Starting phenix.real_space_refine
on Tue Jul 29 03:02:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ky8_23071/07_2025/7ky8_23071.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ky8_23071/07_2025/7ky8_23071.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2025/7ky8_23071.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2025/7ky8_23071.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2025/7ky8_23071.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2025/7ky8_23071.cif"
  }
  resolution = 3.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      53      5.16       5
     C    6798      2.51       5
     N    1693      2.21       5
     O    1972      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10520
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 7237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 910, 7237
          Classifications: {'peptide': 910}
          Link IDs: {'PTRANS': 25, 'TRANS': 884}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2950
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 19, 'TRANS': 344}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 51
          Unusual residues: {'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "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: "F"
      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: 156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 156
          Unusual residues: {' MG': 1, 'ACP': 1, 'CLR': 4, 'MAN': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 42
          Unusual residues: {'CLR': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.34, per 1000 atoms: 0.60
  Number of scatterers: 10520
  At special positions: 0
  Unit cell: (132.16, 120.596, 131.334, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      53     16.00
     P       3     15.00
     Mg      1     11.99
     O    1972      8.00
     N    1693      7.00
     C    6798      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Links applied
    ALPHA1-4
      " NAG D   2 " - " MAN D   3 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG B 502 " - " ASN B 113 "
      " NAG C   1 " - " ASN B 298 "
      " NAG D   1 " - " ASN B 240 "
      " NAG E   1 " - " ASN B 256 "
      " NAG F   1 " - " ASN B 332 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.77
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2382

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 9 sheets defined
      49.9% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 283 through 299
      removed outlier: 4.015A  pdb=" N   VAL A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE A 288 " --> pdb=" O   PRO A 284 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A 290 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ALA A 293 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 616
      removed outlier: 4.306A  pdb=" N   GLU A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 622
    Processing helix  chain 'A' and resid 641 through 655
    Processing helix  chain 'A' and resid 656 through 658
      No H-bonds generated for 'chain 'A' and resid 656 through 658'
    Processing helix  chain 'A' and resid 661 through 679
      removed outlier: 4.015A  pdb=" N   GLU A 667 " --> pdb=" O   TYR A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 682
      No H-bonds generated for 'chain 'A' and resid 680 through 682'
    Processing helix  chain 'A' and resid 701 through 706
      removed outlier: 3.619A  pdb=" N   GLN A 705 " --> pdb=" O   ASP A 702 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ILE A 706 " --> pdb=" O   LEU A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 750
    Processing helix  chain 'A' and resid 754 through 779
    Processing helix  chain 'A' and resid 793 through 802
      removed outlier: 4.129A  pdb=" N   VAL A 797 " --> pdb=" O   SER A 793 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLU A 798 " --> pdb=" O   LYS A 794 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASP A 799 " --> pdb=" O   GLU A 795 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   LYS A 801 " --> pdb=" O   VAL A 797 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLY A 802 " --> pdb=" O   GLU A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 822
    Processing helix  chain 'A' and resid 843 through 857
    Processing helix  chain 'A' and resid 918 through 925
    Processing helix  chain 'A' and resid 934 through 949
      removed outlier: 3.592A  pdb=" N   GLU A 949 " --> pdb=" O   GLU A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 962 through 977
    Processing helix  chain 'A' and resid 982 through 995
      removed outlier: 4.420A  pdb=" N   GLU A 986 " --> pdb=" O   ASN A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1024
    Processing helix  chain 'A' and resid 1035 through 1046
    Processing helix  chain 'A' and resid 1071 through 1088
    Processing helix  chain 'A' and resid 1095 through 1103
    Processing helix  chain 'A' and resid 1116 through 1124
    Processing helix  chain 'A' and resid 1126 through 1137
    Processing helix  chain 'A' and resid 1149 through 1163
    Processing helix  chain 'A' and resid 1177 through 1183
    Processing helix  chain 'A' and resid 1196 through 1201
      removed outlier: 3.522A  pdb=" N   CYS A1201 " --> pdb=" O   GLN A1197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1208 through 1210
