.7773 (t70) cc_final: 0.7421 (t70)
REVERT: A  695 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5874 (tm-30)
REVERT: A  795 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7656 (mmtp)
REVERT: A  849 MET cc_start: 0.8426 (ttm) cc_final: 0.8072 (ttt)
REVERT: A  954 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6081 (tp30)
REVERT: A  976 GLU cc_start: 0.8372 (tp30) cc_final: 0.8125 (tp30)
REVERT: A 1087 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7337 (mtm-85)
REVERT: A 1098 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7495 (mtt180)
REVERT: A 1153 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7724 (mtp85)
REVERT: A 1196 MET cc_start: 0.8398 (ttt) cc_final: 0.8138 (ttt)
REVERT: A 1227 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7618 (mp)
REVERT: A 1391 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7721 (tp)
REVERT: A 1409 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7012 (mt-10)
REVERT: B  181 LYS cc_start: 0.8710 (mttt) cc_final: 0.8446 (mttm)
REVERT: B  188 ARG cc_start: 0.8521 (tpm170) cc_final: 0.7787 (ttp-170)
REVERT: B  190 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8631 (m)
  outliers start: 55
  outliers final: 40
  residues processed: 159
  average time/residue: 0.0904
  time to fit residues: 20.9893
Evaluate side-chains
  153 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 104
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  747 VAL
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue  920 TRP
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1098 ARG
Chi-restraints excluded: chain A residue 1133 ASN
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1193 TYR
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1227 LEU
Chi-restraints excluded: chain A residue 1266 ASN
Chi-restraints excluded: chain A residue 1274 MET
Chi-restraints excluded: chain A residue 1291 VAL
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1387 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain A residue 1409 GLU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   chunk 5 optimal weight:    9.9990
   chunk 129 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 116 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.173103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.132320 restraints weight = 11431.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.87
r_work: 0.2976 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11080  Z= 0.156
  Angle     :  0.580  14.197  15036  Z= 0.289
  Chirality :  0.042   0.177   1672
  Planarity :  0.004   0.040   1882
  Dihedral  : 11.110 174.741   1722
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 20.89 %
    Favored  : 73.78 %
  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: -0.29 (0.23), residues: 1314
  helix:  1.02 (0.21), residues: 636
  sheet: -0.40 (0.39), residues: 153
  loop : -1.67 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 723 
 TYR   0.019   0.001   TYR B 280 
 PHE   0.015   0.001   PHE A1285 
 TRP   0.012   0.001   TRP A 926 
 HIS   0.003   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (11069)
  covalent geometry    : angle       0.57224 (15005)
  SS BOND              : bond        0.00361 (    2)
  SS BOND              : angle       0.77898 (    4)
  hydrogen bonds       : bond        0.04539 (  537)
  hydrogen bonds       : angle       4.49797 ( 1563)
  link_ALPHA1-4        : bond        0.01373 (    1)
  link_ALPHA1-4        : angle       3.68738 (    3)
  link_BETA1-4         : bond        0.00126 (    3)
  link_BETA1-4         : angle       1.48223 (    9)
  link_NAG-ASN         : bond        0.00501 (    5)
  link_NAG-ASN         : angle       2.35333 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 107
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 HIS cc_start: 0.4202 (OUTLIER) cc_final: 0.3039 (p-80)
REVERT: A  576 ASP cc_start: 0.7799 (t70) cc_final: 0.7449 (t70)
REVERT: A  695 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5860 (tm-30)
REVERT: A  747 VAL cc_start: 0.7236 (OUTLIER) cc_final: 0.6876 (t)
REVERT: A  795 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7630 (mmtp)
REVERT: A  849 MET cc_start: 0.8417 (ttm) cc_final: 0.8052 (ttt)
REVERT: A  954 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6097 (tp30)
REVERT: A 1087 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7381 (mtm-85)
REVERT: A 1098 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7433 (mtt180)
REVERT: A 1153 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7707 (mtp85)
REVERT: A 1196 MET cc_start: 0.8358 (ttt) cc_final: 0.8107 (ttt)
REVERT: A 1227 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7615 (mp)
REVERT: A 1391 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7747 (tp)
REVERT: A 1409 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7009 (mt-10)
REVERT: B  181 LYS cc_start: 0.8719 (mttt) cc_final: 0.8466 (mttm)
REVERT: B  188 ARG cc_start: 0.8511 (tpm170) cc_final: 0.7803 (ttp-170)
REVERT: B  190 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8608 (m)
  outliers start: 61
