Starting phenix.real_space_refine
on Wed Mar  4 12:14:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jgj_22328/03_2026/7jgj_22328.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jgj_22328/03_2026/7jgj_22328.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jgj_22328/03_2026/7jgj_22328.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jgj_22328/03_2026/7jgj_22328.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jgj_22328/03_2026/7jgj_22328.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jgj_22328/03_2026/7jgj_22328.cif"
  }
  resolution = 4.8
  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=   0.001 sd=   0.021
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    8393      2.51       5
     N    2239      2.21       5
     O    2656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13324
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 10070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1277, 10070
          Classifications: {'peptide': 1277}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 33, 'TRANS': 1243}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "L"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1626
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 201}
    Chain: "H"
      Number of atoms: 1628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1628
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 202}
  Time building chain proxies: 2.79, per 1000 atoms: 0.21
  Number of scatterers: 13324
  At special positions: 0
  Unit cell: (82.368, 136.448, 143.936, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    2656      8.00
     N    2239      7.00
     C    8393      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  87 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L 133 " - pdb=" SG  CYS L 193 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 146 " - pdb=" SG  CYS H 201 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 641.6 milliseconds
  

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  GLN A 979 "
        pdb=" CB  TYR A1141 "
        pdb=" CB  VAL A1465 "
        pdb=" CB  ALA A1478 "
        pdb=" CB  GLN A1612 "
        pdb=" CB  ARG A1622 "
        pdb=" CB  VAL A1905 "
        pdb=" CB  SER L 115 "
        pdb=" CB  PRO L 118 "
        pdb=" CB  ASN L 136 "
        pdb=" CB  SER L 173 "
        pdb=" CB  PRO H 132 "
  Number of C-beta restraints generated:  3154

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 28 sheets defined
      27.0% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 782 through 793
    Processing helix  chain 'A' and resid 807 through 809
      No H-bonds generated for 'chain 'A' and resid 807 through 809'
    Processing helix  chain 'A' and resid 1075 through 1082
      removed outlier: 3.506A  pdb=" N   VAL A1082 " --> pdb=" O   ALA A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1119 through 1130
      removed outlier: 3.653A  pdb=" N   LEU A1129 " --> pdb=" O   ASN A1125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1134 through 1144
      removed outlier: 3.629A  pdb=" N   LEU A1144 " --> pdb=" O   LYS A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1174
    Processing helix  chain 'A' and resid 1224 through 1238
      removed outlier: 4.348A  pdb=" N   ILE A1228 " --> pdb=" O   ASP A1224 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A1231 " --> pdb=" O   SER A1227 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A1233 " --> pdb=" O   VAL A1229 " (cutoff:3.500A)
      Proline residue:  A1234  - end of helix
    Processing helix  chain 'A' and resid 1243 through 1250
    Processing helix  chain 'A' and resid 1257 through 1262
      removed outlier: 4.440A  pdb=" N   GLU A1260 " --> pdb=" O   LYS A1257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1263 through 1273
    Processing helix  chain 'A' and resid 1273 through 1283
    Processing helix  chain 'A' and resid 1292 through 1306
      removed outlier: 4.095A  pdb=" N   ARG A1296 " --> pdb=" O   ASN A1292 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   TYR A1298 " --> pdb=" O   VAL A1294 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LEU A1299 " --> pdb=" O   THR A1295 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN A1305 " --> pdb=" O   ASP A1301 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   ASN A1306 " --> pdb=" O   LYS A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1321
    Processing helix  chain 'A' and resid 1330 through 1336
    Processing helix  chain 'A' and resid 1337 through 1342
      removed outlier: 3.713A  pdb=" N   PHE A1341 " --> pdb=" O   PRO A1338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1358
      removed outlier: 3.662A  pdb=" N   LEU A1352 " --> pdb=" O   PRO A1348 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE A1353 " --> pdb=" O   LEU A1349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1359 through 1364
    Processing helix  chain 'A' and resid 1367 through 1375
    Processing helix  chain 'A' and resid 1384 through 1395
      removed outlier: 3.690A  pdb=" N   LYS A1394 " --> pdb=" O   GLU A1390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1401 through 1410
    Processing helix  chain 'A' and resid 1421 through 1430
    Processing helix  chain 'A' and resid 1438 through 1445
    Processing helix  chain 'A' and resid 1448 through 1452
      removed outlier: 4.506A  pdb=" N   ASN A1452 " --> pdb=" O   LYS A1449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1453 through 1459
    Processing helix  chain 'A' and resid 1480 through 1483
    Processing helix  chain 'A' and resid 1491 through 1519
    Processing helix  chain 'A' and resid 1522 through 1527
      removed outlier: 3.516A  pdb=" N   GLU A1525 " --> pdb=" O   GLN A1522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1558 through 1564
    Processing helix  chain 'A' and resid 1597 through 1610
      removed outlier: 3.773A  pdb=" N   THR A1601 " --> pdb=" O   ASP A1597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1658 through 1662
    Processing helix  chain 'A' and resid 1676 through 1705
      removed outlier: 3.635A  pdb=" N   TYR A1696 " --> pdb=" O   TYR A1692 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER A1701 " --> pdb=" O   LEU A1697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1707 through 1714
    Processing helix  chain 'A' and resid 1742 through 1749
      removed outlier: 3.800A  pdb=" N   LEU A1749 " --> pdb=" O   GLU A1745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1751 through 1759
    Processing helix  chain 'A' and resid 1798 through 1810
    Processing helix  chain 'A' and resid 1817 through 1823
    Processing helix  chain 'A' and resid 1826 through 1834
    Processing helix  chain 'A' and resid 1848 through 1857
    Processing helix  chain 'A' and resid 1863 through 1882
      removed outlier: 3.940A  pdb=" N   LEU A1882 " --> pdb=" O   GLN A1878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1904 through 1921
      removed outlier: 3.522A  pdb=" N   GLN A1914 " --> pdb=" O   ALA A1910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1934 through 1951
    Processing helix  chain 'L' and resid 120 through 127
      removed outlier: 3.634A  pdb=" N   SER L 126 " --> pdb=" O   GLU L 122 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 182 through 188
    Processing helix  chain 'H' and resid 135 through 139
    Processing sheet with id=AA1, first strand: chain 'A' and resid 699 through 700
