Starting phenix.real_space_refine
on Wed Mar  4 04:45:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ky8_23071/03_2026/7ky8_23071.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ky8_23071/03_2026/7ky8_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_23071/03_2026/7ky8_23071.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ky8_23071/03_2026/7ky8_23071.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ky8_23071/03_2026/7ky8_23071.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ky8_23071/03_2026/7ky8_23071.cif"
  }
  resolution = 3.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.35, per 1000 atoms: 0.22
  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: 0.92
  Conformation dependent library (CDL) restraints added in 464.4 milliseconds
  

  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: 0.33
  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: 1.63

  Time building geometry restraints manager: 1.21 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:             1.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.590
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.410
-------------------------------------------------------------------------------
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 : 13.00
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.25), 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
 ARG   0.007   0.000   ARG A1131 
 TYR   0.020   0.001   TYR B 378 
 PHE   0.017   0.001   PHE A 791 
 TRP   0.052   0.002   TRP B 142 
 HIS   0.003   0.001   HIS B 125 

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

*********************** 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  : 0.299 
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: 0.0897
  time to fit residues: 19.6334
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  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    8.9990
   chunk 123 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.153265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.115880 restraints weight = 13122.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.114416 restraints weight = 17540.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.111950 restraints weight = 19123.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.109376 restraints weight = 17430.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.110567 restraints weight = 15290.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.0941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10783  Z= 0.173
  Angle     :  0.643  11.070  14677  Z= 0.322
  Chirality :  0.045   0.181   1673
  Planarity :  0.004   0.035   1805
  Dihedral  : 11.229 118.167   1997
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.62 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.24), residues: 1266
  helix:  0.43 (0.22), residues: 578
  sheet: -1.44 (0.43), residues: 146
  loop : -2.09 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1147 
 TYR   0.021   0.002   TYR A1299 
 PHE   0.017   0.001   PHE A1408 
 TRP   0.026   0.001   TRP B 142 
 HIS   0.006   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (10770)
  covalent geometry    : angle       0.63678 (14643)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       0.62786 (    4)
  hydrogen bonds       : bond        0.04420 (  490)
  hydrogen bonds       : angle       4.62041 ( 1362)
  Misc. bond           : bond        0.00009 (    1)
  link_ALPHA1-4        : bond        0.01139 (    1)
  link_ALPHA1-4        : angle       2.85593 (    3)
  link_BETA1-4         : bond        0.00375 (    4)
  link_BETA1-4         : angle       1.51331 (   12)
  link_NAG-ASN         : bond        0.00196 (    5)
  link_NAG-ASN         : angle       2.20583 (   15)

*********************** 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: 17
    poor density    : 122
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8544 (t80) cc_final: 0.8331 (t80)
REVERT: A  771 MET cc_start: 0.6701 (ttp) cc_final: 0.5955 (ttt)
REVERT: A  845 ASP cc_start: 0.7978 (p0) cc_final: 0.7673 (p0)
REVERT: A  949 GLU cc_start: 0.7629 (pm20) cc_final: 0.7426 (mt-10)
REVERT: B  121 ILE cc_start: 0.8548 (mt) cc_final: 0.8159 (mt)
  outliers start: 17
  outliers final: 15
  residues processed: 130
  average time/residue: 0.0872
  time to fit residues: 16.7521
Evaluate side-chains
  124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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 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  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 34 optimal weight:    0.8980
   chunk 116 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 119 optimal weight:    0.5980
   chunk 100 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 107 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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  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 = 0.3665 r_free = 0.3665 target = 0.155315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.115161 restraints weight = 12995.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.114110 restraints weight = 20650.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.115276 restraints weight = 18786.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.114420 restraints weight = 14122.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.114996 restraints weight = 12393.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10783  Z= 0.122
  Angle     :  0.583   8.625  14677  Z= 0.292
  Chirality :  0.043   0.174   1673
  Planarity :  0.003   0.034   1805
  Dihedral  : 10.780 117.226   1997
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.96 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.24), residues: 1266
  helix:  0.51 (0.22), residues: 588
  sheet: -1.43 (0.42), residues: 146
  loop : -2.01 (0.28), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1147 
 TYR   0.018   0.001   TYR B 280 
 PHE   0.013   0.001   PHE A1328 
 TRP   0.017   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10770)
  covalent geometry    : angle       0.57610 (14643)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       0.54761 (    4)
  hydrogen bonds       : bond        0.03948 (  490)
  hydrogen bonds       : angle       4.38544 ( 1362)
  Misc. bond           : bond        0.00008 (    1)
  link_ALPHA1-4        : bond        0.01311 (    1)
  link_ALPHA1-4        : angle       3.24980 (    3)
  link_BETA1-4         : bond        0.00539 (    4)
  link_BETA1-4         : angle       1.57433 (   12)
  link_NAG-ASN         : bond        0.00085 (    5)
  link_NAG-ASN         : angle       2.00438 (   15)

