Starting phenix.real_space_refine
on Thu Jul  2 23:40:37 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7ky8_23071/07_2026/7ky8_23071.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ky8_23071/07_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2026/7ky8_23071.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2026/7ky8_23071.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2026/7ky8_23071.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2026/7ky8_23071.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2026/7ky8_23071.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ky8_23071/07_2026/7ky8_23071.map"
  }
  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-6108/lib/python3.11/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 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 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 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 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 chiralities: 1
  Time building chain proxies: 2.60, per 1000 atoms: 0.25
  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: 0.96
  Conformation dependent library (CDL) restraints added in 319.9 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: 0.32
  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: 1.65

  Time building geometry restraints manager: 1.25 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 -    21.32: 5770
       21.32 -    42.64: 399
       42.64 -    63.96: 43
       63.96 -    85.27: 9
       85.27 -   106.59: 4
  Dihedral angle restraints: 6225
    sinusoidal: 2511
      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 6222 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:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.620
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
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  : 14.200 106.592   3837
  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/Z
  covalent geometry    : bond        0.00467 /  0.22 (10770)
  covalent geometry    : angle       0.74144 /  0.36 (14643)
  SS BOND              : bond        0.00185 /  0.12 (    2)
  SS BOND              : angle       0.54991 /  0.20 (    4)
  hydrogen bonds       : bond        0.13621 /  8.83 (  490)
  hydrogen bonds       : angle       5.70977 /  4.00 ( 1362)
  Misc. bond           : bond        0.00048 /  0.03 (    1)
  link_ALPHA1-4        : bond        0.00362 /  0.23 (    1)
  link_ALPHA1-4        : angle       2.60758 /  1.31 (    3)
  link_BETA1-4         : bond        0.00542 /  0.31 (    4)
  link_BETA1-4         : angle       0.94561 /  0.59 (   12)
  link_NAG-ASN         : bond        0.00171 /  0.09 (    5)
  link_NAG-ASN         : angle       2.38861 /  1.20 (   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  : 0.375 
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: 0.0846
  time to fit residues: 18.5594
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  : 0.351 
-------------------------------------------------------------------------------
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...
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 = 0.3644 r_free = 0.3644 target = 0.153213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.115799 restraints weight = 13111.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.114329 restraints weight = 17892.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.110961 restraints weight = 18833.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.107967 restraints weight = 15475.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.108947 restraints weight = 13590.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.0937

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= 0.172
  Angle     :  0.635  11.122  14677  Z= 0.320
  Chirality :  0.044   0.178   1673
  Planarity :  0.004   0.034   1805
  Dihedral  :  6.568 119.377   1437
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.44 %
    Favored  : 89.03 %
  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:  0.44 (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 A1376 
 TYR   0.021   0.001   TYR A1299 
 PHE   0.016   0.001   PHE A1408 
 TRP   0.024   0.001   TRP B 142 
 HIS   0.006   0.001   HIS A1336 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.17 (10770)
  covalent geometry    : angle       0.63030 /  0.32 (14643)
  SS BOND              : bond        0.00249 /  0.16 (    2)
  SS BOND              : angle       0.59676 /  0.22 (    4)
  hydrogen bonds       : bond        0.04396 /  2.84 (  490)
  hydrogen bonds       : angle       4.61526 /  3.29 ( 1362)
  Misc. bond           : bond        0.00019 /  0.01 (    1)
  link_ALPHA1-4        : bond        0.00572 /  0.36 (    1)
  link_ALPHA1-4        : angle       2.14563 /  1.11 (    3)
  link_BETA1-4         : bond        0.00353 /  0.22 (    4)
