Starting phenix.real_space_refine
on Thu Jul 31 15:02:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jgj_22328/07_2025/7jgj_22328.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jgj_22328/07_2025/7jgj_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_22328/07_2025/7jgj_22328.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jgj_22328/07_2025/7jgj_22328.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jgj_22328/07_2025/7jgj_22328.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jgj_22328/07_2025/7jgj_22328.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.79, per 1000 atoms: 0.66
  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: 3.06
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 2.01
  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: 6.44

  Time building geometry restraints manager: 3.67 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:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     36.810
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.070
  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:3.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.910
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.043   0.004   TRP H 194 
 HIS   0.012   0.002   HIS A1487 
 PHE   0.028   0.003   PHE L 138 
 TYR   0.053   0.004   TYR L  35 
 ARG   0.010   0.002   ARG A 699 

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

*********************** 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  : 1.608 
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: 0.9221 (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: 0.9749 (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: 0.4338 (OUTLIER) cc_final: 0.3863 (m-30)
REVERT: A 1561 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8651 (ppp)
REVERT: A 1593 MET cc_start: 0.9108 (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: 0.2637
  time to fit residues: 168.0914
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  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 142 optimal weight:    0.5980
   chunk 128 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 132 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 153 optimal weight:    9.9990
   overall best weight:    3.1188

-------------------------------------------------------------------------------
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
A1044 ASN
A1166 GLN
A1203 ASN
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.042175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2579 r_free = 0.2579 target = 0.028793 restraints weight = 92442.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.030646 restraints weight = 52505.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.032107 restraints weight = 34969.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4777
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  13597  Z= 0.218
  Angle     :  0.797   9.418  18413  Z= 0.436
  Chirality :  0.059   1.096   2033
  Planarity :  0.006   0.070   2378
  Dihedral  :  6.221  57.958   1852
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 22.22
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.71 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.89 %
    Favored  : 94.83 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.75 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.19), residues: 1699
  helix: -0.41 (0.23), residues: 436
  sheet: -1.67 (0.25), residues: 376
  loop : -1.84 (0.19), residues: 887

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1894 
 HIS   0.010   0.002   HIS A 977 
 PHE   0.023   0.003   PHE A 993 
 TYR   0.048   0.003   TYR A1861 
 ARG   0.007   0.001   ARG A1592 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05468 (  403)
  hydrogen bonds       : angle       7.71411 ( 1110)
  SS BOND              : bond        0.00946 (    4)
  SS BOND              : angle       2.02485 (    8)
  covalent geometry    : bond        0.00454 (13593)
  covalent geometry    : angle       0.79562 (18405)