*********************** 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
  144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8586 (t80) cc_final: 0.8333 (t80)
REVERT: A  771 MET cc_start: 0.6784 (ttp) cc_final: 0.6014 (ttt)
REVERT: A  845 ASP cc_start: 0.7803 (p0) cc_final: 0.7530 (p0)
REVERT: A 1410 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7945 (mmtm)
REVERT: B  121 ILE cc_start: 0.8498 (mt) cc_final: 0.8140 (mt)
  outliers start: 24
  outliers final: 15
  residues processed: 134
  average time/residue: 0.0925
  time to fit residues: 18.2859
Evaluate side-chains
  125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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 1287 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
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 126 optimal weight:    0.0270
   chunk 123 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    1.8044

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.151088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.110882 restraints weight = 13320.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.107266 restraints weight = 23467.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.109020 restraints weight = 21925.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.108998 restraints weight = 14369.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.109147 restraints weight = 14291.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10783  Z= 0.202
  Angle     :  0.638   8.447  14677  Z= 0.320
  Chirality :  0.045   0.176   1673
  Planarity :  0.004   0.038   1805
  Dihedral  : 10.790 120.757   1997
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.57 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.24), residues: 1266
  helix:  0.57 (0.22), residues: 576
  sheet: -1.47 (0.42), residues: 146
  loop : -1.99 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 162 
 TYR   0.018   0.001   TYR B 280 
 PHE   0.018   0.002   PHE A1408 
 TRP   0.016   0.001   TRP B 142 
 HIS   0.007   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (10770)
  covalent geometry    : angle       0.62915 (14643)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       0.61674 (    4)
  hydrogen bonds       : bond        0.04161 (  490)
  hydrogen bonds       : angle       4.44450 ( 1362)
  Misc. bond           : bond        0.00030 (    1)
  link_ALPHA1-4        : bond        0.01084 (    1)
  link_ALPHA1-4        : angle       3.35962 (    3)
  link_BETA1-4         : bond        0.00397 (    4)
  link_BETA1-4         : angle       1.67562 (   12)
  link_NAG-ASN         : bond        0.00364 (    5)
  link_NAG-ASN         : angle       2.77693 (   15)

*********************** 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
  145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8695 (t80) cc_final: 0.8490 (t80)
REVERT: A  771 MET cc_start: 0.7001 (ttp) cc_final: 0.6204 (ttt)
REVERT: A  809 GLN cc_start: 0.6594 (tm-30) cc_final: 0.6375 (tm-30)
REVERT: A  845 ASP cc_start: 0.7976 (p0) cc_final: 0.7696 (p0)
REVERT: A  878 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6526 (tm-30)
REVERT: A  949 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7466 (pm20)
REVERT: A 1059 LYS cc_start: 0.8147 (ptmm) cc_final: 0.7875 (ptmm)
REVERT: B  121 ILE cc_start: 0.8608 (mt) cc_final: 0.8234 (mt)
REVERT: B  316 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8582 (ptp-170)
  outliers start: 31
  outliers final: 22
  residues processed: 132
  average time/residue: 0.1016
  time to fit residues: 19.5027
Evaluate side-chains
  132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
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 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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 108 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 89 optimal weight:    0.6980
   chunk 83 optimal weight:    0.7980
   chunk 22 optimal weight:    9.9990
   chunk 80 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.3624 r_free = 0.3624 target = 0.152101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.111708 restraints weight = 13191.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.109590 restraints weight = 21572.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.111006 restraints weight = 20451.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.111151 restraints weight = 13184.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.111219 restraints weight = 13345.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10783  Z= 0.149
  Angle     :  0.605   8.503  14677  Z= 0.300
  Chirality :  0.043   0.160   1673
  Planarity :  0.004   0.046   1805
  Dihedral  : 10.614 120.503   1997
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.73 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.24), residues: 1266
  helix:  0.59 (0.22), residues: 578
  sheet: -1.41 (0.43), residues: 146
  loop : -1.96 (0.28), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1131 
 TYR   0.018   0.001   TYR B 280 
 PHE   0.013   0.001   PHE A1408 
 TRP   0.013   0.001   TRP B 142 
 HIS   0.004   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10770)
  covalent geometry    : angle       0.59808 (14643)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       0.57523 (    4)
  hydrogen bonds       : bond        0.03917 (  490)
  hydrogen bonds       : angle       4.35728 ( 1362)
  Misc. bond           : bond        0.00008 (    1)
  link_ALPHA1-4        : bond        0.01377 (    1)
  link_ALPHA1-4        : angle       3.39547 (    3)
  link_BETA1-4         : bond        0.00489 (    4)
  link_BETA1-4         : angle       1.68510 (   12)
  link_NAG-ASN         : bond        0.00113 (    5)
  link_NAG-ASN         : angle       2.04169 (   15)