  link_BETA1-4         : angle       1.10141 /  0.70 (   12)
  link_NAG-ASN         : bond        0.00219 /  0.13 (    5)
  link_NAG-ASN         : angle       2.12471 /  1.09 (   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
  140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8540 (t80) cc_final: 0.8317 (t80)
REVERT: A  771 MET cc_start: 0.6549 (ttp) cc_final: 0.5801 (ttt)
REVERT: A  845 ASP cc_start: 0.8155 (p0) cc_final: 0.7847 (p0)
REVERT: A  949 GLU cc_start: 0.7763 (pm20) cc_final: 0.7392 (mt-10)
REVERT: A 1129 MET cc_start: 0.6575 (mmt) cc_final: 0.6374 (mmt)
REVERT: B  121 ILE cc_start: 0.8552 (mt) cc_final: 0.8158 (mt)
REVERT: B  147 ASP cc_start: 0.8563 (t0) cc_final: 0.8362 (t0)
  outliers start: 17
  outliers final: 15
  residues processed: 131
  average time/residue: 0.0854
  time to fit residues: 16.5285
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 116 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9980
   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:    1.2182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3639 r_free = 0.3639 target = 0.152825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.111830 restraints weight = 13093.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.108957 restraints weight = 23436.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.110485 restraints weight = 20447.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.110963 restraints weight = 14637.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.111083 restraints weight = 14723.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10783  Z= 0.153
  Angle     :  0.595   8.453  14677  Z= 0.301
  Chirality :  0.043   0.179   1673
  Planarity :  0.003   0.034   1805
  Dihedral  :  6.589 122.408   1437
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 12.23 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.24), residues: 1266
  helix:  0.52 (0.22), residues: 579
  sheet: -1.49 (0.42), residues: 146
  loop : -2.04 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1131 
 TYR   0.018   0.001   TYR B 280 
 PHE   0.015   0.001   PHE A1408 
 TRP   0.018   0.001   TRP B 142 
 HIS   0.005   0.001   HIS A1336 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 (10770)
  covalent geometry    : angle       0.59032 /  0.30 (14643)
  SS BOND              : bond        0.00233 /  0.15 (    2)
  SS BOND              : angle       0.55607 /  0.22 (    4)
  hydrogen bonds       : bond        0.04112 /  2.66 (  490)
  hydrogen bonds       : angle       4.43528 /  3.17 ( 1362)
  Misc. bond           : bond        0.00025 /  0.02 (    1)
  link_ALPHA1-4        : bond        0.00593 /  0.37 (    1)
  link_ALPHA1-4        : angle       2.00488 /  1.04 (    3)
  link_BETA1-4         : bond        0.00465 /  0.28 (    4)
  link_BETA1-4         : angle       1.09258 /  0.73 (   12)
  link_NAG-ASN         : bond        0.00261 /  0.16 (    5)
  link_NAG-ASN         : angle       2.15127 /  1.16 (   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
  153 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8615 (t80) cc_final: 0.8345 (t80)
REVERT: A  771 MET cc_start: 0.6867 (ttp) cc_final: 0.6034 (ttt)
REVERT: A  845 ASP cc_start: 0.7858 (p0) cc_final: 0.7610 (p0)
REVERT: B  121 ILE cc_start: 0.8557 (mt) cc_final: 0.8199 (mt)
  outliers start: 30
  outliers final: 19
  residues processed: 140
  average time/residue: 0.0903
  time to fit residues: 18.7673
Evaluate side-chains
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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 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  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:    0.8980
   chunk 123 optimal weight:    0.7980
   chunk 111 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 30 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 48 optimal weight:    0.3980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3650 r_free = 0.3650 target = 0.154425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.114370 restraints weight = 13080.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.112552 restraints weight = 22869.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.114675 restraints weight = 19137.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.113641 restraints weight = 13416.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.114364 restraints weight = 13254.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1351

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= 0.119
  Angle     :  0.570   8.772  14677  Z= 0.287
  Chirality :  0.042   0.167   1673
  Planarity :  0.003   0.035   1805
  Dihedral  :  6.502 123.991   1437
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.20 %
    Favored  : 82.55 %
  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: 585