      removed outlier: 5.894A  pdb=" N   TYR A 714 " --> pdb=" O   VAL A 730 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A 732 " --> pdb=" O   THR A 747 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 736 through 737
      removed outlier: 3.550A  pdb=" N   GLU A 736 " --> pdb=" O   VAL A 743 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A 732 " --> pdb=" O   THR A 747 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 756 through 757
    Processing sheet with id=AA4, first strand: chain 'A' and resid 797 through 799
      removed outlier: 6.397A  pdb=" N   TYR A 798 " --> pdb=" O   GLY A 829 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE A 828 " --> pdb=" O   THR A 853 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLU A 855 " --> pdb=" O   ILE A 828 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LYS A 884 " --> pdb=" O   VAL A 854 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 804 through 805
      removed outlier: 7.046A  pdb=" N   LEU A 804 " --> pdb=" O   TYR A 839 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   SER A 858 " --> pdb=" O   TYR A 836 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 864
      removed outlier: 5.095A  pdb=" N   VAL A 862 " --> pdb=" O   VAL A 891 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   PHE A 915 " --> pdb=" O   THR A 951 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   THR A 953 " --> pdb=" O   PHE A 915 " (cutoff:3.500A)
      removed outlier: 8.402A  pdb=" N   GLY A 917 " --> pdb=" O   THR A 953 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   SER A 955 " --> pdb=" O   GLY A 917 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ASP A 986 " --> pdb=" O   ALA A 950 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   VAL A 952 " --> pdb=" O   ASP A 986 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   ASN A 988 " --> pdb=" O   VAL A 952 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   ILE A 954 " --> pdb=" O   ASN A 988 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 869 through 871
    Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 905
    Processing sheet with id=AA9, first strand: chain 'A' and resid 944 through 946
    Processing sheet with id=AB1, first strand: chain 'A' and resid 964 through 965
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1054 through 1055
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1159 through 1161
      removed outlier: 3.621A  pdb=" N   MET A1161 " --> pdb=" O   LYS A1180 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LYS A1180 " --> pdb=" O   MET A1161 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1207 through 1209
      removed outlier: 4.014A  pdb=" N   LEU A1214 " --> pdb=" O   LEU A1209 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1324 through 1325
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1465 through 1467
      removed outlier: 3.533A  pdb=" N   PHE A1476 " --> pdb=" O   LEU A1533 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   LEU A1532 " --> pdb=" O   VAL A1586 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1736 through 1739
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1836 through 1839
    Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13
      removed outlier: 5.728A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 104 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 47 through 48
    Processing sheet with id=AC3, first strand: chain 'L' and resid 128 through 134
    Processing sheet with id=AC4, first strand: chain 'L' and resid 152 through 154
      removed outlier: 3.614A  pdb=" N   THR L 192 " --> pdb=" O   LYS L 148 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR L 191 " --> pdb=" O   PHE L 208 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE L 208 " --> pdb=" O   TYR L 191 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.602A  pdb=" N   THR H 113 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   MET H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   SER H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 16 through 23
      removed outlier: 5.240A  pdb=" N   ALA H  16 " --> pdb=" O   SER H  85 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'H' and resid 129 through 130
    Processing sheet with id=AC8, first strand: chain 'H' and resid 141 through 143
    Processing sheet with id=AC9, first strand: chain 'H' and resid 171 through 177
      removed outlier: 4.434A  pdb=" N   SER H 184 " --> pdb=" O   PRO H 173 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'H' and resid 203 through 205
      removed outlier: 3.905A  pdb=" N   VAL H 203 " --> pdb=" O   VAL H 212 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   VAL H 212 " --> pdb=" O   VAL H 203 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1110 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: 2.93

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.16 -     1.30: 2274
        1.30 -     1.45: 3670
        1.45 -     1.59: 7585
        1.59 -     1.74: 0
        1.74 -     1.88: 64
  Bond restraints: 13593
  Sorted by residual:
  bond pdb=" CA  CYS L  23 "
       pdb=" C   CYS L  23 "
    ideal  model  delta    sigma   weight residual
    1.522  1.406  0.116 1.20e-02 6.94e+03 9.38e+01
  bond pdb=" C   CYS L  23 "
       pdb=" O   CYS L  23 "
    ideal  model  delta    sigma   weight residual
    1.236  1.346 -0.110 1.21e-02 6.83e+03 8.26e+01
  bond pdb=" CA  CYS L  23 "
       pdb=" CB  CYS L  23 "
    ideal  model  delta    sigma   weight residual
    1.531  1.403  0.127 1.52e-02 4.33e+03 7.02e+01
  bond pdb=" C   TYR A1440 "
       pdb=" O   TYR A1440 "
    ideal  model  delta    sigma   weight residual
    1.236  1.160  0.076 1.15e-02 7.56e+03 4.41e+01
  bond pdb=" C   LEU A1209 "
       pdb=" O   LEU A1209 "
    ideal  model  delta    sigma   weight residual
    1.232  1.159  0.073 1.35e-02 5.49e+03 2.92e+01
  ... (remaining 13588 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.42: 18392
       13.42 -    26.84: 11
       26.84 -    40.26: 1
       40.26 -    53.68: 0
       53.68 -    67.10: 1
  Bond angle restraints: 18405
  Sorted by residual:
  angle pdb=" CA  TYR A1392 "
        pdb=" C   TYR A1392 "
        pdb=" O   TYR A1392 "
      ideal   model   delta    sigma   weight residual
     120.55   53.45   67.10 1.06e+00 8.90e-01 4.01e+03
  angle pdb=" O   TYR A1392 "
        pdb=" C   TYR A1392 "
        pdb=" N   ARG A1393 "
      ideal   model   delta    sigma   weight residual
     122.12   87.43   34.69 1.06e+00 8.90e-01 1.07e+03
  angle pdb=" CA  TYR A1392 "
        pdb=" C   TYR A1392 "
        pdb=" N   ARG A1393 "
      ideal   model   delta    sigma   weight residual
     117.30  140.73  -23.43 1.16e+00 7.43e-01 4.08e+02
  angle pdb=" C   PRO L 118 "
        pdb=" CA  PRO L 118 "
        pdb=" CB  PRO L 118 "
      ideal   model   delta    sigma   weight residual
     110.92  132.43  -21.51 1.22e+00 6.72e-01 3.11e+02
  angle pdb=" C   GLY A1801 "
        pdb=" N   ARG A1802 "
        pdb=" CA  ARG A1802 "
      ideal   model   delta    sigma   weight residual
     120.44  139.14  -18.70 1.36e+00 5.41e-01 1.89e+02
  ... (remaining 18400 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.52: 7467
       25.52 -    51.05: 568
       51.05 -    76.57: 90
       76.57 -   102.09: 11
      102.09 -   127.61: 2
  Dihedral angle restraints: 8138
    sinusoidal: 3183
      harmonic: 4955
  Sorted by residual:
  dihedral pdb=" CA  ALA H 105 "
           pdb=" C   ALA H 105 "
           pdb=" N   MET H 106 "
           pdb=" CA  MET H 106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -52.39 -127.61     0      5.00e+00 4.00e-02 6.51e+02