*********************** 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
  137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.7039 (ttp) cc_final: 0.6203 (ttt)
REVERT: A  809 GLN cc_start: 0.6791 (tm-30) cc_final: 0.6546 (tm-30)
REVERT: A  810 LYS cc_start: 0.7345 (tptt) cc_final: 0.6275 (ptpt)
REVERT: A  845 ASP cc_start: 0.7949 (p0) cc_final: 0.7664 (p0)
REVERT: A  871 GLU cc_start: 0.7468 (mp0) cc_final: 0.6151 (mm-30)
REVERT: A  949 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7470 (pm20)
REVERT: A 1059 LYS cc_start: 0.8145 (ptmm) cc_final: 0.7900 (ptmm)
REVERT: B  121 ILE cc_start: 0.8596 (mt) cc_final: 0.8243 (mt)
REVERT: B  236 ASN cc_start: 0.9415 (t0) cc_final: 0.9084 (t0)
  outliers start: 27
  outliers final: 20
  residues processed: 127
  average time/residue: 0.0890
  time to fit residues: 16.7150
Evaluate side-chains
  125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
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 1212 VAL
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1287 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   94 LEU
Chi-restraints excluded: chain B residue  111 MET
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  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 29 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 123 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.153708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.117253 restraints weight = 13131.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.116131 restraints weight = 17512.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.112325 restraints weight = 17436.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.109356 restraints weight = 14410.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.110426 restraints weight = 12621.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1575

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= 0.122
  Angle     :  0.594  10.660  14677  Z= 0.293
  Chirality :  0.042   0.154   1673
  Planarity :  0.003   0.042   1805
  Dihedral  : 10.401 120.957   1997
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.81 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.25), residues: 1266
  helix:  0.65 (0.22), residues: 581
  sheet: -1.41 (0.41), residues: 156
  loop : -1.87 (0.29), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1131 
 TYR   0.025   0.001   TYR A 684 
 PHE   0.013   0.001   PHE A1328 
 TRP   0.013   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10770)
  covalent geometry    : angle       0.58792 (14643)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.48266 (    4)
  hydrogen bonds       : bond        0.03733 (  490)
  hydrogen bonds       : angle       4.26029 ( 1362)
  Misc. bond           : bond        0.00006 (    1)
  link_ALPHA1-4        : bond        0.01401 (    1)
  link_ALPHA1-4        : angle       3.45983 (    3)
  link_BETA1-4         : bond        0.00515 (    4)
  link_BETA1-4         : angle       1.74435 (   12)
  link_NAG-ASN         : bond        0.00096 (    5)
  link_NAG-ASN         : angle       1.83296 (   15)