*********************** 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
  263 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 259
  time to evaluate  : 1.591 
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  857 LEU cc_start: 0.9755 (tt) cc_final: 0.9478 (mp)
REVERT: A  870 ILE cc_start: 0.8293 (mm) cc_final: 0.8081 (pt)
REVERT: A  878 THR cc_start: 0.8507 (p) cc_final: 0.8178 (p)
REVERT: A  934 LEU cc_start: 0.8043 (mm) cc_final: 0.7764 (tp)
REVERT: A 1003 LEU cc_start: 0.9408 (mm) cc_final: 0.9035 (tp)
REVERT: A 1207 TYR cc_start: 0.9472 (m-10) cc_final: 0.9159 (m-80)
REVERT: A 1316 TYR cc_start: 0.9246 (t80) cc_final: 0.8833 (t80)
REVERT: A 1332 ASP cc_start: 0.8353 (m-30) cc_final: 0.8097 (m-30)
REVERT: A 1352 LEU cc_start: 0.7852 (tt) cc_final: 0.7593 (tt)
REVERT: A 1371 THR cc_start: 0.8477 (m) cc_final: 0.7374 (m)
REVERT: A 1443 ILE cc_start: 0.8202 (tt) cc_final: 0.7578 (tt)
REVERT: A 1471 MET cc_start: 0.9157 (tmm) cc_final: 0.8642 (tmm)
REVERT: A 1531 ILE cc_start: 0.5469 (pt) cc_final: 0.4875 (pt)
REVERT: A 1532 LEU cc_start: 0.8347 (pp) cc_final: 0.6301 (pp)
REVERT: A 1534 TYR cc_start: 0.9293 (m-10) cc_final: 0.9042 (m-10)
REVERT: A 1561 MET cc_start: 0.8575 (ppp) cc_final: 0.8136 (ppp)
REVERT: A 1593 MET cc_start: 0.8389 (ppp) cc_final: 0.8127 (ppp)
REVERT: A 1630 PHE cc_start: 0.8602 (m-10) cc_final: 0.8292 (m-10)
REVERT: A 1635 LEU cc_start: 0.6988 (tp) cc_final: 0.6782 (tp)
REVERT: A 1693 MET cc_start: 0.9279 (tmm) cc_final: 0.8854 (ptp)
REVERT: A 1694 MET cc_start: 0.9314 (ppp) cc_final: 0.9071 (ppp)
REVERT: A 1806 TYR cc_start: 0.7764 (m-10) cc_final: 0.7211 (m-80)
REVERT: A 1808 LEU cc_start: 0.8969 (tp) cc_final: 0.8670 (tp)
REVERT: A 1818 MET cc_start: 0.8652 (mtp) cc_final: 0.8364 (mtm)
REVERT: L   34 TRP cc_start: 0.7551 (m100) cc_final: 0.6019 (m100)
REVERT: L   87 CYS cc_start: 0.8191 (p) cc_final: 0.7287 (p)
REVERT: L  134 PHE cc_start: 0.7962 (m-10) cc_final: 0.7758 (m-80)
REVERT: H   11 LEU cc_start: 0.6831 (tp) cc_final: 0.6590 (tp)
REVERT: H   59 ASN cc_start: 0.6584 (m-40) cc_final: 0.5664 (m-40)
REVERT: H   83 LEU cc_start: 0.8994 (mp) cc_final: 0.8249 (mm)
REVERT: H  183 LEU cc_start: 0.9380 (tt) cc_final: 0.9107 (pp)
  outliers start: 4
  outliers final: 2
  residues processed: 261
  average time/residue: 0.2388
  time to fit residues: 93.9454
Evaluate side-chains
  191 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 189
  time to evaluate  : 1.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 160 optimal weight:    9.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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
** 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**
A1686 ASN
** A1833 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.042507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.028797 restraints weight = 92987.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.030692 restraints weight = 52501.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.032146 restraints weight = 34739.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4711
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13597  Z= 0.157
  Angle     :  0.699   7.840  18413  Z= 0.376
  Chirality :  0.048   0.490   2033
  Planarity :  0.005   0.059   2378
  Dihedral  :  5.890  50.648   1852
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.71 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.14 %
    Favored  : 95.59 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.75 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.19), residues: 1699
  helix: -0.29 (0.23), residues: 425
  sheet: -1.70 (0.25), residues: 376
  loop : -1.77 (0.19), residues: 898

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1864 
 HIS   0.012   0.002   HIS A1511 
 PHE   0.052   0.003   PHE L 117 
 TYR   0.038   0.002   TYR A1392 
 ARG   0.006   0.001   ARG A 960 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04465 (  403)
  hydrogen bonds       : angle       7.02329 ( 1110)
  SS BOND              : bond        0.00454 (    4)
  SS BOND              : angle       1.90754 (    8)
  covalent geometry    : bond        0.00339 (13593)
  covalent geometry    : angle       0.69829 (18405)