  dihedral pdb=" CA  GLU H 154 "
           pdb=" C   GLU H 154 "
           pdb=" N   PRO H 155 "
           pdb=" CA  PRO H 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   71.88  108.12     0      5.00e+00 4.00e-02 4.68e+02
  dihedral pdb=" CA  PHE H 152 "
           pdb=" C   PHE H 152 "
           pdb=" N   PRO H 153 "
           pdb=" CA  PRO H 153 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -44.96   44.96     0      5.00e+00 4.00e-02 8.08e+01
  ... (remaining 8135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.995: 2020
       0.995 -    1.989: 0
       1.989 -    2.983: 1
       2.983 -    3.978: 11
       3.978 -    4.972: 1
  Chirality restraints: 2033
  Sorted by residual:
  chirality pdb=" CB  THR A1018 "
            pdb=" CA  THR A1018 "
            pdb=" OG1 THR A1018 "
            pdb=" CG2 THR A1018 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.42    4.97 2.00e-01 2.50e+01 6.18e+02
  chirality pdb=" CA  SER L 173 "
            pdb=" N   SER L 173 "
            pdb=" C   SER L 173 "
            pdb=" CB  SER L 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.37    3.88 2.00e-01 2.50e+01 3.76e+02
  chirality pdb=" CA  TYR A1141 "
            pdb=" N   TYR A1141 "
            pdb=" C   TYR A1141 "
            pdb=" CB  TYR A1141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.20    3.71 2.00e-01 2.50e+01 3.45e+02
  ... (remaining 2030 not shown)

  Planarity restraints: 2378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A1627 "   -0.043 2.00e-02 2.50e+03   8.59e-02 7.38e+01
        pdb=" C   PRO A1627 "    0.149 2.00e-02 2.50e+03
        pdb=" O   PRO A1627 "   -0.057 2.00e-02 2.50e+03
        pdb=" N   GLU A1628 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 940 "    0.036 2.00e-02 2.50e+03   7.21e-02 5.20e+01
        pdb=" C   GLY A 940 "   -0.125 2.00e-02 2.50e+03
        pdb=" O   GLY A 940 "    0.048 2.00e-02 2.50e+03
        pdb=" N   LYS A 941 "    0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1358 "    0.029 2.00e-02 2.50e+03   5.97e-02 3.57e+01
        pdb=" C   SER A1358 "   -0.103 2.00e-02 2.50e+03
        pdb=" O   SER A1358 "    0.038 2.00e-02 2.50e+03
        pdb=" N   GLY A1359 "    0.036 2.00e-02 2.50e+03
  ... (remaining 2375 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.30: 2
        2.30 -     2.95: 6468
        2.95 -     3.60: 21866
        3.60 -     4.25: 34373
        4.25 -     4.90: 54023
  Nonbonded interactions: 116732
  Sorted by model distance:
  nonbonded pdb=" N   TYR A1392 "
            pdb=" O   TYR A1392 "
     model   vdw
     1.656 2.496
  nonbonded pdb=" O   TYR A1392 "
            pdb=" CB  TYR A1392 "
     model   vdw
     2.131 2.752
  nonbonded pdb=" N   TYR H  94 "
            pdb=" O   TYR H  94 "
     model   vdw
     2.382 2.496
  nonbonded pdb=" OD1 ASN A1402 "
            pdb=" N   ASN A1403 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" O   GLU H  12 "
            pdb=" N   SER H 118 "
     model   vdw
     2.430 3.120
  ... (remaining 116727 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.530
  Find NCS groups from input model:        0.050
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
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      :  0.013   0.127  13597  Z= 0.976
  Angle     :  2.215  67.103  18413  Z= 1.662
  Chirality :  0.307   4.972   2033
  Planarity :  0.009   0.086   2378
  Dihedral  : 17.489 127.612   4972
  Min Nonbonded Distance : 1.656

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  :  7.24 %
    Favored  : 91.58 %
  Rotamer:
    Outliers : 12.68 %
    Allowed  : 16.33 %
    Favored  : 70.99 %
  Cbeta Deviations :  1.07 %
  Peptide Plane:
    Cis-proline     : 7.02 %
    Cis-general     : 0.06 %
    Twisted Proline : 3.51 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.18), residues: 1699
  helix: -0.08 (0.24), residues: 416
  sheet: -1.92 (0.27), residues: 298
  loop : -1.83 (0.17), residues: 985

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG A 699 
 TYR   0.053   0.004   TYR L  35 
 PHE   0.028   0.003   PHE L 138 
 TRP   0.043   0.004   TRP H 194 
 HIS   0.012   0.002   HIS A1487 

Details of bonding type rmsd
  covalent geometry    : bond        0.01292 (13593)
  covalent geometry    : angle       2.21526 (18405)
  SS BOND              : bond        0.01556 (    4)
  SS BOND              : angle       1.65847 (    8)
  hydrogen bonds       : bond        0.23762 (  403)
  hydrogen bonds       : angle      11.15096 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  485 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 184
    poor density    : 301
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  727 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8723 (m-80)
REVERT: A  733 ILE cc_start: 0.8162 (pt) cc_final: 0.7905 (mm)
REVERT: A  768 TYR cc_start: 0.9460 (OUTLIER) cc_final: 0.9204 (m-10)
REVERT: A  783 PHE cc_start: 0.9236 (t80) cc_final: 0.8953 (t80)
REVERT: A  835 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8165 (p0)
REVERT: A  870 ILE cc_start: 0.9378 (mm) cc_final: 0.9063 (mm)
REVERT: A  915 PHE cc_start: 0.9031 (t80) cc_final: 0.8278 (t80)
REVERT: A  930 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7787 (p0)
REVERT: A  972 VAL cc_start: 0.9641 (OUTLIER) cc_final: 0.9365 (t)
REVERT: A  980 ASN cc_start: 0.9769 (OUTLIER) cc_final: 0.9339 (t0)
REVERT: A 1003 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9118 (tp)
REVERT: A 1048 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7711 (p)
REVERT: A 1133 TYR cc_start: 0.9334 (m-80) cc_final: 0.8812 (m-80)
REVERT: A 1204 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8887 (pp)
REVERT: A 1206 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7113 (pm20)
REVERT: A 1207 TYR cc_start: 0.9798 (m-10) cc_final: 0.9515 (m-80)
REVERT: A 1209 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9283 (mt)
REVERT: A 1221 PHE cc_start: 0.9220 (m-80) cc_final: 0.9019 (t80)
REVERT: A 1263 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9076 (mm)
REVERT: A 1308 GLU cc_start: 0.9462 (OUTLIER) cc_final: 0.9128 (pm20)
REVERT: A 1316 TYR cc_start: 0.9740 (t80) cc_final: 0.9484 (t80)
REVERT: A 1352 LEU cc_start: 0.9460 (tt) cc_final: 0.9160 (tt)
REVERT: A 1390 GLU cc_start: 0.9778 (mm-30) cc_final: 0.9293 (mm-30)
REVERT: A 1397 LEU cc_start: 0.9114 (mp) cc_final: 0.8858 (mp)
REVERT: A 1405 TRP cc_start: 0.9186 (t60) cc_final: 0.8701 (t60)
REVERT: A 1406 PHE cc_start: 0.9643 (t80) cc_final: 0.9289 (t80)
REVERT: A 1466 PHE cc_start: 0.8466 (p90) cc_final: 0.7658 (p90)
REVERT: A 1480 ASP cc_start: 0.9712 (m-30) cc_final: 0.9498 (m-30)
REVERT: A 1510 ASP cc_start: 0.9649 (m-30) cc_final: 0.9174 (p0)
REVERT: A 1511 HIS cc_start: 0.9750 (t70) cc_final: 0.9434 (t-90)
REVERT: A 1532 LEU cc_start: 0.9429 (pp) cc_final: 0.8908 (pp)
REVERT: A 1535 ASP cc_start: 0.4339 (OUTLIER) cc_final: 0.3864 (m-30)
REVERT: A 1561 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8651 (ppp)
REVERT: A 1593 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8391 (ptt)
REVERT: A 1605 GLU cc_start: 0.8976 (mp0) cc_final: 0.8628 (mt-10)
REVERT: A 1610 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8465 (p)
REVERT: A 1616 LEU cc_start: 0.9171 (mt) cc_final: 0.8808 (mp)
REVERT: A 1625 LEU cc_start: 0.8498 (mt) cc_final: 0.8170 (mt)
REVERT: A 1643 ASP cc_start: 0.9541 (m-30) cc_final: 0.8943 (p0)
REVERT: A 1688 PHE cc_start: 0.9656 (m-80) cc_final: 0.9236 (m-80)
REVERT: A 1692 TYR cc_start: 0.9189 (m-10) cc_final: 0.8829 (m-80)
REVERT: A 1694 MET cc_start: 0.9762 (ppp) cc_final: 0.9297 (ppp)