      No H-bonds generated for 'chain 'A' and resid 1208 through 1210'
    Processing helix  chain 'A' and resid 1211 through 1216
    Processing helix  chain 'A' and resid 1218 through 1251
      Proline residue:  A1232  - end of helix
      removed outlier: 3.681A  pdb=" N   ASN A1238 " --> pdb=" O   PHE A1234 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   PHE A1241 " --> pdb=" O   LYS A1237 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   SER A1244 " --> pdb=" O   ILE A1240 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   TYR A1251 " --> pdb=" O   TRP A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1252 through 1255
    Processing helix  chain 'A' and resid 1274 through 1283
      removed outlier: 3.881A  pdb=" N   ILE A1278 " --> pdb=" O   SER A1274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1288 through 1295
    Processing helix  chain 'A' and resid 1296 through 1303
    Processing helix  chain 'A' and resid 1309 through 1336
      removed outlier: 3.533A  pdb=" N   PHE A1313 " --> pdb=" O   ASN A1309 " (cutoff:3.500A)
      Proline residue:  A1331  - end of helix
    Processing helix  chain 'A' and resid 1350 through 1373
    Processing helix  chain 'A' and resid 1380 through 1401
    Processing helix  chain 'A' and resid 1402 through 1406
      removed outlier: 3.624A  pdb=" N   ASN A1406 " --> pdb=" O   SER A1403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1416
    Processing helix  chain 'A' and resid 1418 through 1442
      removed outlier: 3.656A  pdb=" N   TRP A1422 " --> pdb=" O   GLN A1418 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL A1427 " --> pdb=" O   ALA A1423 " (cutoff:3.500A)
      Proline residue:  A1435  - end of helix
    Processing helix  chain 'A' and resid 1449 through 1461
    Processing helix  chain 'B' and resid 71 through 74
    Processing helix  chain 'B' and resid 75 through 98
    Processing helix  chain 'B' and resid 186 through 191
    Processing helix  chain 'B' and resid 194 through 200
      removed outlier: 3.564A  pdb=" N   ILE B 198 " --> pdb=" O   SER B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 208
      removed outlier: 3.655A  pdb=" N   VAL B 208 " --> pdb=" O   TYR B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 238
      removed outlier: 3.739A  pdb=" N   MET B 238 " --> pdb=" O   ALA B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 272
    Processing helix  chain 'B' and resid 286 through 290
      removed outlier: 3.757A  pdb=" N   GLU B 290 " --> pdb=" O   PRO B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 315
    Processing helix  chain 'B' and resid 350 through 354
    Processing helix  chain 'B' and resid 372 through 399
    Processing helix  chain 'B' and resid 405 through 409
      removed outlier: 3.805A  pdb=" N   LEU B 409 " --> pdb=" O   ALA B 406 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 684 through 685
      removed outlier: 3.717A  pdb=" N   ASN A 685 " --> pdb=" O   TYR A 690 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR A 690 " --> pdb=" O   ASN A 685 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1055 through 1057
      removed outlier: 6.398A  pdb=" N   VAL A1030 " --> pdb=" O   CYS A1145 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 732 through 734
      removed outlier: 6.857A  pdb=" N   ALA A1005 " --> pdb=" O   LYS A 725 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   CYS A 727 " --> pdb=" O   GLY A1003 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   GLY A1003 " --> pdb=" O   CYS A 727 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   ILE A 729 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
      removed outlier: 9.352A  pdb=" N   LEU A1001 " --> pdb=" O   ILE A 729 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LEU A 956 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   GLY A1003 " --> pdb=" O   LEU A 954 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU A 954 " --> pdb=" O   GLY A1003 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   ALA A1005 " --> pdb=" O   ARG A 952 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ARG A 952 " --> pdb=" O   ALA A1005 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LYS A 899 " --> pdb=" O   VAL A 881 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   VAL A 881 " --> pdb=" O   LYS A 899 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 858 through 860
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1188 through 1190
      removed outlier: 6.548A  pdb=" N   GLY A1189 " --> pdb=" O   ILE A1206 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1377 through 1378
    Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 129
      removed outlier: 6.179A  pdb=" N   TYR B 177 " --> pdb=" O   LEU B 326 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   LEU B 326 " --> pdb=" O   TYR B 177 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   LEU B 179 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   THR B 324 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 120
      removed outlier: 5.691A  pdb=" N   ASP B 343 " --> pdb=" O   GLN B 246 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   GLN B 246 " --> pdb=" O   ASP B 343 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 228
      removed outlier: 6.342A  pdb=" N   ILE B 227 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    490 hydrogen bonds defined for protein.