  outliers final: 46
  residues processed: 160
  average time/residue: 0.1031
  time to fit residues: 23.8653
Evaluate side-chains
  160 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 104
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  574 TYR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  747 VAL
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue  920 TRP
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1098 ARG
Chi-restraints excluded: chain A residue 1133 ASN
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1193 TYR
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1227 LEU
Chi-restraints excluded: chain A residue 1266 ASN
Chi-restraints excluded: chain A residue 1274 MET
Chi-restraints excluded: chain A residue 1291 VAL
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1387 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain A residue 1409 GLU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  172 ASN
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  216 CYS
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0980
   chunk 23 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 89 optimal weight:    0.8980
   chunk 25 optimal weight:   20.0000
   chunk 114 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
B  97 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.172370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.132535 restraints weight = 11399.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.74
r_work: 0.2959 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11080  Z= 0.126
  Angle     :  0.559  14.328  15036  Z= 0.279
  Chirality :  0.041   0.168   1672
  Planarity :  0.003   0.039   1882
  Dihedral  : 10.775 174.509   1720
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 20.89 %
    Favored  : 73.95 %
  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: -0.19 (0.23), residues: 1314
  helix:  1.10 (0.21), residues: 641
  sheet: -0.33 (0.39), residues: 153
  loop : -1.64 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 723 
 TYR   0.020   0.001   TYR B 280 
 PHE   0.014   0.001   PHE A1285 
 TRP   0.012   0.001   TRP A 926 
 HIS   0.002   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (11069)
  covalent geometry    : angle       0.55260 (15005)
  SS BOND              : bond        0.00279 (    2)
  SS BOND              : angle       0.61553 (    4)
  hydrogen bonds       : bond        0.04240 (  537)
  hydrogen bonds       : angle       4.44580 ( 1563)
  link_ALPHA1-4        : bond        0.01506 (    1)
  link_ALPHA1-4        : angle       3.55488 (    3)
  link_BETA1-4         : bond        0.00181 (    3)
  link_BETA1-4         : angle       1.32837 (    9)
  link_NAG-ASN         : bond        0.00516 (    5)
  link_NAG-ASN         : angle       2.13786 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 106
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 HIS cc_start: 0.4148 (OUTLIER) cc_final: 0.3008 (p-80)
REVERT: A  576 ASP cc_start: 0.7689 (t70) cc_final: 0.7324 (t70)
REVERT: A  695 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5868 (tm-30)
REVERT: A  795 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7640 (mmtp)
REVERT: A  849 MET cc_start: 0.8366 (ttm) cc_final: 0.7957 (ttt)
REVERT: A  943 GLU cc_start: 0.8093 (mp0) cc_final: 0.7674 (mp0)
REVERT: A  954 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6066 (tp30)
REVERT: A 1087 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7306 (mtm-85)
REVERT: A 1153 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7790 (mtp85)
REVERT: A 1196 MET cc_start: 0.8318 (ttt) cc_final: 0.8069 (ttt)
REVERT: A 1208 TYR cc_start: 0.9121 (m-80) cc_final: 0.8617 (m-80)
REVERT: A 1227 LEU cc_start: 0.7874 (tp) cc_final: 0.7498 (mp)
REVERT: A 1391 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7703 (tp)
REVERT: A 1409 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6937 (mt-10)
REVERT: B  181 LYS cc_start: 0.8686 (mttt) cc_final: 0.8397 (mttm)
REVERT: B  188 ARG cc_start: 0.8504 (tpm170) cc_final: 0.7824 (ttt180)
REVERT: B  190 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8653 (m)
REVERT: B  236 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8660 (t0)
  outliers start: 59
  outliers final: 42
  residues processed: 159
  average time/residue: 0.1045
  time to fit residues: 23.6893
Evaluate side-chains
  152 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 102
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  574 TYR
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue  920 TRP
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1133 ASN
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1193 TYR
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1266 ASN
Chi-restraints excluded: chain A residue 1274 MET
Chi-restraints excluded: chain A residue 1291 VAL
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1387 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain A residue 1409 GLU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  172 ASN
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  216 CYS