REVERT: A 1741 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6375 (pp)
REVERT: A 1760 ILE cc_start: 0.9454 (pt) cc_final: 0.9224 (pt)
REVERT: A 1789 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7227 (tt)
REVERT: A 1798 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8706 (p0)
REVERT: A 1808 LEU cc_start: 0.9632 (tp) cc_final: 0.9412 (tp)
REVERT: A 1818 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8704 (mtm)
REVERT: A 1889 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.7979 (p0)
REVERT: A 1912 MET cc_start: 0.9779 (tpp) cc_final: 0.9234 (ttp)
REVERT: A 1940 LYS cc_start: 0.9530 (mttm) cc_final: 0.9294 (mtmm)
REVERT: A 1945 LYS cc_start: 0.9620 (pttm) cc_final: 0.9372 (tptp)
REVERT: A 1947 TYR cc_start: 0.9416 (t80) cc_final: 0.8920 (t80)
REVERT: L   32 ILE cc_start: 0.9779 (OUTLIER) cc_final: 0.9563 (tp)
REVERT: L   88 PHE cc_start: 0.9584 (t80) cc_final: 0.8644 (t80)
REVERT: L   95 PHE cc_start: 0.9213 (m-10) cc_final: 0.8893 (m-10)
REVERT: L  190 SER cc_start: 0.0372 (OUTLIER) cc_final: -0.0052 (p)
REVERT: L  191 TYR cc_start: 0.8143 (m-80) cc_final: 0.7753 (m-10)
REVERT: L  208 PHE cc_start: 0.4221 (OUTLIER) cc_final: 0.3438 (m-80)
REVERT: H   44 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8845 (t)
REVERT: H   64 PHE cc_start: 0.9175 (m-80) cc_final: 0.8921 (m-80)
REVERT: H  126 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8341 (p)
REVERT: H  184 SER cc_start: 0.9727 (OUTLIER) cc_final: 0.9517 (p)
  outliers start: 184
  outliers final: 37
  residues processed: 437
  average time/residue: 0.1080
  time to fit residues: 69.3674
Evaluate side-chains
  283 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 218
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:   20.0000
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 875 ASN
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 ASN
A 963 GLN
** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN
A1166 GLN
A1203 ASN
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
A1508 GLN
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1623 ASN
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1950 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  62 GLN
H 139 ASN
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.043103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.029367 restraints weight = 91128.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.031299 restraints weight = 51430.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.032803 restraints weight = 33956.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.033985 restraints weight = 24497.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.034914 restraints weight = 18678.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4647
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13597  Z= 0.199
  Angle     :  0.797   9.479  18413  Z= 0.435
  Chirality :  0.060   1.151   2033
  Planarity :  0.006   0.070   2378
  Dihedral  :  6.176  58.804   1852
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 20.62
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.65 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.69 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.75 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.18), residues: 1699
  helix: -0.43 (0.23), residues: 437
  sheet: -1.68 (0.25), residues: 376
  loop : -1.85 (0.19), residues: 886

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1621 
 TYR   0.047   0.002   TYR A1861 
 PHE   0.027   0.003   PHE A 993 
 TRP   0.014   0.002   TRP A1894 
 HIS   0.009   0.002   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (13593)
  covalent geometry    : angle       0.79582 (18405)
  SS BOND              : bond        0.00574 (    4)
  SS BOND              : angle       2.13249 (    8)
  hydrogen bonds       : bond        0.05485 (  403)
  hydrogen bonds       : angle       7.73403 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 263
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  857 LEU cc_start: 0.9724 (tt) cc_final: 0.9436 (mp)
REVERT: A 1003 LEU cc_start: 0.9406 (mm) cc_final: 0.9032 (tp)
REVERT: A 1161 MET cc_start: 0.8229 (pmm) cc_final: 0.7994 (pmm)
REVERT: A 1207 TYR cc_start: 0.9442 (m-10) cc_final: 0.9134 (m-80)
REVERT: A 1316 TYR cc_start: 0.9224 (t80) cc_final: 0.8629 (t80)
REVERT: A 1332 ASP cc_start: 0.8248 (m-30) cc_final: 0.7912 (m-30)
REVERT: A 1371 THR cc_start: 0.8226 (m) cc_final: 0.7080 (m)
REVERT: A 1443 ILE cc_start: 0.8149 (tt) cc_final: 0.7506 (tt)
REVERT: A 1531 ILE cc_start: 0.5213 (pt) cc_final: 0.4589 (pt)
REVERT: A 1532 LEU cc_start: 0.8253 (pp) cc_final: 0.6161 (pp)
REVERT: A 1534 TYR cc_start: 0.9294 (m-10) cc_final: 0.8994 (m-10)
REVERT: A 1561 MET cc_start: 0.8540 (ppp) cc_final: 0.8106 (ppp)
REVERT: A 1630 PHE cc_start: 0.8543 (m-10) cc_final: 0.8189 (m-10)
REVERT: A 1800 MET cc_start: 0.7997 (mmm) cc_final: 0.7796 (mmt)
REVERT: A 1806 TYR cc_start: 0.7695 (m-10) cc_final: 0.7127 (m-80)
REVERT: A 1808 LEU cc_start: 0.9022 (tp) cc_final: 0.8720 (tp)
REVERT: A 1818 MET cc_start: 0.8608 (mtp) cc_final: 0.8318 (mtm)
REVERT: A 1908 LEU cc_start: 0.9844 (tt) cc_final: 0.9598 (tp)
REVERT: L   34 TRP cc_start: 0.7252 (m100) cc_final: 0.5905 (m100)
REVERT: L   87 CYS cc_start: 0.8194 (p) cc_final: 0.7435 (p)
REVERT: H   11 LEU cc_start: 0.6752 (tp) cc_final: 0.6503 (tp)
REVERT: H   59 ASN cc_start: 0.6622 (m-40) cc_final: 0.5681 (m-40)
REVERT: H   83 LEU cc_start: 0.8873 (mp) cc_final: 0.8060 (mm)
REVERT: H  183 LEU cc_start: 0.9351 (tt) cc_final: 0.9087 (pp)
  outliers start: 4
  outliers final: 3
  residues processed: 265
  average time/residue: 0.0994
  time to fit residues: 40.0832
Evaluate side-chains
  191 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 188
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 127 optimal weight:    6.9990
   chunk 99 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9980
   chunk 144 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 126 optimal weight:    0.9990
   chunk 34 optimal weight:   20.0000
   chunk 100 optimal weight:    8.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 754 GLN
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
A1362 ASN
** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  89 GLN
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.041540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.028169 restraints weight = 94775.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.029987 restraints weight = 53570.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.031409 restraints weight = 35593.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.032519 restraints weight = 25775.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.033431 restraints weight = 19831.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4800
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  13597  Z= 0.176
  Angle     :  0.716   7.950  18413  Z= 0.387
  Chirality :  0.048   0.478   2033
  Planarity :  0.005   0.055   2378
  Dihedral  :  5.937  51.259   1852
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 20.09
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.77 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  4.62 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.75 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.19), residues: 1699
  helix: -0.39 (0.23), residues: 427
  sheet: -1.74 (0.25), residues: 373
  loop : -1.76 (0.19), residues: 899

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1507 
 TYR   0.034   0.002   TYR A1861 
 PHE   0.041   0.003   PHE L 117 