    1362 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.46

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3273
        1.34 -     1.46: 2276
        1.46 -     1.58: 5137
        1.58 -     1.69: 6
        1.69 -     1.81: 78
  Bond restraints: 10770
  Sorted by residual:
  bond pdb=" O2B ACP A1706 "
       pdb=" PB  ACP A1706 "
    ideal  model  delta    sigma   weight residual
    1.507  1.610 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" O3A ACP A1706 "
       pdb=" PB  ACP A1706 "
    ideal  model  delta    sigma   weight residual
    1.698  1.610  0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" C4  ACP A1706 "
       pdb=" C5  ACP A1706 "
    ideal  model  delta    sigma   weight residual
    1.386  1.470 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" O3G ACP A1706 "
       pdb=" PG  ACP A1706 "
    ideal  model  delta    sigma   weight residual
    1.532  1.610 -0.078 2.00e-02 2.50e+03 1.51e+01
  bond pdb=" C5  ACP A1706 "
       pdb=" C6  ACP A1706 "
    ideal  model  delta    sigma   weight residual
    1.407  1.482 -0.075 2.00e-02 2.50e+03 1.40e+01
  ... (remaining 10765 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 14343
        2.29 -     4.57: 240
        4.57 -     6.86: 52
        6.86 -     9.14: 5
        9.14 -    11.43: 3
  Bond angle restraints: 14643
  Sorted by residual:
  angle pdb=" N   LEU A1164 "
        pdb=" CA  LEU A1164 "
        pdb=" C   LEU A1164 "
      ideal   model   delta    sigma   weight residual
     111.02  104.71    6.31 1.25e+00 6.40e-01 2.54e+01
  angle pdb=" C3B ACP A1706 "
        pdb=" PB  ACP A1706 "
        pdb=" O3A ACP A1706 "
      ideal   model   delta    sigma   weight residual
      98.05  109.48  -11.43 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" C   ARG B 316 "
        pdb=" CA  ARG B 316 "
        pdb=" CB  ARG B 316 "
      ideal   model   delta    sigma   weight residual
     110.44  113.63   -3.19 9.00e-01 1.23e+00 1.26e+01
  angle pdb=" O1B ACP A1706 "
        pdb=" PB  ACP A1706 "
        pdb=" O2B ACP A1706 "
      ideal   model   delta    sigma   weight residual
     119.60  109.45   10.15 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" C   PHE A1408 "
        pdb=" N   TYR A1409 "
        pdb=" CA  TYR A1409 "
      ideal   model   delta    sigma   weight residual
     121.54  127.60   -6.06 1.91e+00 2.74e-01 1.01e+01
  ... (remaining 14638 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.89: 6325
       23.89 -    47.78: 391
       47.78 -    71.67: 46
       71.67 -    95.57: 17
       95.57 -   119.46: 6
  Dihedral angle restraints: 6785
    sinusoidal: 3071
      harmonic: 3714
  Sorted by residual:
  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  157.40   22.60     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  GLY A 802 "
           pdb=" C   GLY A 802 "
           pdb=" N   SER A 803 "
           pdb=" CA  SER A 803 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.97  -22.03     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  LEU A1348 "
           pdb=" C   LEU A1348 "
           pdb=" N   ASP A1349 "
           pdb=" CA  ASP A1349 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.63   20.37     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 6782 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1451
       0.071 -    0.141: 199
       0.141 -    0.212: 8
       0.212 -    0.282: 9
       0.282 -    0.353: 6
  Chirality restraints: 1673
  Sorted by residual:
  chirality pdb=" C14 CLR A1704 "
            pdb=" C13 CLR A1704 "
            pdb=" C15 CLR A1704 "
            pdb=" C8  CLR A1704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.67    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" C14 CLR B 501 "
            pdb=" C13 CLR B 501 "
            pdb=" C15 CLR B 501 "
            pdb=" C8  CLR B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.66    0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" C14 CLR A1703 "
            pdb=" C13 CLR A1703 "
            pdb=" C15 CLR A1703 "
            pdb=" C8  CLR A1703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.64    0.32 2.00e-01 2.50e+01 2.62e+00
  ... (remaining 1670 not shown)

  Planarity restraints: 1810
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A1461 "    0.020 2.00e-02 2.50e+03   3.83e-02 1.47e+01
        pdb=" C   GLY A1461 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   GLY A1461 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ASP A1462 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 398 "    0.016 2.00e-02 2.50e+03   3.05e-02 9.28e+00
        pdb=" C   PHE B 398 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   PHE B 398 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLY B 399 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 142 "    0.021 2.00e-02 2.50e+03   1.92e-02 9.21e+00
        pdb=" CG  TRP B 142 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 142 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 142 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 142 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 142 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 142 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 142 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 142 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 142 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1807 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1263
        2.75 -     3.28: 10765
        3.28 -     3.82: 17322
        3.82 -     4.36: 20255
        4.36 -     4.90: 34921
  Nonbonded interactions: 84526
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 588 "
            pdb=" OD1 ASP A 701 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG  SER A 588 "