  sheet: -1.47 (0.42), residues: 146
  loop : -1.96 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1131 
 TYR   0.017   0.001   TYR B 280 
 PHE   0.018   0.001   PHE A1111 
 TRP   0.014   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 (10770)
  covalent geometry    : angle       0.56487 /  0.29 (14643)
  SS BOND              : bond        0.00161 /  0.10 (    2)
  SS BOND              : angle       0.53099 /  0.22 (    4)
  hydrogen bonds       : bond        0.03790 /  2.45 (  490)
  hydrogen bonds       : angle       4.31421 /  3.10 ( 1362)
  Misc. bond           : bond        0.00008 /  0.00 (    1)
  link_ALPHA1-4        : bond        0.00621 /  0.39 (    1)
  link_ALPHA1-4        : angle       1.89045 /  0.96 (    3)
  link_BETA1-4         : bond        0.00513 /  0.31 (    4)
  link_BETA1-4         : angle       1.08746 /  0.73 (   12)
  link_NAG-ASN         : bond        0.00140 /  0.08 (    5)
  link_NAG-ASN         : angle       2.16777 /  1.23 (   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
  141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8651 (t80) cc_final: 0.8431 (t80)
REVERT: A  771 MET cc_start: 0.6944 (ttp) cc_final: 0.6166 (ttt)
REVERT: A  845 ASP cc_start: 0.7915 (p0) cc_final: 0.7629 (p0)
REVERT: A  871 GLU cc_start: 0.7626 (mp0) cc_final: 0.6226 (mm-30)
REVERT: A  944 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7604 (mm-30)
REVERT: A  949 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7451 (pm20)
REVERT: A 1059 LYS cc_start: 0.8118 (ptmm) cc_final: 0.7818 (ptmm)
REVERT: A 1410 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7928 (mmtm)
REVERT: B  121 ILE cc_start: 0.8550 (mt) cc_final: 0.8197 (mt)
REVERT: B  236 ASN cc_start: 0.9403 (t0) cc_final: 0.9059 (t0)
  outliers start: 25
  outliers final: 17
  residues processed: 130
  average time/residue: 0.0969
  time to fit residues: 18.5575
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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 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  111 MET
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  343 ASP
Chi-restraints excluded: chain B residue  393 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 92 optimal weight:    0.0980
   chunk 47 optimal weight:    0.7980
   chunk 108 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3650 r_free = 0.3650 target = 0.154403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.114808 restraints weight = 13054.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.113220 restraints weight = 22164.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.114953 restraints weight = 19267.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.114540 restraints weight = 13590.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.115005 restraints weight = 13297.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10783  Z= 0.121
  Angle     :  0.572   8.512  14677  Z= 0.288
  Chirality :  0.042   0.158   1673
  Planarity :  0.003   0.044   1805
  Dihedral  :  6.453 124.284   1437
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.19 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.01 (0.24), residues: 1266
  helix:  0.64 (0.22), residues: 586
  sheet: -1.46 (0.42), residues: 146
  loop : -1.93 (0.28), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1131 
 TYR   0.018   0.001   TYR B 280 
 PHE   0.014   0.001   PHE A1408 
 TRP   0.012   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 (10770)
  covalent geometry    : angle       0.56615 /  0.29 (14643)
  SS BOND              : bond        0.00180 /  0.11 (    2)
  SS BOND              : angle       0.47072 /  0.19 (    4)
  hydrogen bonds       : bond        0.03714 /  2.41 (  490)
  hydrogen bonds       : angle       4.25586 /  3.05 ( 1362)
  Misc. bond           : bond        0.00006 /  0.00 (    1)
  link_ALPHA1-4        : bond        0.00627 /  0.39 (    1)
  link_ALPHA1-4        : angle       1.92703 /  0.99 (    3)
  link_BETA1-4         : bond        0.00544 /  0.33 (    4)
  link_BETA1-4         : angle       1.11522 /  0.76 (   12)
  link_NAG-ASN         : bond        0.00153 /  0.09 (    5)
  link_NAG-ASN         : angle       2.43023 /  1.43 (   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
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8684 (t80) cc_final: 0.8473 (t80)
REVERT: A  771 MET cc_start: 0.7077 (ttp) cc_final: 0.6267 (ttt)
REVERT: A  845 ASP cc_start: 0.7853 (p0) cc_final: 0.7563 (p0)
REVERT: A  949 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7431 (pm20)
REVERT: A 1059 LYS cc_start: 0.8142 (ptmm) cc_final: 0.7914 (ptmm)
REVERT: A 1410 LYS cc_start: 0.8402 (mmtt) cc_final: 0.7940 (mmtm)
REVERT: B  121 ILE cc_start: 0.8562 (mt) cc_final: 0.8191 (mt)
REVERT: B  236 ASN cc_start: 0.9390 (t0) cc_final: 0.9041 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 126