 TRP   0.026   0.002   TRP A1864 
 HIS   0.012   0.002   HIS A1608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (13593)
  covalent geometry    : angle       0.71529 (18405)
  SS BOND              : bond        0.00686 (    4)
  SS BOND              : angle       1.87851 (    8)
  hydrogen bonds       : bond        0.04559 (  403)
  hydrogen bonds       : angle       7.04804 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 228
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  898 VAL cc_start: 0.7417 (t) cc_final: 0.7178 (t)
REVERT: A 1003 LEU cc_start: 0.9418 (mm) cc_final: 0.8957 (tp)
REVERT: A 1161 MET cc_start: 0.8256 (pmm) cc_final: 0.8033 (pmm)
REVERT: A 1207 TYR cc_start: 0.9441 (m-10) cc_final: 0.9100 (m-80)
REVERT: A 1316 TYR cc_start: 0.8952 (t80) cc_final: 0.8691 (t80)
REVERT: A 1443 ILE cc_start: 0.8272 (tt) cc_final: 0.7581 (tt)
REVERT: A 1455 LEU cc_start: 0.8153 (tp) cc_final: 0.7886 (tp)
REVERT: A 1466 PHE cc_start: 0.8021 (p90) cc_final: 0.7208 (p90)
REVERT: A 1471 MET cc_start: 0.9132 (tmm) cc_final: 0.8633 (tmm)
REVERT: A 1531 ILE cc_start: 0.5230 (pt) cc_final: 0.4901 (pt)
REVERT: A 1532 LEU cc_start: 0.8237 (pp) cc_final: 0.6257 (pp)
REVERT: A 1534 TYR cc_start: 0.9321 (m-10) cc_final: 0.8955 (m-10)
REVERT: A 1561 MET cc_start: 0.8374 (ppp) cc_final: 0.8115 (ppp)
REVERT: A 1586 VAL cc_start: 0.9549 (t) cc_final: 0.9344 (t)
REVERT: A 1630 PHE cc_start: 0.8520 (m-10) cc_final: 0.8224 (m-10)
REVERT: A 1635 LEU cc_start: 0.6852 (tp) cc_final: 0.6623 (tp)
REVERT: A 1688 PHE cc_start: 0.8989 (m-80) cc_final: 0.8766 (m-80)
REVERT: A 1806 TYR cc_start: 0.7258 (m-10) cc_final: 0.6775 (m-80)
REVERT: A 1808 LEU cc_start: 0.8746 (tp) cc_final: 0.8527 (tp)
REVERT: A 1818 MET cc_start: 0.8648 (mtp) cc_final: 0.8366 (mtm)
REVERT: L   34 TRP cc_start: 0.7270 (m100) cc_final: 0.5504 (m100)
REVERT: L   72 LEU cc_start: 0.8010 (tt) cc_final: 0.7806 (tt)
REVERT: L   87 CYS cc_start: 0.8137 (p) cc_final: 0.7275 (p)
REVERT: L  117 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.6241 (m-10)
REVERT: H  183 LEU cc_start: 0.9347 (tt) cc_final: 0.9107 (pp)
  outliers start: 5
  outliers final: 2
  residues processed: 232
  average time/residue: 0.0953
  time to fit residues: 34.1591
Evaluate side-chains
  169 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 166
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 138 optimal weight:    9.9990
   chunk 88 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 163 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 153 optimal weight:    0.0970
   overall best weight:    2.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 ASN
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1759 ASN
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.040961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2548 r_free = 0.2548 target = 0.027880 restraints weight = 95081.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.029678 restraints weight = 53607.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.031067 restraints weight = 35535.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.032185 restraints weight = 25793.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.033059 restraints weight = 19680.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4919
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13597  Z= 0.164
  Angle     :  0.668   7.442  18413  Z= 0.363
  Chirality :  0.046   0.320   2033
  Planarity :  0.005   0.050   2378
  Dihedral  :  5.711  44.619   1852
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 20.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.58 %
    Favored  : 96.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.75 %
    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: -1.98 (0.19), residues: 1699
  helix: -0.26 (0.24), residues: 416
  sheet: -1.56 (0.26), residues: 364
  loop : -1.71 (0.19), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1802 
 TYR   0.027   0.002   TYR A1861 
 PHE   0.040   0.002   PHE L 117 
 TRP   0.013   0.002   TRP H 194 
 HIS   0.011   0.002   HIS A1511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (13593)
  covalent geometry    : angle       0.66723 (18405)
  SS BOND              : bond        0.00524 (    4)
  SS BOND              : angle       1.53376 (    8)
  hydrogen bonds       : bond        0.04201 (  403)
  hydrogen bonds       : angle       6.78225 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 219
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  878 THR cc_start: 0.8460 (p) cc_final: 0.8131 (p)
REVERT: A 1003 LEU cc_start: 0.9390 (mm) cc_final: 0.8863 (tp)
REVERT: A 1133 TYR cc_start: 0.9204 (m-80) cc_final: 0.8901 (m-80)
REVERT: A 1161 MET cc_start: 0.8240 (pmm) cc_final: 0.7964 (pmm)
REVERT: A 1207 TYR cc_start: 0.9469 (m-10) cc_final: 0.9118 (m-80)
REVERT: A 1443 ILE cc_start: 0.8301 (tt) cc_final: 0.7654 (tt)
REVERT: A 1455 LEU cc_start: 0.8175 (tp) cc_final: 0.7939 (tp)
REVERT: A 1471 MET cc_start: 0.9080 (tmm) cc_final: 0.8553 (tmm)
REVERT: A 1531 ILE cc_start: 0.5212 (pt) cc_final: 0.4907 (pt)
REVERT: A 1532 LEU cc_start: 0.8424 (pp) cc_final: 0.6567 (pp)
REVERT: A 1534 TYR cc_start: 0.9357 (m-10) cc_final: 0.9060 (m-10)
REVERT: A 1561 MET cc_start: 0.8517 (ppp) cc_final: 0.8144 (ppp)
REVERT: A 1800 MET cc_start: 0.8202 (mmm) cc_final: 0.7944 (mmm)
REVERT: A 1806 TYR cc_start: 0.7268 (m-10) cc_final: 0.7021 (m-80)
REVERT: A 1912 MET cc_start: 0.8964 (mtm) cc_final: 0.8497 (ptm)
REVERT: L   34 TRP cc_start: 0.7198 (m100) cc_final: 0.4937 (m100)
REVERT: L   87 CYS cc_start: 0.8049 (p) cc_final: 0.7107 (p)
REVERT: L  117 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.6436 (m-80)
REVERT: H   81 MET cc_start: 0.9153 (tpt) cc_final: 0.8783 (tpt)
REVERT: H  141 MET cc_start: 0.7524 (tpt) cc_final: 0.7110 (tpp)
REVERT: H  183 LEU cc_start: 0.9344 (tt) cc_final: 0.9080 (pp)
  outliers start: 4
  outliers final: 2
  residues processed: 223
  average time/residue: 0.0946
  time to fit residues: 32.8591
Evaluate side-chains
  161 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 35 optimal weight:    0.2980
   chunk 23 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 164 optimal weight:    9.9990
   chunk 147 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    4.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 ASN
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1612 GLN
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  68 ASN
** H   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.038984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2504 r_free = 0.2504 target = 0.026553 restraints weight = 101546.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.028234 restraints weight = 57993.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.029530 restraints weight = 38619.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.030578 restraints weight = 28086.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.031401 restraints weight = 21491.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5116
moved from start:          0.4899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13597  Z= 0.241
  Angle     :  0.710   9.309  18413  Z= 0.388
  Chirality :  0.045   0.326   2033
  Planarity :  0.005   0.077   2378
  Dihedral  :  5.866  41.118   1852
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 26.03
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.65 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.83 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.75 %