            pdb=" OD1 ASP A 702 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG1 THR A 929 "
            pdb=" OE1 GLN A 930 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" NH1 ARG A1226 "
            pdb=" O   VAL A1282 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" ND2 ASN A1252 "
            pdb=" OG  SER A1257 "
     model   vdw
     2.241 3.120
  ... (remaining 84521 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 'C'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     26.450
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
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      :  0.005   0.103  10783  Z= 0.222
  Angle     :  0.746  11.425  14677  Z= 0.365
  Chirality :  0.053   0.353   1673
  Planarity :  0.003   0.038   1805
  Dihedral  : 15.267 119.457   4397
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.25), residues: 1266
  helix:  0.39 (0.22), residues: 581
  sheet: -1.48 (0.42), residues: 159
  loop : -2.05 (0.29), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP B 142 
 HIS   0.003   0.001   HIS B 125 
 PHE   0.017   0.001   PHE A 791 
 TYR   0.020   0.001   TYR B 378 
 ARG   0.007   0.000   ARG A1131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00171 (    5)
  link_NAG-ASN         : angle       2.38861 (   15)
  link_ALPHA1-4        : bond        0.00362 (    1)
  link_ALPHA1-4        : angle       2.60758 (    3)
  link_BETA1-4         : bond        0.00542 (    4)
  link_BETA1-4         : angle       0.94561 (   12)
  hydrogen bonds       : bond        0.13621 (  490)
  hydrogen bonds       : angle       5.70977 ( 1362)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.54991 (    4)
  covalent geometry    : bond        0.00467 (10770)
  covalent geometry    : angle       0.74144 (14643)
  Misc. bond           : bond        0.00048 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.076 
Fit side-chains
REVERT: A  771 MET cc_start: 0.6518 (ttp) cc_final: 0.5904 (ttt)
REVERT: B  112 THR cc_start: 0.8338 (p) cc_final: 0.8127 (p)
REVERT: B  261 ASN cc_start: 0.8935 (p0) cc_final: 0.8677 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2189
  time to fit residues: 47.4494
Evaluate side-chains
  110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    0.2980
   chunk 96 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 115 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN
A1253 ASN
** B  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.156369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.116082 restraints weight = 12851.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.114517 restraints weight = 19680.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.115194 restraints weight = 17993.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10783  Z= 0.127
  Angle     :  0.610  11.148  14677  Z= 0.305
  Chirality :  0.043   0.172   1673
  Planarity :  0.004   0.035   1805
  Dihedral  : 11.118 115.783   1997
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.72 %
    Favored  : 89.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.24), residues: 1266
  helix:  0.48 (0.22), residues: 585
  sheet: -1.47 (0.43), residues: 144
  loop : -2.05 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 
 PHE   0.014   0.001   PHE A1328 
 TYR   0.020   0.001   TYR A1299 
 ARG   0.002   0.000   ARG A1226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00183 (    5)
  link_NAG-ASN         : angle       1.99723 (   15)
  link_ALPHA1-4        : bond        0.01170 (    1)
  link_ALPHA1-4        : angle       2.67664 (    3)
  link_BETA1-4         : bond        0.00431 (    4)
  link_BETA1-4         : angle       1.50370 (   12)
  hydrogen bonds       : bond        0.04258 (  490)
  hydrogen bonds       : angle       4.57290 ( 1362)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       0.57008 (    4)
  covalent geometry    : bond        0.00278 (10770)
  covalent geometry    : angle       0.60421 (14643)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8474 (t80) cc_final: 0.8264 (t80)
REVERT: A  771 MET cc_start: 0.6688 (ttp) cc_final: 0.6009 (ttt)
REVERT: A  845 ASP cc_start: 0.7821 (p0) cc_final: 0.7516 (p0)
REVERT: A 1410 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7983 (mmtm)
  outliers start: 15
  outliers final: 12
  residues processed: 132
  average time/residue: 0.2324
  time to fit residues: 45.0594
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  888 ASN
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1086 GLU
Chi-restraints excluded: chain A residue 1325 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 123 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 84 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 642 ASN
A1253 ASN
B  60 GLN
** B  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.153358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.116506 restraints weight = 13104.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.114602 restraints weight = 17993.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.114326 restraints weight = 17870.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10783  Z= 0.162
  Angle     :  0.608   8.287  14677  Z= 0.305
  Chirality :  0.044   0.172   1673
  Planarity :  0.003   0.035   1805
  Dihedral  : 10.845 117.743   1997
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.96 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.24), residues: 1266
  helix:  0.59 (0.22), residues: 579
  sheet: -1.43 (0.43), residues: 146
  loop : -2.03 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 142 
 HIS   0.005   0.001   HIS A1336 
 PHE   0.017   0.001   PHE A1408 
 TYR   0.018   0.001   TYR B 280 
 ARG   0.005   0.000   ARG B 162 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00282 (    5)