  average time/residue: 0.1020
  time to fit residues: 18.8549
Evaluate side-chains
  126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  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 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  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:    0.3980
   chunk 107 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 123 optimal weight:    0.7980
   chunk 110 optimal weight:    0.6980
   chunk 104 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.154844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.117047 restraints weight = 13087.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.115511 restraints weight = 21703.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.117283 restraints weight = 17668.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.114101 restraints weight = 9480.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.114253 restraints weight = 8818.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10783  Z= 0.117
  Angle     :  0.572  10.232  14677  Z= 0.285
  Chirality :  0.041   0.147   1673
  Planarity :  0.003   0.039   1805
  Dihedral  :  6.410 124.686   1437
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.09 %
    Favored  : 80.76 %
  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: -1.01 (0.24), residues: 1266
  helix:  0.59 (0.22), residues: 593
  sheet: -1.41 (0.42), residues: 146
  loop : -1.92 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1131 
 TYR   0.018   0.001   TYR B 280 
 PHE   0.030   0.001   PHE A1111 
 TRP   0.011   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 (10770)
  covalent geometry    : angle       0.56862 /  0.28 (14643)
  SS BOND              : bond        0.00167 /  0.10 (    2)
  SS BOND              : angle       0.44555 /  0.19 (    4)
  hydrogen bonds       : bond        0.03664 /  2.36 (  490)
  hydrogen bonds       : angle       4.21056 /  3.03 ( 1362)
  Misc. bond           : bond        0.00004 /  0.00 (    1)
  link_ALPHA1-4        : bond        0.00642 /  0.40 (    1)
  link_ALPHA1-4        : angle       1.91033 /  0.97 (    3)
  link_BETA1-4         : bond        0.00518 /  0.31 (    4)
  link_BETA1-4         : angle       1.10692 /  0.75 (   12)
  link_NAG-ASN         : bond        0.00069 /  0.04 (    5)
  link_NAG-ASN         : angle       1.80121 /  0.94 (   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: 24
    poor density    : 120
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.6870 (ttp) cc_final: 0.6411 (ttt)
REVERT: A  845 ASP cc_start: 0.8184 (p0) cc_final: 0.7967 (p0)
REVERT: A  871 GLU cc_start: 0.7535 (mp0) cc_final: 0.5966 (mm-30)
REVERT: A  954 LEU cc_start: 0.8707 (tp) cc_final: 0.8404 (tp)
REVERT: A 1410 LYS cc_start: 0.8401 (mmtt) cc_final: 0.7893 (mmtm)
REVERT: B  121 ILE cc_start: 0.8569 (mt) cc_final: 0.8220 (mt)
REVERT: B  236 ASN cc_start: 0.9407 (t0) cc_final: 0.9060 (t0)
REVERT: B  348 TRP cc_start: 0.9107 (OUTLIER) cc_final: 0.8645 (t60)
  outliers start: 24
  outliers final: 18
  residues processed: 133
  average time/residue: 0.1007
  time to fit residues: 19.8381
Evaluate side-chains
  129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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 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 1325 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  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  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:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 119 optimal weight:    0.9980
   chunk 111 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1285 GLN
B  60 GLN
** 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 = 0.153904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.113682 restraints weight = 13010.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.112106 restraints weight = 22731.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.113125 restraints weight = 19157.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.113186 restraints weight = 14243.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.113543 restraints weight = 12702.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10783  Z= 0.128
  Angle     :  0.572   8.471  14677  Z= 0.288
  Chirality :  0.042   0.138   1673
  Planarity :  0.004   0.041   1805
  Dihedral  :  6.415 125.222   1437
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.99 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.58 (0.22), residues: 594
  sheet: -1.37 (0.41), residues: 156
  loop : -1.89 (0.29), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 893 
 TYR   0.026   0.001   TYR A 684 
 PHE   0.013   0.001   PHE A1408 
 TRP   0.011   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 (10770)
  covalent geometry    : angle       0.56840 /  0.29 (14643)