    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: -2.17 (0.19), residues: 1699
  helix: -0.59 (0.23), residues: 428
  sheet: -1.74 (0.26), residues: 361
  loop : -1.71 (0.20), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1621 
 TYR   0.027   0.002   TYR A1861 
 PHE   0.041   0.003   PHE L 117 
 TRP   0.016   0.002   TRP A1448 
 HIS   0.007   0.002   HIS A1511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (13593)
  covalent geometry    : angle       0.70948 (18405)
  SS BOND              : bond        0.00515 (    4)
  SS BOND              : angle       1.61852 (    8)
  hydrogen bonds       : bond        0.04376 (  403)
  hydrogen bonds       : angle       6.89233 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  783 PHE cc_start: 0.8935 (t80) cc_final: 0.8621 (t80)
REVERT: A  846 PHE cc_start: 0.8647 (m-80) cc_final: 0.8433 (m-80)
REVERT: A  849 LEU cc_start: 0.9524 (mt) cc_final: 0.9289 (mt)
REVERT: A 1003 LEU cc_start: 0.9427 (mm) cc_final: 0.8940 (tp)
REVERT: A 1133 TYR cc_start: 0.9236 (m-80) cc_final: 0.8960 (m-80)
REVERT: A 1161 MET cc_start: 0.8236 (pmm) cc_final: 0.7882 (pmm)
REVERT: A 1207 TYR cc_start: 0.9439 (m-10) cc_final: 0.9033 (m-80)
REVERT: A 1455 LEU cc_start: 0.8288 (tp) cc_final: 0.8033 (tp)
REVERT: A 1532 LEU cc_start: 0.8505 (pp) cc_final: 0.7643 (pp)
REVERT: A 1534 TYR cc_start: 0.9411 (m-10) cc_final: 0.9199 (m-10)
REVERT: A 1561 MET cc_start: 0.8645 (ppp) cc_final: 0.8346 (ppp)
REVERT: A 1593 MET cc_start: 0.8393 (ppp) cc_final: 0.7807 (ppp)
REVERT: A 1806 TYR cc_start: 0.7436 (m-10) cc_final: 0.6601 (m-80)
REVERT: L   34 TRP cc_start: 0.7205 (m100) cc_final: 0.5699 (m100)
REVERT: L   87 CYS cc_start: 0.7745 (p) cc_final: 0.7232 (p)
REVERT: L  117 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.6248 (m-10)
REVERT: H   81 MET cc_start: 0.9163 (tpt) cc_final: 0.8865 (tpt)
REVERT: H  115 VAL cc_start: 0.4579 (t) cc_final: 0.3861 (t)
REVERT: H  183 LEU cc_start: 0.9324 (tt) cc_final: 0.9034 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0926
  time to fit residues: 28.8461
Evaluate side-chains
  151 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 141 optimal weight:    5.9990
   chunk 72 optimal weight:    0.4980
   chunk 125 optimal weight:    7.9990
   chunk 108 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 160 optimal weight:    6.9990
   chunk 29 optimal weight:   20.0000
   chunk 32 optimal weight:    0.9990
   chunk 139 optimal weight:   10.0000
   chunk 126 optimal weight:    1.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 764 ASN
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 ASN
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
A1508 GLN
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.039175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2509 r_free = 0.2509 target = 0.026646 restraints weight = 100147.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.028320 restraints weight = 57209.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.029627 restraints weight = 38206.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.030656 restraints weight = 27855.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.031489 restraints weight = 21495.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5083
moved from start:          0.5194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13597  Z= 0.183
  Angle     :  0.657   8.018  18413  Z= 0.357
  Chirality :  0.044   0.292   2033
  Planarity :  0.005   0.047   2378
  Dihedral  :  5.761  39.314   1852
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 23.97
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.47 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.51 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.75 %
    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: -2.11 (0.19), residues: 1699
  helix: -0.55 (0.23), residues: 433
  sheet: -1.64 (0.28), residues: 327
  loop : -1.73 (0.20), residues: 939

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1621 
 TYR   0.022   0.002   TYR A1861 
 PHE   0.040   0.002   PHE L 117 
 TRP   0.015   0.002   TRP A1448 
 HIS   0.007   0.002   HIS A1604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (13593)
  covalent geometry    : angle       0.65632 (18405)
  SS BOND              : bond        0.00508 (    4)
  SS BOND              : angle       1.59070 (    8)
  hydrogen bonds       : bond        0.03815 (  403)
  hydrogen bonds       : angle       6.68317 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 204
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  680 LEU cc_start: 0.9684 (mt) cc_final: 0.9480 (mt)
REVERT: A  849 LEU cc_start: 0.9510 (mt) cc_final: 0.9178 (mt)
REVERT: A  898 VAL cc_start: 0.7436 (t) cc_final: 0.7224 (t)
REVERT: A  915 PHE cc_start: 0.9322 (t80) cc_final: 0.9017 (t80)
REVERT: A  926 THR cc_start: 0.7135 (p) cc_final: 0.6738 (p)
REVERT: A  980 ASN cc_start: 0.9382 (m-40) cc_final: 0.8756 (t0)
REVERT: A 1003 LEU cc_start: 0.9403 (mm) cc_final: 0.8939 (tp)
REVERT: A 1052 ARG cc_start: 0.4549 (mtm-85) cc_final: 0.4214 (mtm-85)
REVERT: A 1133 TYR cc_start: 0.9203 (m-80) cc_final: 0.8895 (m-80)
REVERT: A 1161 MET cc_start: 0.8041 (pmm) cc_final: 0.7762 (pmm)
REVERT: A 1207 TYR cc_start: 0.9424 (m-10) cc_final: 0.9019 (m-80)
REVERT: A 1455 LEU cc_start: 0.8264 (tp) cc_final: 0.8033 (tp)
REVERT: A 1532 LEU cc_start: 0.8581 (pp) cc_final: 0.7752 (pp)
REVERT: A 1561 MET cc_start: 0.8630 (ppp) cc_final: 0.8379 (ppp)
REVERT: A 1593 MET cc_start: 0.8166 (ppp) cc_final: 0.7458 (ppp)
REVERT: A 1808 LEU cc_start: 0.8955 (tp) cc_final: 0.8753 (tp)
REVERT: A 1912 MET cc_start: 0.9111 (mtm) cc_final: 0.8674 (ptm)
REVERT: L   34 TRP cc_start: 0.6932 (m100) cc_final: 0.5501 (m100)
REVERT: L   87 CYS cc_start: 0.7695 (p) cc_final: 0.7219 (p)
REVERT: L   88 PHE cc_start: 0.9055 (t80) cc_final: 0.8833 (t80)
REVERT: H   81 MET cc_start: 0.9160 (tpt) cc_final: 0.8883 (tpt)
REVERT: H  130 LEU cc_start: 0.9263 (mt) cc_final: 0.9024 (mt)
REVERT: H  183 LEU cc_start: 0.9333 (tt) cc_final: 0.9051 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0966
  time to fit residues: 30.7796
Evaluate side-chains
  147 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 150 optimal weight:    1.9990
   chunk 116 optimal weight:   20.0000
   chunk 126 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 130 optimal weight:    5.9990
   chunk 42 optimal weight:   20.0000
   chunk 115 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 134 optimal weight:   20.0000
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 885 GLN
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 ASN
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
A1508 GLN
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.039007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.026607 restraints weight = 103463.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2568 r_free = 0.2568 target = 0.028278 restraints weight = 58723.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.029565 restraints weight = 39326.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.030599 restraints weight = 28734.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.031407 restraints weight = 22073.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5106
moved from start:          0.5466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13597  Z= 0.176
  Angle     :  0.669  12.662  18413  Z= 0.359
  Chirality :  0.044   0.275   2033
  Planarity :  0.005   0.049   2378
  Dihedral  :  5.707  30.624   1852
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 23.71