  link_NAG-ASN         : angle       2.31305 (   15)
  link_ALPHA1-4        : bond        0.01139 (    1)
  link_ALPHA1-4        : angle       3.18321 (    3)
  link_BETA1-4         : bond        0.00468 (    4)
  link_BETA1-4         : angle       1.59351 (   12)
  hydrogen bonds       : bond        0.04091 (  490)
  hydrogen bonds       : angle       4.42551 ( 1362)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       0.58373 (    4)
  covalent geometry    : bond        0.00378 (10770)
  covalent geometry    : angle       0.60059 (14643)
  Misc. bond           : bond        0.00026 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8645 (t80) cc_final: 0.8415 (t80)
REVERT: A  771 MET cc_start: 0.6840 (ttp) cc_final: 0.6054 (ttt)
REVERT: A  845 ASP cc_start: 0.7774 (p0) cc_final: 0.7485 (p0)
REVERT: A  949 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7419 (pm20)
REVERT: A 1059 LYS cc_start: 0.8161 (ptmm) cc_final: 0.7890 (ptmm)
REVERT: A 1410 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7956 (mmtm)
REVERT: B  121 ILE cc_start: 0.8552 (mt) cc_final: 0.8185 (mt)
  outliers start: 27
  outliers final: 19
  residues processed: 137
  average time/residue: 0.2249
  time to fit residues: 45.0633
Evaluate side-chains
  125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  985 GLU
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1086 GLU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1250 ILE
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   chunk 104 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 90 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9980
   chunk 107 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.4384

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.152491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.112037 restraints weight = 13069.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.109042 restraints weight = 23606.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.110730 restraints weight = 21107.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10783  Z= 0.170
  Angle     :  0.615   8.673  14677  Z= 0.307
  Chirality :  0.044   0.171   1673
  Planarity :  0.004   0.038   1805
  Dihedral  : 10.728 119.844   1997
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.57 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.24), residues: 1266
  helix:  0.54 (0.22), residues: 585
  sheet: -1.50 (0.42), residues: 146
  loop : -2.03 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 142 
 HIS   0.006   0.001   HIS A1336 
 PHE   0.015   0.001   PHE A1408 
 TYR   0.017   0.001   TYR B 280 
 ARG   0.004   0.000   ARG A1131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00316 (    5)
  link_NAG-ASN         : angle       2.66820 (   15)
  link_ALPHA1-4        : bond        0.01146 (    1)
  link_ALPHA1-4        : angle       3.29992 (    3)
  link_BETA1-4         : bond        0.00432 (    4)
  link_BETA1-4         : angle       1.63366 (   12)
  hydrogen bonds       : bond        0.04034 (  490)
  hydrogen bonds       : angle       4.39633 ( 1362)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       0.56315 (    4)
  covalent geometry    : bond        0.00396 (10770)
  covalent geometry    : angle       0.60562 (14643)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.7029 (ttp) cc_final: 0.6220 (ttt)
REVERT: A  810 LYS cc_start: 0.7318 (tptt) cc_final: 0.6219 (ptpt)
REVERT: A  845 ASP cc_start: 0.7861 (p0) cc_final: 0.7591 (p0)
REVERT: A  878 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6542 (tm-30)
REVERT: A  949 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7533 (pm20)
REVERT: A 1059 LYS cc_start: 0.8124 (ptmm) cc_final: 0.7879 (ptmm)
REVERT: B  121 ILE cc_start: 0.8581 (mt) cc_final: 0.8217 (mt)
  outliers start: 29
  outliers final: 22
  residues processed: 132
  average time/residue: 0.2126
  time to fit residues: 41.9042
Evaluate side-chains
  130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  985 GLU
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1074 GLN
Chi-restraints excluded: chain A residue 1086 GLU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1250 ILE
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1287 VAL
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 111 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 685 ASN
** B  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.147240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.107473 restraints weight = 13329.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.103926 restraints weight = 23348.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.105228 restraints weight = 21236.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  10783  Z= 0.274
  Angle     :  0.712   8.956  14677  Z= 0.357
  Chirality :  0.048   0.179   1673
  Planarity :  0.004   0.046   1805
  Dihedral  : 11.077 123.345   1997
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.00 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.24), residues: 1266
  helix:  0.33 (0.22), residues: 577
  sheet: -1.54 (0.42), residues: 150
  loop : -2.11 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 142 
 HIS   0.009   0.002   HIS A1336 
 PHE   0.021   0.002   PHE A1408 
 TYR   0.024   0.002   TYR A 684 
 ARG   0.006   0.000   ARG A1131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00386 (    5)
  link_NAG-ASN         : angle       2.73748 (   15)
  link_ALPHA1-4        : bond        0.00927 (    1)
  link_ALPHA1-4        : angle       3.44033 (    3)
  link_BETA1-4         : bond        0.00331 (    4)
  link_BETA1-4         : angle       1.74417 (   12)
  hydrogen bonds       : bond        0.04571 (  490)
  hydrogen bonds       : angle       4.62046 ( 1362)