*********************** 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
  144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8337 (t80) cc_final: 0.7999 (t80)
REVERT: A  685 ASN cc_start: 0.8588 (t0) cc_final: 0.8112 (p0)
REVERT: A  771 MET cc_start: 0.6795 (ttp) cc_final: 0.6337 (ttt)
REVERT: A  810 LYS cc_start: 0.7137 (tptt) cc_final: 0.6030 (ptpt)
REVERT: A  845 ASP cc_start: 0.8263 (p0) cc_final: 0.7993 (p0)
REVERT: A  871 GLU cc_start: 0.7397 (mp0) cc_final: 0.5941 (mm-30)
REVERT: A  949 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7482 (pm20)
REVERT: A 1410 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7941 (mmtm)
REVERT: B  121 ILE cc_start: 0.8617 (mt) cc_final: 0.8274 (mt)
REVERT: B  236 ASN cc_start: 0.9436 (t0) cc_final: 0.9091 (t0)
REVERT: B  316 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8568 (ptp-170)
REVERT: B  348 TRP cc_start: 0.9174 (OUTLIER) cc_final: 0.8708 (t60)
  outliers start: 28
  outliers final: 17
  residues processed: 131
  average time/residue: 0.0991
  time to fit residues: 18.9259
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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 1250 ILE
Chi-restraints excluded: chain A residue 1266 THR
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  176 ASN
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  316 ARG
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 125 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 119 optimal weight:    7.9990
   chunk 111 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 37 optimal weight:    7.9990
   chunk 113 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.151814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.112337 restraints weight = 13137.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.109800 restraints weight = 21526.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.111043 restraints weight = 20108.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.110953 restraints weight = 13252.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.111088 restraints weight = 13743.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1668

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= 0.159
  Angle     :  0.614   9.056  14677  Z= 0.305
  Chirality :  0.043   0.135   1673
  Planarity :  0.004   0.045   1805
  Dihedral  : 10.448 121.772   1997
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.44 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.24), residues: 1266
  helix:  0.55 (0.22), residues: 586
  sheet: -1.40 (0.41), residues: 156
  loop : -1.92 (0.29), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1131 
 TYR   0.018   0.001   TYR B 280 
 PHE   0.032   0.001   PHE A1111 
 TRP   0.012   0.001   TRP B 142 
 HIS   0.004   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (10770)
  covalent geometry    : angle       0.60725 (14643)
  SS BOND              : bond        0.00241 (    2)
  SS BOND              : angle       0.55335 (    4)
  hydrogen bonds       : bond        0.03879 (  490)
  hydrogen bonds       : angle       4.28304 ( 1362)
  Misc. bond           : bond        0.00010 (    1)
  link_ALPHA1-4        : bond        0.01304 (    1)
  link_ALPHA1-4        : angle       3.48155 (    3)
  link_BETA1-4         : bond        0.00420 (    4)
  link_BETA1-4         : angle       1.76418 (   12)
  link_NAG-ASN         : bond        0.00132 (    5)
  link_NAG-ASN         : angle       2.04572 (   15)

*********************** 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
  142 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8363 (t80) cc_final: 0.8086 (t80)
REVERT: A  685 ASN cc_start: 0.8576 (t0) cc_final: 0.8144 (p0)
REVERT: A  771 MET cc_start: 0.7116 (ttp) cc_final: 0.6659 (ttt)
REVERT: A  810 LYS cc_start: 0.7341 (tptt) cc_final: 0.6181 (ptpt)
REVERT: A  845 ASP cc_start: 0.7929 (p0) cc_final: 0.7716 (p0)
REVERT: A  949 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7433 (pm20)
REVERT: B  316 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8578 (ptp-170)
REVERT: B  348 TRP cc_start: 0.9180 (OUTLIER) cc_final: 0.8730 (t60)
  outliers start: 27
  outliers final: 23
  residues processed: 131
  average time/residue: 0.0888
  time to fit residues: 17.1162
Evaluate side-chains
  131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
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 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 1212 VAL
Chi-restraints excluded: chain A residue 1250 ILE
Chi-restraints excluded: chain A residue 1266 THR
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   94 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  176 ASN
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  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 80 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 120 optimal weight:    0.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.152372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.113140 restraints weight = 13103.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.110332 restraints weight = 22563.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.112287 restraints weight = 20731.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.111582 restraints weight = 14026.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.112369 restraints weight = 13536.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10783  Z= 0.143
  Angle     :  0.607   8.580  14677  Z= 0.301
  Chirality :  0.043   0.158   1673
  Planarity :  0.003   0.045   1805
  Dihedral  : 10.380 121.289   1997
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 19.15 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.25), residues: 1266
  helix:  0.61 (0.22), residues: 582
  sheet: -1.36 (0.41), residues: 156
  loop : -1.88 (0.29), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1131 
 TYR   0.018   0.001   TYR B 280 
 PHE   0.013   0.001   PHE A1133 
 TRP   0.012   0.001   TRP B 142 
 HIS   0.004   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10770)
  covalent geometry    : angle       0.59999 (14643)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       0.57599 (    4)
  hydrogen bonds       : bond        0.03805 (  490)
  hydrogen bonds       : angle       4.25335 ( 1362)
  Misc. bond           : bond        0.00003 (    1)
  link_ALPHA1-4        : bond        0.01366 (    1)
  link_ALPHA1-4        : angle       3.48881 (    3)
  link_BETA1-4         : bond        0.00459 (    4)
  link_BETA1-4         : angle       1.76521 (   12)
  link_NAG-ASN         : bond        0.00113 (    5)
  link_NAG-ASN         : angle       1.89666 (   15)