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.95 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.75 %
    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: -2.21 (0.19), residues: 1699
  helix: -0.55 (0.23), residues: 440
  sheet: -1.67 (0.27), residues: 327
  loop : -1.86 (0.19), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1052 
 TYR   0.025   0.002   TYR A1806 
 PHE   0.031   0.002   PHE L 117 
 TRP   0.024   0.002   TRP H 109 
 HIS   0.009   0.002   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (13593)
  covalent geometry    : angle       0.66885 (18405)
  SS BOND              : bond        0.00436 (    4)
  SS BOND              : angle       1.51430 (    8)
  hydrogen bonds       : bond        0.03835 (  403)
  hydrogen bonds       : angle       6.64411 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  849 LEU cc_start: 0.9543 (mt) cc_final: 0.9293 (mt)
REVERT: A  898 VAL cc_start: 0.7406 (t) cc_final: 0.7173 (t)
REVERT: A  915 PHE cc_start: 0.9260 (t80) cc_final: 0.8997 (t80)
REVERT: A  926 THR cc_start: 0.7043 (p) cc_final: 0.6611 (p)
REVERT: A  980 ASN cc_start: 0.9359 (m-40) cc_final: 0.8719 (t0)
REVERT: A 1003 LEU cc_start: 0.9364 (mm) cc_final: 0.8868 (tp)
REVERT: A 1052 ARG cc_start: 0.5540 (mpp-170) cc_final: 0.5106 (mtm180)
REVERT: A 1133 TYR cc_start: 0.9189 (m-80) cc_final: 0.8860 (m-80)
REVERT: A 1177 THR cc_start: 0.7156 (m) cc_final: 0.6333 (m)
REVERT: A 1207 TYR cc_start: 0.9357 (m-10) cc_final: 0.9018 (m-80)
REVERT: A 1455 LEU cc_start: 0.8277 (tp) cc_final: 0.8007 (tp)
REVERT: A 1532 LEU cc_start: 0.8509 (pp) cc_final: 0.7751 (pp)
REVERT: A 1561 MET cc_start: 0.8680 (ppp) cc_final: 0.8419 (ppp)
REVERT: A 1593 MET cc_start: 0.7991 (ppp) cc_final: 0.7348 (ppp)
REVERT: A 1694 MET cc_start: 0.9592 (ppp) cc_final: 0.9374 (ppp)
REVERT: A 1800 MET cc_start: 0.8223 (tpp) cc_final: 0.8021 (ttm)
REVERT: A 1912 MET cc_start: 0.9117 (mtm) cc_final: 0.8672 (ptm)
REVERT: A 1925 TRP cc_start: 0.6649 (t-100) cc_final: 0.6423 (t-100)
REVERT: L   34 TRP cc_start: 0.6568 (m100) cc_final: 0.6072 (m100)
REVERT: L   87 CYS cc_start: 0.7429 (p) cc_final: 0.7075 (p)
REVERT: H   81 MET cc_start: 0.9148 (tpt) cc_final: 0.8701 (tpt)
REVERT: H  106 MET cc_start: 0.8017 (ppp) cc_final: 0.7429 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0928
  time to fit residues: 29.7164
Evaluate side-chains
  147 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 16 optimal weight:   20.0000
   chunk 118 optimal weight:    8.9990
   chunk 154 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 147 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 161 optimal weight:    8.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 791 ASN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 840 ASN
A 885 GLN
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1220 GLN
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
A1379 GLN
** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1686 ASN
** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 211 ASN
** H   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.036793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.025348 restraints weight = 111957.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2521 r_free = 0.2521 target = 0.026919 restraints weight = 62950.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.028113 restraints weight = 41825.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.029063 restraints weight = 30494.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.029798 restraints weight = 23406.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5326
moved from start:          0.5848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.098  13597  Z= 0.319
  Angle     :  0.815  11.226  18413  Z= 0.443
  Chirality :  0.047   0.291   2033
  Planarity :  0.006   0.054   2378
  Dihedral  :  6.374  27.433   1852
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 36.19
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.83 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    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: -2.74 (0.19), residues: 1699
  helix: -1.26 (0.22), residues: 443
  sheet: -1.93 (0.26), residues: 342
  loop : -2.06 (0.19), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1393 
 TYR   0.028   0.003   TYR A1861 
 PHE   0.037   0.003   PHE L 117 
 TRP   0.029   0.003   TRP A1448 
 HIS   0.010   0.003   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 (13593)
  covalent geometry    : angle       0.81366 (18405)
  SS BOND              : bond        0.00515 (    4)
  SS BOND              : angle       1.98097 (    8)
  hydrogen bonds       : bond        0.04640 (  403)
  hydrogen bonds       : angle       7.09996 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  849 LEU cc_start: 0.9519 (mt) cc_final: 0.9159 (mt)
REVERT: A 1003 LEU cc_start: 0.9339 (mm) cc_final: 0.8889 (tp)
REVERT: A 1133 TYR cc_start: 0.9242 (m-80) cc_final: 0.8962 (m-10)
REVERT: A 1207 TYR cc_start: 0.9365 (m-10) cc_final: 0.9010 (m-10)
REVERT: A 1532 LEU cc_start: 0.8573 (pp) cc_final: 0.7864 (pp)
REVERT: A 1561 MET cc_start: 0.8850 (ppp) cc_final: 0.8600 (ppp)
REVERT: A 1925 TRP cc_start: 0.6628 (t-100) cc_final: 0.6400 (t-100)
REVERT: L   21 MET cc_start: 0.6097 (pmm) cc_final: 0.5889 (pmm)
REVERT: L   34 TRP cc_start: 0.7095 (m100) cc_final: 0.6114 (m100)
REVERT: L   87 CYS cc_start: 0.7183 (p) cc_final: 0.6972 (p)
REVERT: H   81 MET cc_start: 0.9238 (tpt) cc_final: 0.8896 (tpt)
REVERT: H  106 MET cc_start: 0.8137 (ppp) cc_final: 0.7769 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.0916
  time to fit residues: 26.5251
Evaluate side-chains
  123 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 147 optimal weight:    9.9990
   chunk 119 optimal weight:    8.9990
   chunk 111 optimal weight:    7.9990
   chunk 78 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 133 optimal weight:   10.0000
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 885 GLN
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1176 GLN
** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
A1508 GLN
A1575 ASN
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 211 ASN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.038336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2491 r_free = 0.2491 target = 0.026135 restraints weight = 105190.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.027806 restraints weight = 59464.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.029062 restraints weight = 39489.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.030064 restraints weight = 28820.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.030871 restraints weight = 22196.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5197
moved from start:          0.5905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13597  Z= 0.176
  Angle     :  0.694  10.346  18413  Z= 0.374
  Chirality :  0.045   0.263   2033
  Planarity :  0.005   0.048   2378
  Dihedral  :  6.045  26.801   1852
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 26.10
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.83 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.03 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    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: -2.43 (0.19), residues: 1699
  helix: -0.75 (0.23), residues: 433
  sheet: -1.73 (0.27), residues: 326
  loop : -2.00 (0.19), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1481 
 TYR   0.044   0.002   TYR A1482 
 PHE   0.066   0.003   PHE L  97 
 TRP   0.046   0.003   TRP A1405 