  SS BOND              : bond        0.00183 /  0.11 (    2)
  SS BOND              : angle       0.46143 /  0.19 (    4)
  hydrogen bonds       : bond        0.03697 /  2.38 (  490)
  hydrogen bonds       : angle       4.18188 /  3.01 ( 1362)
  Misc. bond           : bond        0.00007 /  0.00 (    1)
  link_ALPHA1-4        : bond        0.00616 /  0.38 (    1)
  link_ALPHA1-4        : angle       1.95342 /  1.00 (    3)
  link_BETA1-4         : bond        0.00523 /  0.32 (    4)
  link_BETA1-4         : angle       1.12518 /  0.76 (   12)
  link_NAG-ASN         : bond        0.00069 /  0.04 (    5)
  link_NAG-ASN         : angle       1.76264 /  0.91 (   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
  144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8316 (t80) cc_final: 0.8071 (t80)
REVERT: A  685 ASN cc_start: 0.8477 (t0) cc_final: 0.8082 (p0)
REVERT: A  771 MET cc_start: 0.7129 (ttp) cc_final: 0.6662 (ttt)
REVERT: A  810 LYS cc_start: 0.7387 (tptp) cc_final: 0.6159 (ptpt)
REVERT: A  845 ASP cc_start: 0.7842 (p0) cc_final: 0.7638 (p0)
REVERT: A  871 GLU cc_start: 0.7444 (mp0) cc_final: 0.6136 (mm-30)
REVERT: A  949 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7412 (pm20)
REVERT: A  954 LEU cc_start: 0.8450 (tp) cc_final: 0.8211 (tp)
REVERT: A 1410 LYS cc_start: 0.8444 (mmtt) cc_final: 0.7963 (mmtm)
REVERT: B  121 ILE cc_start: 0.8573 (mt) cc_final: 0.8235 (mt)
REVERT: B  236 ASN cc_start: 0.9387 (t0) cc_final: 0.9026 (t0)
REVERT: B  348 TRP cc_start: 0.9147 (OUTLIER) cc_final: 0.8713 (t60)
  outliers start: 24
  outliers final: 18
  residues processed: 135
  average time/residue: 0.0951
  time to fit residues: 19.0579
Evaluate side-chains
  131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
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 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 1287 VAL
Chi-restraints excluded: chain A residue 1325 VAL
Chi-restraints excluded: chain A residue 1458 TRP
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  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:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 111 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0570
   chunk 100 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 120 optimal weight:    2.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    1.0500

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3638 r_free = 0.3638 target = 0.153392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.113789 restraints weight = 13075.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.111385 restraints weight = 20609.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.113227 restraints weight = 20134.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.112700 restraints weight = 13166.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.113221 restraints weight = 12844.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10783  Z= 0.138
  Angle     :  0.583   8.515  14677  Z= 0.294
  Chirality :  0.042   0.165   1673
  Planarity :  0.004   0.043   1805
  Dihedral  :  6.435 125.695   1437
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.53 %
    Favored  : 79.32 %
  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: -0.96 (0.25), residues: 1266
  helix:  0.63 (0.22), residues: 588
  sheet: -1.36 (0.41), residues: 156
  loop : -1.87 (0.29), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1131 
 TYR   0.017   0.001   TYR B 280 
 PHE   0.030   0.001   PHE A1111 
 TRP   0.012   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 (10770)
  covalent geometry    : angle       0.57958 /  0.29 (14643)
  SS BOND              : bond        0.00197 /  0.12 (    2)
  SS BOND              : angle       0.51376 /  0.21 (    4)
  hydrogen bonds       : bond        0.03720 /  2.38 (  490)
  hydrogen bonds       : angle       4.18776 /  3.02 ( 1362)
  Misc. bond           : bond        0.00009 /  0.01 (    1)
  link_ALPHA1-4        : bond        0.00565 /  0.35 (    1)
  link_ALPHA1-4        : angle       1.97082 /  1.00 (    3)
  link_BETA1-4         : bond        0.00494 /  0.30 (    4)
  link_BETA1-4         : angle       1.13266 /  0.76 (   12)
  link_NAG-ASN         : bond        0.00091 /  0.05 (    5)
  link_NAG-ASN         : angle       1.81200 /  0.91 (   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
  140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8318 (t80) cc_final: 0.8074 (t80)
REVERT: A  685 ASN cc_start: 0.8516 (t0) cc_final: 0.8141 (p0)
REVERT: A  771 MET cc_start: 0.7120 (ttp) cc_final: 0.6673 (ttt)
REVERT: A  810 LYS cc_start: 0.7384 (tptp) cc_final: 0.6188 (ptpt)
REVERT: A  871 GLU cc_start: 0.7416 (mp0) cc_final: 0.6136 (mm-30)
REVERT: A  956 LEU cc_start: 0.8342 (mp) cc_final: 0.8120 (mp)
REVERT: A 1410 LYS cc_start: 0.8482 (mmtt) cc_final: 0.7964 (mmtm)