*********************** 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
  143 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8430 (t80) cc_final: 0.8149 (t80)
REVERT: A  685 ASN cc_start: 0.8572 (t0) cc_final: 0.8137 (p0)
REVERT: A  771 MET cc_start: 0.7119 (ttp) cc_final: 0.6682 (ttt)
REVERT: A  810 LYS cc_start: 0.7331 (tptt) cc_final: 0.6221 (ptpt)
REVERT: A  871 GLU cc_start: 0.7411 (mp0) cc_final: 0.6005 (mm-30)
REVERT: A  956 LEU cc_start: 0.8400 (mt) cc_final: 0.8183 (mp)
REVERT: B  316 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8555 (ptp-170)
REVERT: B  348 TRP cc_start: 0.9147 (OUTLIER) cc_final: 0.8678 (t60)
  outliers start: 29
  outliers final: 24
  residues processed: 133
  average time/residue: 0.0940
  time to fit residues: 18.0970
Evaluate side-chains
  135 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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 1115 ILE
Chi-restraints excluded: chain A residue 1206 ILE
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 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 VAL
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  348 TRP
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:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 28 optimal weight:    9.9990
   chunk 116 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0770
   chunk 74 optimal weight:    0.4980
   chunk 96 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.154864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.117092 restraints weight = 12966.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.116775 restraints weight = 19427.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.116975 restraints weight = 18026.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.114967 restraints weight = 11673.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.115572 restraints weight = 10279.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1789

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= 0.114
  Angle     :  0.590   8.848  14677  Z= 0.294
  Chirality :  0.042   0.150   1673
  Planarity :  0.003   0.042   1805
  Dihedral  : 10.215 120.744   1997
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 19.78 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.25), residues: 1266
  helix:  0.70 (0.22), residues: 582
  sheet: -1.39 (0.42), residues: 154
  loop : -1.83 (0.29), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1131 
 TYR   0.020   0.001   TYR B 280 
 PHE   0.035   0.001   PHE A1111 
 TRP   0.012   0.001   TRP B 142 
 HIS   0.002   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10770)
  covalent geometry    : angle       0.58367 (14643)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       0.55384 (    4)
  hydrogen bonds       : bond        0.03633 (  490)
  hydrogen bonds       : angle       4.17815 ( 1362)
  Misc. bond           : bond        0.00010 (    1)
  link_ALPHA1-4        : bond        0.01567 (    1)
  link_ALPHA1-4        : angle       3.54786 (    3)
  link_BETA1-4         : bond        0.00522 (    4)
  link_BETA1-4         : angle       1.78735 (   12)
  link_NAG-ASN         : bond        0.00091 (    5)
  link_NAG-ASN         : angle       1.67086 (   15)

*********************** 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
  143 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8426 (t80) cc_final: 0.8115 (t80)
REVERT: A  685 ASN cc_start: 0.8526 (t0) cc_final: 0.8158 (p0)
REVERT: A  771 MET cc_start: 0.6985 (ttp) cc_final: 0.6285 (ttt)
REVERT: A  810 LYS cc_start: 0.7243 (tptt) cc_final: 0.6132 (ptpt)
REVERT: A  871 GLU cc_start: 0.7432 (mp0) cc_final: 0.5915 (mm-30)
REVERT: A  949 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7364 (pm20)
REVERT: A 1338 ASN cc_start: 0.8610 (p0) cc_final: 0.8239 (p0)
REVERT: A 1410 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7898 (mmtm)
REVERT: B  236 ASN cc_start: 0.9386 (t0) cc_final: 0.9010 (t0)
REVERT: B  348 TRP cc_start: 0.9090 (OUTLIER) cc_final: 0.8591 (t60)
  outliers start: 23
  outliers final: 19
  residues processed: 135
  average time/residue: 0.0974
  time to fit residues: 19.0266
Evaluate side-chains
  134 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
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 1086 GLU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1212 VAL
Chi-restraints excluded: chain A residue 1250 ILE
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   94 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  176 ASN
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  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 75 optimal weight:    0.6980
   chunk 122 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 124 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A1285 GLN
B  60 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.152384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.112599 restraints weight = 12954.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.111216 restraints weight = 22277.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.112336 restraints weight = 20016.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.112515 restraints weight = 13246.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.112534 restraints weight = 13426.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1832