  SS BOND              : bond        0.00458 (    2)
  SS BOND              : angle       0.80223 (    4)
  covalent geometry    : bond        0.00648 (10770)
  covalent geometry    : angle       0.70428 (14643)
  Misc. bond           : bond        0.00037 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.7119 (ttp) cc_final: 0.6619 (ttt)
REVERT: A  810 LYS cc_start: 0.7350 (tptt) cc_final: 0.6190 (ptpt)
REVERT: A  845 ASP cc_start: 0.8068 (p0) cc_final: 0.7808 (p0)
REVERT: A  871 GLU cc_start: 0.7476 (mp0) cc_final: 0.6051 (mm-30)
REVERT: A  878 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6613 (tm-30)
REVERT: A 1059 LYS cc_start: 0.8209 (ptmm) cc_final: 0.7920 (ptmm)
REVERT: B  121 ILE cc_start: 0.8622 (mt) cc_final: 0.8277 (mt)
REVERT: B  316 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8596 (ptp-170)
  outliers start: 35
  outliers final: 29
  residues processed: 133
  average time/residue: 0.2161
  time to fit residues: 42.2812
Evaluate side-chains
  137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  985 GLU
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1074 GLN
Chi-restraints excluded: chain A residue 1086 GLU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1203 ASP
Chi-restraints excluded: chain A residue 1206 ILE
Chi-restraints excluded: chain A residue 1250 ILE
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1287 VAL
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 VAL
Chi-restraints excluded: chain A residue 1339 MET
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  316 ARG
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.151821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.112025 restraints weight = 13200.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.109759 restraints weight = 22384.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.111106 restraints weight = 20608.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10783  Z= 0.132
  Angle     :  0.603   9.677  14677  Z= 0.301
  Chirality :  0.043   0.146   1673
  Planarity :  0.004   0.046   1805
  Dihedral  : 10.694 121.084   1997
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.17 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.24), residues: 1266
  helix:  0.58 (0.22), residues: 573
  sheet: -1.45 (0.42), residues: 146
  loop : -1.99 (0.27), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 
 PHE   0.014   0.001   PHE A1133 
 TYR   0.021   0.001   TYR A 684 
 ARG   0.006   0.000   ARG A1131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00107 (    5)
  link_NAG-ASN         : angle       1.95714 (   15)
  link_ALPHA1-4        : bond        0.01422 (    1)
  link_ALPHA1-4        : angle       3.41941 (    3)
  link_BETA1-4         : bond        0.00470 (    4)
  link_BETA1-4         : angle       1.69197 (   12)
  hydrogen bonds       : bond        0.03921 (  490)
  hydrogen bonds       : angle       4.38601 ( 1362)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       0.63118 (    4)
  covalent geometry    : bond        0.00297 (10770)
  covalent geometry    : angle       0.59644 (14643)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.7094 (ttp) cc_final: 0.6298 (ttt)
REVERT: A  810 LYS cc_start: 0.7274 (tptt) cc_final: 0.6138 (ptpt)
REVERT: A  845 ASP cc_start: 0.8032 (p0) cc_final: 0.7832 (p0)
REVERT: A  871 GLU cc_start: 0.7481 (mp0) cc_final: 0.6159 (mm-30)
REVERT: A  878 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6715 (tm-30)
REVERT: A  949 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7714 (pm20)
REVERT: B  121 ILE cc_start: 0.8609 (mt) cc_final: 0.8274 (mt)
REVERT: B  236 ASN cc_start: 0.9412 (t0) cc_final: 0.9075 (t0)
REVERT: B  238 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8054 (tmm)
REVERT: B  348 TRP cc_start: 0.9124 (OUTLIER) cc_final: 0.8601 (t60)
  outliers start: 26
  outliers final: 18
  residues processed: 130
  average time/residue: 0.2262
  time to fit residues: 43.2747
Evaluate side-chains
  129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1074 GLN
Chi-restraints excluded: chain A residue 1086 GLU
Chi-restraints excluded: chain A residue 1212 VAL
Chi-restraints excluded: chain A residue 1250 ILE
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1287 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  238 MET
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 60 optimal weight:    0.0050
   chunk 90 optimal weight:    0.0970
   chunk 11 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 83 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0470
   chunk 106 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.3290

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.155610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.117993 restraints weight = 13144.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.117958 restraints weight = 18502.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.118430 restraints weight = 17260.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10783  Z= 0.107
  Angle     :  0.580   8.964  14677  Z= 0.290
  Chirality :  0.042   0.156   1673
  Planarity :  0.003   0.039   1805
  Dihedral  : 10.271 119.961   1997
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 19.33 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.25), residues: 1266
  helix:  0.68 (0.22), residues: 582
  sheet: -1.41 (0.41), residues: 154
  loop : -1.92 (0.28), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 142 
 HIS   0.003   0.001   HIS B 347 
 PHE   0.014   0.001   PHE A1328 
 TYR   0.019   0.001   TYR A 684 
 ARG   0.007   0.000   ARG A1131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00107 (    5)
  link_NAG-ASN         : angle       1.67312 (   15)
  link_ALPHA1-4        : bond        0.01650 (    1)