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 122 optimal weight:    0.0980
   chunk 27 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 23 optimal weight:    8.9990
   chunk 81 optimal weight:    0.0060
   chunk 72 optimal weight:    0.7980
   chunk 108 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
B  97 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.174448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.134016 restraints weight = 11245.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.75
r_work: 0.3100 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  11080  Z= 0.112
  Angle     :  0.555  15.753  15036  Z= 0.276
  Chirality :  0.041   0.172   1672
  Planarity :  0.003   0.039   1882
  Dihedral  : 10.323 172.650   1719
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 21.94 %
    Favored  : 73.78 %
  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: -0.08 (0.23), residues: 1314
  helix:  1.19 (0.21), residues: 642
  sheet: -0.18 (0.40), residues: 151
  loop : -1.62 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 723 
 TYR   0.020   0.001   TYR B 280 
 PHE   0.013   0.001   PHE A1285 
 TRP   0.011   0.001   TRP A 926 
 HIS   0.001   0.000   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (11069)
  covalent geometry    : angle       0.54864 (15005)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       0.59548 (    4)
  hydrogen bonds       : bond        0.03953 (  537)
  hydrogen bonds       : angle       4.36684 ( 1563)
  link_ALPHA1-4        : bond        0.01494 (    1)
  link_ALPHA1-4        : angle       3.43503 (    3)
  link_BETA1-4         : bond        0.00309 (    3)
  link_BETA1-4         : angle       1.23375 (    9)
  link_NAG-ASN         : bond        0.00642 (    5)
  link_NAG-ASN         : angle       1.98542 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 109
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 HIS cc_start: 0.4090 (OUTLIER) cc_final: 0.2956 (p-80)
REVERT: A  576 ASP cc_start: 0.7648 (t70) cc_final: 0.7334 (t70)
REVERT: A  585 TYR cc_start: 0.8815 (m-80) cc_final: 0.8482 (m-80)
REVERT: A  685 ASN cc_start: 0.8218 (t0) cc_final: 0.7807 (t0)
REVERT: A  695 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5933 (tm-30)
REVERT: A  718 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7505 (mt-10)
REVERT: A  826 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6886 (tp30)
REVERT: A  849 MET cc_start: 0.8410 (ttm) cc_final: 0.8037 (ttt)
REVERT: A  943 GLU cc_start: 0.8135 (mp0) cc_final: 0.7756 (mp0)
REVERT: A  949 ASP cc_start: 0.7545 (m-30) cc_final: 0.7213 (t70)
REVERT: A  954 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6044 (tp30)
REVERT: A 1051 GLU cc_start: 0.7558 (pm20) cc_final: 0.7355 (pm20)
REVERT: A 1087 ARG cc_start: 0.7952 (mtm180) cc_final: 0.7356 (mtm-85)
REVERT: A 1153 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7470 (mtp85)
REVERT: A 1196 MET cc_start: 0.8310 (ttt) cc_final: 0.8097 (ttt)
REVERT: A 1208 TYR cc_start: 0.9077 (m-80) cc_final: 0.8669 (m-80)
REVERT: A 1323 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7338 (m)
REVERT: A 1391 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7635 (tp)
REVERT: A 1409 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6900 (mt-10)
REVERT: B  181 LYS cc_start: 0.8677 (mttt) cc_final: 0.8370 (mttm)
REVERT: B  188 ARG cc_start: 0.8532 (tpm170) cc_final: 0.7879 (ttt180)
REVERT: B  190 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8644 (m)
  outliers start: 49
  outliers final: 36
  residues processed: 154
  average time/residue: 0.1015
  time to fit residues: 22.6226
Evaluate side-chains
  144 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 100
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  574 TYR
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1133 ASN
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1193 TYR
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1266 ASN
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1387 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain A residue 1409 GLU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  216 CYS
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 125 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0050
   chunk 45 optimal weight:    0.0170
   chunk 39 optimal weight:    8.9990
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.4232

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
B  97 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.175632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.137998 restraints weight = 11259.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.56
r_work: 0.3123 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11080  Z= 0.108
  Angle     :  0.550  15.811  15036  Z= 0.274
  Chirality :  0.041   0.172   1672
  Planarity :  0.003   0.039   1882
  Dihedral  :  9.983 169.638   1716
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.38 %
    Favored  : 73.69 %
  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:  0.02 (0.23), residues: 1314