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= 0.153
  Angle     :  0.623   8.408  14677  Z= 0.310
  Chirality :  0.044   0.151   1673
  Planarity :  0.004   0.044   1805
  Dihedral  : 10.219 121.682   1997
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.14 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.25), residues: 1266
  helix:  0.59 (0.22), residues: 589
  sheet: -1.32 (0.42), residues: 156
  loop : -1.87 (0.29), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1131 
 TYR   0.019   0.001   TYR B 280 
 PHE   0.014   0.001   PHE A1408 
 TRP   0.012   0.001   TRP B 142 
 HIS   0.004   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10770)
  covalent geometry    : angle       0.61669 (14643)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       0.53651 (    4)
  hydrogen bonds       : bond        0.03763 (  490)
  hydrogen bonds       : angle       4.22083 ( 1362)
  Misc. bond           : bond        0.00010 (    1)
  link_ALPHA1-4        : bond        0.01368 (    1)
  link_ALPHA1-4        : angle       3.55448 (    3)
  link_BETA1-4         : bond        0.00462 (    4)
  link_BETA1-4         : angle       1.82064 (   12)
  link_NAG-ASN         : bond        0.00120 (    5)
  link_NAG-ASN         : angle       1.88900 (   15)

********************** 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: 21
    poor density    : 114
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8450 (t80) cc_final: 0.8125 (t80)
REVERT: A  685 ASN cc_start: 0.8542 (t0) cc_final: 0.8173 (p0)
REVERT: A  771 MET cc_start: 0.7079 (ttp) cc_final: 0.6386 (ttt)
REVERT: A  810 LYS cc_start: 0.7309 (tptt) cc_final: 0.6214 (ptpt)
REVERT: A  856 LEU cc_start: 0.8848 (tp) cc_final: 0.8604 (tt)
REVERT: A  871 GLU cc_start: 0.7461 (mp0) cc_final: 0.5990 (mm-30)
REVERT: A  949 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7447 (pm20)
REVERT: B  348 TRP cc_start: 0.9134 (OUTLIER) cc_final: 0.8673 (t60)
  outliers start: 21
  outliers final: 19
  residues processed: 128
  average time/residue: 0.0922
  time to fit residues: 17.3670
Evaluate side-chains
  132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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 1086 GLU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1212 VAL
Chi-restraints excluded: chain A residue 1250 ILE
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   94 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  176 ASN
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  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 88 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0980
   chunk 35 optimal weight:    6.9990
   chunk 110 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0370
   chunk 126 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.155545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.118047 restraints weight = 13016.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.116674 restraints weight = 17162.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.115105 restraints weight = 16329.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.112870 restraints weight = 12619.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.113374 restraints weight = 11515.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10783  Z= 0.114
  Angle     :  0.599   8.876  14677  Z= 0.297
  Chirality :  0.042   0.150   1673
  Planarity :  0.003   0.042   1805
  Dihedral  :  9.978 120.036   1997
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 20.50 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.25), residues: 1266
  helix:  0.74 (0.22), residues: 583
  sheet: -1.32 (0.42), residues: 154
  loop : -1.80 (0.29), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1131 
 TYR   0.020   0.001   TYR B 280 
 PHE   0.014   0.001   PHE A1328 
 TRP   0.010   0.001   TRP B 142 
 HIS   0.002   0.001   HIS A1336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10770)
  covalent geometry    : angle       0.59252 (14643)
  SS BOND              : bond        0.00120 (    2)
  SS BOND              : angle       0.53638 (    4)
  hydrogen bonds       : bond        0.03567 (  490)
  hydrogen bonds       : angle       4.16506 ( 1362)
  Misc. bond           : bond        0.00008 (    1)
  link_ALPHA1-4        : bond        0.01709 (    1)
  link_ALPHA1-4        : angle       3.69331 (    3)
  link_BETA1-4         : bond        0.00586 (    4)
  link_BETA1-4         : angle       1.85224 (   12)
  link_NAG-ASN         : bond        0.00100 (    5)
  link_NAG-ASN         : angle       1.61921 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1610.59 seconds
wall clock time: 28 minutes 42.67 seconds (1722.67 seconds total)