 HIS   0.010   0.002   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (13593)
  covalent geometry    : angle       0.69310 (18405)
  SS BOND              : bond        0.00446 (    4)
  SS BOND              : angle       1.73434 (    8)
  hydrogen bonds       : bond        0.03829 (  403)
  hydrogen bonds       : angle       6.70870 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  680 LEU cc_start: 0.9678 (mt) cc_final: 0.9435 (mt)
REVERT: A  926 THR cc_start: 0.6622 (p) cc_final: 0.6234 (p)
REVERT: A  980 ASN cc_start: 0.9372 (m-40) cc_final: 0.8729 (t0)
REVERT: A 1003 LEU cc_start: 0.9299 (mm) cc_final: 0.8871 (tp)
REVERT: A 1020 VAL cc_start: 0.8449 (m) cc_final: 0.7885 (t)
REVERT: A 1052 ARG cc_start: 0.6158 (mtm-85) cc_final: 0.5798 (mtm-85)
REVERT: A 1133 TYR cc_start: 0.9188 (m-80) cc_final: 0.8841 (m-80)
REVERT: A 1207 TYR cc_start: 0.9320 (m-10) cc_final: 0.8966 (m-10)
REVERT: A 1455 LEU cc_start: 0.8314 (tp) cc_final: 0.8092 (tp)
REVERT: A 1532 LEU cc_start: 0.8550 (pp) cc_final: 0.7867 (pp)
REVERT: A 1534 TYR cc_start: 0.9304 (m-10) cc_final: 0.9080 (m-10)
REVERT: A 1561 MET cc_start: 0.8758 (ppp) cc_final: 0.8520 (ppp)
REVERT: A 1806 TYR cc_start: 0.8996 (m-80) cc_final: 0.8763 (m-10)
REVERT: A 1925 TRP cc_start: 0.6221 (t-100) cc_final: 0.6003 (t-100)
REVERT: H   81 MET cc_start: 0.9124 (tpt) cc_final: 0.8664 (tpt)
REVERT: H  103 VAL cc_start: 0.6626 (t) cc_final: 0.6290 (t)
REVERT: H  106 MET cc_start: 0.8128 (ppp) cc_final: 0.7591 (ptt)
  outliers start: 1
  outliers final: 1
  residues processed: 199
  average time/residue: 0.0900
  time to fit residues: 28.2301
Evaluate side-chains
  145 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 20 optimal weight:   20.0000
   chunk 138 optimal weight:    3.9990
   chunk 148 optimal weight:    9.9990
   chunk 95 optimal weight:    0.9980
   chunk 117 optimal weight:    0.9990
   chunk 115 optimal weight:    0.0970
   chunk 137 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 147 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A 791 ASN
A 885 GLN
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 ASN
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
A1508 GLN
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.039648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2522 r_free = 0.2522 target = 0.026940 restraints weight = 100942.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.028682 restraints weight = 56933.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.030008 restraints weight = 37759.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.031060 restraints weight = 27458.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.031915 restraints weight = 21131.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5115
moved from start:          0.6029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13597  Z= 0.138
  Angle     :  0.677   9.738  18413  Z= 0.360
  Chirality :  0.045   0.241   2033
  Planarity :  0.004   0.042   2378
  Dihedral  :  5.698  23.998   1852
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 20.43
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.00 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    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: -2.20 (0.19), residues: 1699
  helix: -0.41 (0.23), residues: 433
  sheet: -1.52 (0.29), residues: 314
  loop : -1.98 (0.19), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1481 
 TYR   0.027   0.002   TYR A1692 
 PHE   0.030   0.002   PHE A1879 
 TRP   0.034   0.002   TRP A1405 
 HIS   0.008   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (13593)
  covalent geometry    : angle       0.67668 (18405)
  SS BOND              : bond        0.00526 (    4)
  SS BOND              : angle       1.35529 (    8)
  hydrogen bonds       : bond        0.03582 (  403)
  hydrogen bonds       : angle       6.42510 ( 1110)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  680 LEU cc_start: 0.9699 (mt) cc_final: 0.9479 (mt)
REVERT: A  926 THR cc_start: 0.6424 (p) cc_final: 0.4903 (p)
REVERT: A  980 ASN cc_start: 0.9404 (m-40) cc_final: 0.8823 (t0)
REVERT: A 1003 LEU cc_start: 0.9281 (mm) cc_final: 0.8842 (tp)
REVERT: A 1020 VAL cc_start: 0.8252 (m) cc_final: 0.7664 (t)
REVERT: A 1052 ARG cc_start: 0.6306 (mtm-85) cc_final: 0.5992 (mtm-85)
REVERT: A 1133 TYR cc_start: 0.9153 (m-80) cc_final: 0.8775 (m-80)
REVERT: A 1207 TYR cc_start: 0.9250 (m-10) cc_final: 0.8934 (m-10)
REVERT: A 1532 LEU cc_start: 0.8535 (pp) cc_final: 0.7831 (pp)
REVERT: A 1561 MET cc_start: 0.8719 (ppp) cc_final: 0.8457 (ppp)
REVERT: A 1568 VAL cc_start: 0.7671 (p) cc_final: 0.7308 (m)
REVERT: A 1606 MET cc_start: 0.9439 (mmp) cc_final: 0.9234 (mmp)
REVERT: A 1800 MET cc_start: 0.8175 (ttm) cc_final: 0.7883 (ttt)
REVERT: A 1912 MET cc_start: 0.9199 (mtm) cc_final: 0.8753 (ptm)
REVERT: H   81 MET cc_start: 0.8956 (tpt) cc_final: 0.8374 (tpt)
REVERT: H  106 MET cc_start: 0.8141 (ppp) cc_final: 0.7667 (ptt)
REVERT: H  130 LEU cc_start: 0.9406 (mt) cc_final: 0.9099 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.0939
  time to fit residues: 29.1578
Evaluate side-chains
  144 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 132 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 136 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9980
   chunk 121 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0570
   chunk 142 optimal weight:   30.0000
   chunk 3 optimal weight:    9.9990
   chunk 123 optimal weight:    0.9980
   chunk 160 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 885 GLN
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1036 HIS
** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 ASN
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1237 GLN
A1345 ASN
A1508 GLN
** A1604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.040001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2532 r_free = 0.2532 target = 0.027126 restraints weight = 99752.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.028886 restraints weight = 56568.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.030255 restraints weight = 37589.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.031340 restraints weight = 27319.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.032193 restraints weight = 20956.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5106
moved from start:          0.6240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  13597  Z= 0.133
  Angle     :  0.680  14.995  18413  Z= 0.358
  Chirality :  0.044   0.233   2033
  Planarity :  0.004   0.045   2378
  Dihedral  :  5.459  24.370   1852
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 18.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.42 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    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: -2.07 (0.20), residues: 1699
  helix: -0.21 (0.24), residues: 434
  sheet: -1.36 (0.28), residues: 329
  loop : -1.98 (0.19), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H 102 
 TYR   0.026   0.002   TYR A1692 
 PHE   0.028   0.002   PHE A1879 
 TRP   0.040   0.002   TRP A1405 
 HIS   0.008   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (13593)
  covalent geometry    : angle       0.67974 (18405)
  SS BOND              : bond        0.00424 (    4)
  SS BOND              : angle       1.16037 (    8)
  hydrogen bonds       : bond        0.03583 (  403)
  hydrogen bonds       : angle       6.26876 ( 1110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1934.58 seconds
wall clock time: 34 minutes 47.64 seconds (2087.64 seconds total)