*********************** 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
  240 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 236
  time to evaluate  : 1.577 
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: A  680 LEU cc_start: 0.9599 (mm) cc_final: 0.9391 (mm)
REVERT: A  870 ILE cc_start: 0.8288 (mm) cc_final: 0.8085 (pt)
REVERT: A  898 VAL cc_start: 0.7678 (t) cc_final: 0.7101 (t)
REVERT: A 1003 LEU cc_start: 0.9399 (mm) cc_final: 0.8925 (tp)
REVERT: A 1161 MET cc_start: 0.8384 (pmm) cc_final: 0.8115 (pmm)
REVERT: A 1207 TYR cc_start: 0.9492 (m-10) cc_final: 0.9163 (m-80)
REVERT: A 1316 TYR cc_start: 0.9047 (t80) cc_final: 0.8652 (t80)
REVERT: A 1335 MET cc_start: 0.8653 (ptp) cc_final: 0.8353 (ptp)
REVERT: A 1352 LEU cc_start: 0.7687 (tt) cc_final: 0.7291 (tt)
REVERT: A 1443 ILE cc_start: 0.8246 (tt) cc_final: 0.7540 (tt)
REVERT: A 1455 LEU cc_start: 0.8197 (tp) cc_final: 0.7909 (tp)
REVERT: A 1466 PHE cc_start: 0.7769 (p90) cc_final: 0.7480 (p90)
REVERT: A 1471 MET cc_start: 0.9160 (tmm) cc_final: 0.8882 (tmm)
REVERT: A 1531 ILE cc_start: 0.5207 (pt) cc_final: 0.4869 (pt)
REVERT: A 1532 LEU cc_start: 0.8310 (pp) cc_final: 0.6390 (pp)
REVERT: A 1534 TYR cc_start: 0.9328 (m-10) cc_final: 0.8926 (m-10)
REVERT: A 1561 MET cc_start: 0.8284 (ppp) cc_final: 0.8029 (ppp)
REVERT: A 1630 PHE cc_start: 0.8532 (m-10) cc_final: 0.8219 (m-10)
REVERT: A 1688 PHE cc_start: 0.8992 (m-80) cc_final: 0.8757 (m-80)
REVERT: A 1806 TYR cc_start: 0.7349 (m-10) cc_final: 0.6864 (m-80)
REVERT: A 1808 LEU cc_start: 0.8703 (tp) cc_final: 0.8481 (tp)
REVERT: A 1818 MET cc_start: 0.8684 (mtp) cc_final: 0.8411 (mtm)
REVERT: A 1912 MET cc_start: 0.8851 (mtp) cc_final: 0.8629 (mtm)
REVERT: L   34 TRP cc_start: 0.6959 (m100) cc_final: 0.5331 (m100)
REVERT: L   72 LEU cc_start: 0.7690 (tt) cc_final: 0.7471 (tt)
REVERT: L   87 CYS cc_start: 0.7824 (p) cc_final: 0.7193 (p)
REVERT: L  117 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6172 (m-10)
REVERT: H   81 MET cc_start: 0.9059 (tpt) cc_final: 0.8510 (tpt)
REVERT: H  183 LEU cc_start: 0.9366 (tt) cc_final: 0.9124 (pp)
  outliers start: 4
  outliers final: 2
  residues processed: 239
  average time/residue: 0.2384
  time to fit residues: 86.5264
Evaluate side-chains
  181 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 178
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 167 optimal weight:    4.9990
   chunk 163 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 98 optimal weight:    3.9990
   chunk 125 optimal weight:    0.1980
   chunk 130 optimal weight:    3.9990
   chunk 151 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 115 optimal weight:    9.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 ** 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**
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1759 ASN
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1835 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 = 0.3000 r_free = 0.3000 target = 0.042082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.028573 restraints weight = 92239.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.030419 restraints weight = 52514.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.031881 restraints weight = 35087.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4758
moved from start:          0.4420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13597  Z= 0.142
  Angle     :  0.665   7.679  18413  Z= 0.357
  Chirality :  0.045   0.319   2033
  Planarity :  0.005   0.059   2378
  Dihedral  :  5.579  44.410   1852
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.38 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.19), residues: 1699
  helix: -0.42 (0.23), residues: 435
  sheet: -1.45 (0.26), residues: 374
  loop : -1.78 (0.20), residues: 890

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 194 
 HIS   0.011   0.002   HIS A1511 
 PHE   0.042   0.002   PHE L 117 
 TYR   0.025   0.002   TYR A1861 
 ARG   0.004   0.001   ARG A1802 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04079 (  403)
  hydrogen bonds       : angle       6.68116 ( 1110)
  SS BOND              : bond        0.00487 (    4)
  SS BOND              : angle       1.45711 (    8)
  covalent geometry    : bond        0.00305 (13593)
  covalent geometry    : angle       0.66424 (18405)

*********************** 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
  231 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 228
  time to evaluate  : 1.501 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  849 LEU cc_start: 0.9346 (mt) cc_final: 0.8986 (mt)
REVERT: A 1003 LEU cc_start: 0.9370 (mm) cc_final: 0.8835 (tp)
REVERT: A 1161 MET cc_start: 0.8460 (pmm) cc_final: 0.8132 (pmm)
REVERT: A 1207 TYR cc_start: 0.9403 (m-10) cc_final: 0.9042 (m-80)
REVERT: A 1310 LEU cc_start: 0.9354 (mt) cc_final: 0.9130 (mt)
REVERT: A 1316 TYR cc_start: 0.8894 (t80) cc_final: 0.8576 (t80)
REVERT: A 1409 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6709 (tt0)
REVERT: A 1443 ILE cc_start: 0.8331 (tt) cc_final: 0.7642 (tt)
REVERT: A 1455 LEU cc_start: 0.8163 (tp) cc_final: 0.7881 (tp)
REVERT: A 1466 PHE cc_start: 0.8972 (p90) cc_final: 0.7556 (p90)
REVERT: A 1471 MET cc_start: 0.9119 (tmm) cc_final: 0.8832 (tmm)
REVERT: A 1531 ILE cc_start: 0.5115 (pt) cc_final: 0.4766 (pt)
REVERT: A 1532 LEU cc_start: 0.8411 (pp) cc_final: 0.6574 (pp)
REVERT: A 1534 TYR cc_start: 0.9335 (m-10) cc_final: 0.8991 (m-10)
REVERT: A 1561 MET cc_start: 0.8406 (ppp) cc_final: 0.8084 (ppp)
REVERT: A 1630 PHE cc_start: 0.8425 (m-10) cc_final: 0.8171 (m-10)
REVERT: A 1800 MET cc_start: 0.7984 (mmm) cc_final: 0.7468 (mmm)
REVERT: A 1808 LEU cc_start: 0.8729 (tp) cc_final: 0.8209 (tp)
REVERT: A 1818 MET cc_start: 0.8743 (mtp) cc_final: 0.8298 (mmm)
REVERT: L   34 TRP cc_start: 0.6770 (m100) cc_final: 0.4495 (m100)
REVERT: L   72 LEU cc_start: 0.7686 (tt) cc_final: 0.7469 (tt)
REVERT: L   87 CYS cc_start: 0.7917 (p) cc_final: 0.6935 (p)
REVERT: H   81 MET cc_start: 0.8983 (tpt) cc_final: 0.8511 (tpt)
REVERT: H  141 MET cc_start: 0.7396 (tpt) cc_final: 0.7000 (tpp)
REVERT: H  183 LEU cc_start: 0.9359 (tt) cc_final: 0.9102 (pp)
  outliers start: 3
  outliers final: 0
  residues processed: 231
  average time/residue: 0.2393
  time to fit residues: 84.1769
Evaluate side-chains
  173 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 128 optimal weight:    0.0980
   chunk 43 optimal weight:    9.9990
   chunk 124 optimal weight:   10.0000
   chunk 105 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 158 optimal weight:    3.9990
   chunk 138 optimal weight:    8.9990
   overall best weight:    2.8188