  helix:  1.28 (0.21), residues: 640
  sheet: -0.03 (0.42), residues: 138
  loop : -1.56 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 723 
 TYR   0.019   0.001   TYR B 280 
 PHE   0.012   0.001   PHE A1285 
 TRP   0.011   0.001   TRP A 926 
 HIS   0.005   0.001   HIS A 769 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (11069)
  covalent geometry    : angle       0.54390 (15005)
  SS BOND              : bond        0.00169 (    2)
  SS BOND              : angle       0.52321 (    4)
  hydrogen bonds       : bond        0.03878 (  537)
  hydrogen bonds       : angle       4.33179 ( 1563)
  link_ALPHA1-4        : bond        0.01590 (    1)
  link_ALPHA1-4        : angle       3.44071 (    3)
  link_BETA1-4         : bond        0.00305 (    3)
  link_BETA1-4         : angle       1.18725 (    9)
  link_NAG-ASN         : bond        0.00504 (    5)
  link_NAG-ASN         : angle       1.96532 (   15)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 106
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 HIS cc_start: 0.4105 (OUTLIER) cc_final: 0.2899 (p-80)
REVERT: A  576 ASP cc_start: 0.7568 (t70) cc_final: 0.7253 (t70)
REVERT: A  685 ASN cc_start: 0.8109 (t0) cc_final: 0.7777 (t0)
REVERT: A  695 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6016 (tm-30)
REVERT: A  718 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7483 (mt-10)
REVERT: A  747 VAL cc_start: 0.7181 (OUTLIER) cc_final: 0.6865 (t)
REVERT: A  849 MET cc_start: 0.8371 (ttm) cc_final: 0.8004 (ttt)
REVERT: A  943 GLU cc_start: 0.8156 (mp0) cc_final: 0.7790 (mp0)
REVERT: A  949 ASP cc_start: 0.7479 (m-30) cc_final: 0.7222 (t0)
REVERT: A  954 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.5991 (tp30)
REVERT: A 1087 ARG cc_start: 0.8006 (mtm180) cc_final: 0.7440 (mtm-85)
REVERT: A 1208 TYR cc_start: 0.9106 (m-80) cc_final: 0.8666 (m-80)
REVERT: A 1323 CYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7340 (m)
REVERT: A 1391 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7678 (tp)
REVERT: A 1409 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7521 (mm-30)
REVERT: B  181 LYS cc_start: 0.8682 (mttt) cc_final: 0.8387 (mttm)
REVERT: B  188 ARG cc_start: 0.8560 (tpm170) cc_final: 0.7933 (ttt180)
REVERT: B  190 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8631 (m)
  outliers start: 45
  outliers final: 33
  residues processed: 147
  average time/residue: 0.1138
  time to fit residues: 23.8434
Evaluate side-chains
  144 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 103
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  574 TYR
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  747 VAL
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1133 ASN
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1153 ARG
Chi-restraints excluded: chain A residue 1169 LEU
Chi-restraints excluded: chain A residue 1190 GLU
Chi-restraints excluded: chain A residue 1193 TYR
Chi-restraints excluded: chain A residue 1218 GLU
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1323 CYS
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1387 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain A residue 1409 GLU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  216 CYS
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 106 optimal weight:    6.9990
   chunk 113 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 119 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 123 optimal weight:    0.0980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.174365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.134849 restraints weight = 11361.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.72
r_work: 0.2973 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  11080  Z= 0.120
  Angle     :  0.559  15.859  15036  Z= 0.278
  Chirality :  0.041   0.185   1672
  Planarity :  0.003   0.039   1882
  Dihedral  :  9.894 167.864   1715
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 22.55 %
    Favored  : 73.60 %
  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:  0.05 (0.23), residues: 1314
  helix:  1.29 (0.21), residues: 641
  sheet: -0.01 (0.42), residues: 138
  loop : -1.55 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 723 
 TYR   0.019   0.001   TYR B 280 
 PHE   0.013   0.001   PHE A1285 
 TRP   0.008   0.001   TRP A 926 
 HIS   0.002   0.001   HIS A1176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11069)
  covalent geometry    : angle       0.55227 (15005)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       0.56829 (    4)
  hydrogen bonds       : bond        0.03969 (  537)
  hydrogen bonds       : angle       4.31926 ( 1563)
  link_ALPHA1-4        : bond        0.01394 (    1)
  link_ALPHA1-4        : angle       3.52188 (    3)
  link_BETA1-4         : bond        0.00196 (    3)
  link_BETA1-4         : angle       1.22367 (    9)
  link_NAG-ASN         : bond        0.00555 (    5)
  link_NAG-ASN         : angle       2.09890 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3063.52 seconds
wall clock time: 53 minutes 9.72 seconds (3189.72 seconds total)