REVERT: B  236 ASN cc_start: 0.9378 (t0) cc_final: 0.9025 (t0)
REVERT: B  348 TRP cc_start: 0.9152 (OUTLIER) cc_final: 0.8718 (t60)
  outliers start: 24
  outliers final: 19
  residues processed: 131
  average time/residue: 0.0995
  time to fit residues: 19.2490
Evaluate side-chains
  130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  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 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 1250 ILE
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 B residue   87 VAL
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  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:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 76 optimal weight:    0.1980
   chunk 28 optimal weight:    3.9990
   chunk 116 optimal weight:    0.2980
   chunk 45 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 96 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3658 r_free = 0.3658 target = 0.155150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.115145 restraints weight = 12977.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.113864 restraints weight = 22180.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.116601 restraints weight = 18498.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.114582 restraints weight = 13218.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.115425 restraints weight = 11296.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1767

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= 0.115
  Angle     :  0.584   9.521  14677  Z= 0.293
  Chirality :  0.042   0.149   1673
  Planarity :  0.003   0.040   1805
  Dihedral  :  6.348 124.919   1437
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.15 %
    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: -0.89 (0.25), residues: 1266
  helix:  0.72 (0.22), residues: 583
  sheet: -1.36 (0.41), residues: 156
  loop : -1.84 (0.29), residues: 527

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 A1328 
 TRP   0.012   0.001   TRP B 142 
 HIS   0.002   0.001   HIS A1336 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 (10770)
  covalent geometry    : angle       0.58131 /  0.29 (14643)
  SS BOND              : bond        0.00141 /  0.09 (    2)
  SS BOND              : angle       0.46345 /  0.19 (    4)
  hydrogen bonds       : bond        0.03616 /  2.33 (  490)
  hydrogen bonds       : angle       4.14830 /  3.00 ( 1362)
  Misc. bond           : bond        0.00003 /  0.00 (    1)
  link_ALPHA1-4        : bond        0.00650 /  0.41 (    1)
  link_ALPHA1-4        : angle       1.88829 /  0.94 (    3)
  link_BETA1-4         : bond        0.00520 /  0.32 (    4)
  link_BETA1-4         : angle       1.08975 /  0.74 (   12)
  link_NAG-ASN         : bond        0.00085 /  0.05 (    5)
  link_NAG-ASN         : angle       1.59797 /  0.83 (   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
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8343 (t80) cc_final: 0.8076 (t80)
REVERT: A  685 ASN cc_start: 0.8525 (t0) cc_final: 0.8151 (p0)
REVERT: A  771 MET cc_start: 0.7095 (ttp) cc_final: 0.6663 (ttt)
REVERT: A  810 LYS cc_start: 0.7371 (tptp) cc_final: 0.6141 (ptpt)
REVERT: A  871 GLU cc_start: 0.7453 (mp0) cc_final: 0.6103 (mm-30)
REVERT: A 1338 ASN cc_start: 0.8600 (p0) cc_final: 0.8230 (p0)
REVERT: A 1410 LYS cc_start: 0.8409 (mmtt) cc_final: 0.7871 (mmtm)
REVERT: B  236 ASN cc_start: 0.9384 (t0) cc_final: 0.9000 (t0)
REVERT: B  315 MET cc_start: 0.8403 (tpt) cc_final: 0.8202 (tpp)
REVERT: B  348 TRP cc_start: 0.9073 (OUTLIER) cc_final: 0.8606 (t60)
  outliers start: 19
  outliers final: 16
  residues processed: 132
  average time/residue: 0.1011
  time to fit residues: 19.7532
Evaluate side-chains
  131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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 1086 GLU
Chi-restraints excluded: chain A residue 1212 VAL
Chi-restraints excluded: chain A residue 1250 ILE
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1287 VAL
Chi-restraints excluded: chain A residue 1458 TRP
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  111 MET
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:    0.7980
   chunk 122 optimal weight:    2.9990
   chunk 24 optimal weight:   20.0000
   chunk 47 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 92 optimal weight:    0.0970
   chunk 18 optimal weight:    4.9990
   chunk 124 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0980
   overall best weight:    0.5378

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.155805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.118072 restraints weight = 12804.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.116916 restraints weight = 17702.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.117112 restraints weight = 16575.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.115838 restraints weight = 15262.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.116454 restraints weight = 13042.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10783  Z= 0.112