  link_ALPHA1-4        : angle       3.55517 (    3)
  link_BETA1-4         : bond        0.00546 (    4)
  link_BETA1-4         : angle       1.78084 (   12)
  hydrogen bonds       : bond        0.03594 (  490)
  hydrogen bonds       : angle       4.20579 ( 1362)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       0.51975 (    4)
  covalent geometry    : bond        0.00227 (10770)
  covalent geometry    : angle       0.57358 (14643)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.7086 (ttp) cc_final: 0.6391 (ttt)
REVERT: A  810 LYS cc_start: 0.7277 (tptt) cc_final: 0.6293 (ptpt)
REVERT: A  845 ASP cc_start: 0.7820 (p0) cc_final: 0.7612 (p0)
REVERT: A  871 GLU cc_start: 0.7449 (mp0) cc_final: 0.6238 (mm-30)
REVERT: A  949 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7336 (mm-30)
REVERT: A 1338 ASN cc_start: 0.8573 (p0) cc_final: 0.8238 (p0)
REVERT: A 1410 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7803 (mmtm)
REVERT: B  121 ILE cc_start: 0.8543 (mt) cc_final: 0.8216 (mt)
REVERT: B  236 ASN cc_start: 0.9381 (t0) cc_final: 0.9024 (t0)
REVERT: B  348 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.8556 (t60)
  outliers start: 20
  outliers final: 13
  residues processed: 136
  average time/residue: 0.2260
  time to fit residues: 44.7783
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1074 GLN
Chi-restraints excluded: chain A residue 1086 GLU
Chi-restraints excluded: chain A residue 1212 VAL
Chi-restraints excluded: chain A residue 1287 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  313 ASN
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 105 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 120 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 118 optimal weight:    0.5980
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A1285 GLN
** B  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.149626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.110134 restraints weight = 13305.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.108160 restraints weight = 23122.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.109167 restraints weight = 21332.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10783  Z= 0.229
  Angle     :  0.675   8.245  14677  Z= 0.338
  Chirality :  0.046   0.146   1673
  Planarity :  0.004   0.046   1805
  Dihedral  : 10.611 123.566   1997
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 19.87 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.24), residues: 1266
  helix:  0.52 (0.22), residues: 579
  sheet: -1.35 (0.44), residues: 148
  loop : -1.97 (0.28), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1458 
 HIS   0.006   0.001   HIS A1336 
 PHE   0.017   0.002   PHE A1408 
 TYR   0.019   0.002   TYR B 280 
 ARG   0.007   0.000   ARG A1131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    5)
  link_NAG-ASN         : angle       2.35119 (   15)
  link_ALPHA1-4        : bond        0.01010 (    1)
  link_ALPHA1-4        : angle       3.47939 (    3)
  link_BETA1-4         : bond        0.00428 (    4)
  link_BETA1-4         : angle       1.82518 (   12)
  hydrogen bonds       : bond        0.04181 (  490)
  hydrogen bonds       : angle       4.38117 ( 1362)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       0.67908 (    4)
  covalent geometry    : bond        0.00538 (10770)
  covalent geometry    : angle       0.66737 (14643)
  Misc. bond           : bond        0.00030 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.7216 (ttp) cc_final: 0.6759 (ttt)
REVERT: A  810 LYS cc_start: 0.7364 (tptt) cc_final: 0.6210 (ptpt)
REVERT: A  949 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7735 (mm-30)
REVERT: B  238 MET cc_start: 0.9162 (tpp) cc_final: 0.8952 (tpt)
  outliers start: 26
  outliers final: 19
  residues processed: 128
  average time/residue: 0.2124
  time to fit residues: 40.2497
Evaluate side-chains
  126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1074 GLN
Chi-restraints excluded: chain A residue 1086 GLU
Chi-restraints excluded: chain A residue 1206 ILE
Chi-restraints excluded: chain A residue 1212 VAL
Chi-restraints excluded: chain A residue 1287 VAL
Chi-restraints excluded: chain A residue 1326 ILE
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  313 ASN
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.152810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.116364 restraints weight = 13215.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.115923 restraints weight = 16219.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.114848 restraints weight = 17737.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10783  Z= 0.130
  Angle     :  0.608   8.714  14677  Z= 0.305
  Chirality :  0.043   0.171   1673
  Planarity :  0.004   0.042   1805
  Dihedral  : 10.436 121.611   1997
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 20.32 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.25), residues: 1266
  helix:  0.60 (0.22), residues: 581
  sheet: -1.37 (0.42), residues: 156
  loop : -1.95 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 
 PHE   0.013   0.001   PHE A1328 
 TYR   0.019   0.001   TYR B 280 
 ARG   0.007   0.000   ARG A1131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00103 (    5)
  link_NAG-ASN         : angle       1.92909 (   15)
  link_ALPHA1-4        : bond        0.01471 (    1)
  link_ALPHA1-4        : angle       3.50448 (    3)
  link_BETA1-4         : bond        0.00485 (    4)
  link_BETA1-4         : angle       1.72708 (   12)
  hydrogen bonds       : bond        0.03831 (  490)
  hydrogen bonds       : angle       4.25899 ( 1362)
  SS BOND              : bond        0.00159 (    2)
  SS BOND              : angle       0.56841 (    4)
  covalent geometry    : bond        0.00294 (10770)