  Angle     :  0.578   8.802  14677  Z= 0.291
  Chirality :  0.042   0.140   1673
  Planarity :  0.003   0.040   1805
  Dihedral  :  6.280 124.711   1437
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 19.60 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.85 (0.25), residues: 1266
  helix:  0.70 (0.22), residues: 590
  sheet: -1.37 (0.41), residues: 154
  loop : -1.78 (0.29), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1131 
 TYR   0.019   0.001   TYR B 280 
 PHE   0.032   0.001   PHE A1111 
 TRP   0.010   0.001   TRP B 142 
 HIS   0.002   0.001   HIS A1350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 (10770)
  covalent geometry    : angle       0.57470 /  0.29 (14643)
  SS BOND              : bond        0.00132 /  0.08 (    2)
  SS BOND              : angle       0.44117 /  0.19 (    4)
  hydrogen bonds       : bond        0.03514 /  2.26 (  490)
  hydrogen bonds       : angle       4.12806 /  2.99 ( 1362)
  Misc. bond           : bond        0.00007 /  0.00 (    1)
  link_ALPHA1-4        : bond        0.00667 /  0.42 (    1)
  link_ALPHA1-4        : angle       1.87785 /  0.96 (    3)
  link_BETA1-4         : bond        0.00571 /  0.35 (    4)
  link_BETA1-4         : angle       1.12203 /  0.77 (   12)
  link_NAG-ASN         : bond        0.00084 /  0.05 (    5)
  link_NAG-ASN         : angle       1.57657 /  0.82 (   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
  137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 TYR cc_start: 0.8350 (t80) cc_final: 0.8099 (t80)
REVERT: A  685 ASN cc_start: 0.8543 (t0) cc_final: 0.8161 (p0)
REVERT: A  771 MET cc_start: 0.7060 (ttp) cc_final: 0.6649 (ttt)
REVERT: A  810 LYS cc_start: 0.7346 (tptp) cc_final: 0.6114 (ptpt)
REVERT: A  871 GLU cc_start: 0.7444 (mp0) cc_final: 0.6669 (tm-30)
REVERT: A 1338 ASN cc_start: 0.8578 (p0) cc_final: 0.8219 (p0)
REVERT: B  236 ASN cc_start: 0.9387 (t0) cc_final: 0.9011 (t0)
REVERT: B  315 MET cc_start: 0.8486 (tpt) cc_final: 0.8225 (tpp)
REVERT: B  348 TRP cc_start: 0.9066 (OUTLIER) cc_final: 0.8602 (t60)
  outliers start: 17
  outliers final: 15
  residues processed: 134
  average time/residue: 0.0963
  time to fit residues: 19.0836
Evaluate side-chains
  130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
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 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 1458 TRP
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  111 MET
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:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 126 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.154541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.115062 restraints weight = 13069.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.113910 restraints weight = 22804.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.115107 restraints weight = 18982.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.114298 restraints weight = 13514.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.114909 restraints weight = 13756.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10783  Z= 0.127
  Angle     :  0.590   8.945  14677  Z= 0.295
  Chirality :  0.042   0.164   1673
  Planarity :  0.003   0.042   1805
  Dihedral  :  6.318 125.393   1437
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.60 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.25), residues: 1266
  helix:  0.67 (0.22), residues: 591
  sheet: -1.28 (0.41), residues: 156
  loop : -1.75 (0.29), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1131 
 TYR   0.019   0.001   TYR B 280 
 PHE   0.013   0.001   PHE A1408 
 TRP   0.011   0.001   TRP B 142 
 HIS   0.003   0.001   HIS A1336 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 (10770)
  covalent geometry    : angle       0.58650 /  0.29 (14643)
  SS BOND              : bond        0.00171 /  0.11 (    2)
  SS BOND              : angle       0.45890 /  0.19 (    4)
  hydrogen bonds       : bond        0.03589 /  2.31 (  490)
  hydrogen bonds       : angle       4.13513 /  2.99 ( 1362)
  Misc. bond           : bond        0.00002 /  0.00 (    1)
  link_ALPHA1-4        : bond        0.00608 /  0.38 (    1)
  link_ALPHA1-4        : angle       1.93526 /  0.99 (    3)
  link_BETA1-4         : bond        0.00524 /  0.32 (    4)
  link_BETA1-4         : angle       1.12777 /  0.77 (   12)
  link_NAG-ASN         : bond        0.00076 /  0.04 (    5)
  link_NAG-ASN         : angle       1.65877 /  0.86 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1730.29 seconds
wall clock time: 30 minutes 49.56 seconds (1849.56 seconds total)