  covalent geometry    : angle       0.60118 (14643)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.7091 (ttp) cc_final: 0.6391 (ttt)
REVERT: A  810 LYS cc_start: 0.7352 (tptt) cc_final: 0.6237 (ptpt)
REVERT: A  871 GLU cc_start: 0.7387 (mp0) cc_final: 0.6014 (mm-30)
REVERT: A  949 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7635 (mm-30)
REVERT: B  348 TRP cc_start: 0.9070 (OUTLIER) cc_final: 0.8442 (t60)
  outliers start: 19
  outliers final: 14
  residues processed: 121
  average time/residue: 0.2309
  time to fit residues: 41.0645
Evaluate side-chains
  121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1074 GLN
Chi-restraints excluded: chain A residue 1086 GLU
Chi-restraints excluded: chain A residue 1212 VAL
Chi-restraints excluded: chain A residue 1287 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  313 ASN
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 123 optimal weight:    0.3980
   chunk 28 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0070
   chunk 106 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0020
   overall best weight:    0.4006

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.155649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.115555 restraints weight = 13023.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.114303 restraints weight = 19796.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.114454 restraints weight = 15677.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10783  Z= 0.112
  Angle     :  0.594   8.835  14677  Z= 0.298
  Chirality :  0.042   0.135   1673
  Planarity :  0.004   0.041   1805
  Dihedral  : 10.100 120.355   1997
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 21.13 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.25), residues: 1266
  helix:  0.82 (0.22), residues: 576
  sheet: -1.36 (0.42), residues: 154
  loop : -1.84 (0.29), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 142 
 HIS   0.002   0.001   HIS B 347 
 PHE   0.013   0.001   PHE A1328 
 TYR   0.020   0.001   TYR B 280 
 ARG   0.012   0.000   ARG A 893 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00087 (    5)
  link_NAG-ASN         : angle       1.71119 (   15)
  link_ALPHA1-4        : bond        0.01615 (    1)
  link_ALPHA1-4        : angle       3.61894 (    3)
  link_BETA1-4         : bond        0.00566 (    4)
  link_BETA1-4         : angle       1.81152 (   12)
  hydrogen bonds       : bond        0.03575 (  490)
  hydrogen bonds       : angle       4.15837 ( 1362)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       0.46800 (    4)
  covalent geometry    : bond        0.00243 (10770)
  covalent geometry    : angle       0.58732 (14643)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.7020 (ttp) cc_final: 0.6349 (ttt)
REVERT: A  810 LYS cc_start: 0.7282 (tptt) cc_final: 0.6163 (ptpt)
REVERT: A  856 LEU cc_start: 0.8795 (tt) cc_final: 0.8402 (tt)
REVERT: A  871 GLU cc_start: 0.7439 (mp0) cc_final: 0.5953 (mm-30)
REVERT: A  891 ARG cc_start: 0.8269 (mtp-110) cc_final: 0.7961 (mtp-110)
REVERT: A  949 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7649 (mm-30)
REVERT: A 1338 ASN cc_start: 0.8581 (p0) cc_final: 0.8232 (p0)
REVERT: A 1410 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7740 (mmtm)
REVERT: B  348 TRP cc_start: 0.9063 (OUTLIER) cc_final: 0.8380 (t60)
  outliers start: 14
  outliers final: 12
  residues processed: 130
  average time/residue: 0.2092
  time to fit residues: 40.2824
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1074 GLN
Chi-restraints excluded: chain A residue 1086 GLU
Chi-restraints excluded: chain A residue 1212 VAL
Chi-restraints excluded: chain A residue 1287 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0670
   chunk 116 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 112 optimal weight:    0.7980
   chunk 122 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 107 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0010
   overall best weight:    0.5124

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.155581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.115190 restraints weight = 12943.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.112826 restraints weight = 20913.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.113504 restraints weight = 16863.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10783  Z= 0.114
  Angle     :  0.598   8.908  14677  Z= 0.298
  Chirality :  0.042   0.212   1673
  Planarity :  0.004   0.042   1805
  Dihedral  :  9.956 120.629   1997
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 21.40 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.25), residues: 1266
  helix:  0.80 (0.22), residues: 582
  sheet: -1.28 (0.42), residues: 154
  loop : -1.86 (0.29), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 142 
 HIS   0.002   0.001   HIS B 347 
 PHE   0.013   0.001   PHE A1328 
 TYR   0.020   0.001   TYR B 280 
 ARG   0.009   0.000   ARG A1131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00081 (    5)
  link_NAG-ASN         : angle       1.72508 (   15)
  link_ALPHA1-4        : bond        0.01632 (    1)
  link_ALPHA1-4        : angle       3.64664 (    3)
  link_BETA1-4         : bond        0.00520 (    4)
  link_BETA1-4         : angle       1.83493 (   12)
  hydrogen bonds       : bond        0.03552 (  490)
  hydrogen bonds       : angle       4.12721 ( 1362)
  SS BOND              : bond        0.00124 (    2)
  SS BOND              : angle       0.44402 (    4)
  covalent geometry    : bond        0.00253 (10770)
  covalent geometry    : angle       0.59150 (14643)
  Misc. bond           : bond        0.00007 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3425.24 seconds
wall clock time: 60 minutes 12.49 seconds (3612.49 seconds total)