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  68 ASN
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.040670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2540 r_free = 0.2540 target = 0.027590 restraints weight = 96880.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.029357 restraints weight = 55472.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.030732 restraints weight = 36969.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4961
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  13597  Z= 0.173
  Angle     :  0.662   8.024  18413  Z= 0.359
  Chirality :  0.044   0.350   2033
  Planarity :  0.005   0.047   2378
  Dihedral  :  5.546  39.967   1852
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 20.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.19), residues: 1699
  helix: -0.42 (0.24), residues: 433
  sheet: -1.47 (0.27), residues: 363
  loop : -1.75 (0.20), residues: 903

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L  46 
 HIS   0.009   0.002   HIS A1511 
 PHE   0.046   0.002   PHE L 117 
 TYR   0.024   0.002   TYR A1861 
 ARG   0.009   0.001   ARG A1924 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03969 (  403)
  hydrogen bonds       : angle       6.48741 ( 1110)
  SS BOND              : bond        0.00512 (    4)
  SS BOND              : angle       1.47365 (    8)
  covalent geometry    : bond        0.00355 (13593)
  covalent geometry    : angle       0.66118 (18405)

*********************** 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
  213 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 1.657 
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: A  727 TYR cc_start: 0.8825 (m-10) cc_final: 0.8596 (m-10)
REVERT: A  783 PHE cc_start: 0.8929 (t80) cc_final: 0.8576 (t80)
REVERT: A  849 LEU cc_start: 0.9460 (mt) cc_final: 0.9169 (mt)
REVERT: A  898 VAL cc_start: 0.7260 (t) cc_final: 0.7028 (t)
REVERT: A  926 THR cc_start: 0.7065 (p) cc_final: 0.6818 (p)
REVERT: A 1003 LEU cc_start: 0.9403 (mm) cc_final: 0.8904 (tp)
REVERT: A 1133 TYR cc_start: 0.9194 (m-80) cc_final: 0.8861 (m-80)
REVERT: A 1161 MET cc_start: 0.8494 (pmm) cc_final: 0.8152 (pmm)
REVERT: A 1207 TYR cc_start: 0.9443 (m-10) cc_final: 0.9096 (m-80)
REVERT: A 1409 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6899 (tt0)
REVERT: A 1443 ILE cc_start: 0.8400 (tt) cc_final: 0.7809 (tt)
REVERT: A 1455 LEU cc_start: 0.8277 (tp) cc_final: 0.8040 (tp)
REVERT: A 1471 MET cc_start: 0.9216 (tmm) cc_final: 0.8985 (tmm)
REVERT: A 1531 ILE cc_start: 0.5251 (pt) cc_final: 0.4952 (pt)
REVERT: A 1532 LEU cc_start: 0.8497 (pp) cc_final: 0.6691 (pp)
REVERT: A 1533 LEU cc_start: 0.9405 (mm) cc_final: 0.9167 (mm)
REVERT: A 1534 TYR cc_start: 0.9359 (m-10) cc_final: 0.9100 (m-10)
REVERT: A 1561 MET cc_start: 0.8485 (ppp) cc_final: 0.8185 (ppp)
REVERT: A 1593 MET cc_start: 0.8483 (tmm) cc_final: 0.8229 (tmm)
REVERT: A 1630 PHE cc_start: 0.8511 (m-10) cc_final: 0.8119 (m-10)
REVERT: A 1800 MET cc_start: 0.8013 (mmm) cc_final: 0.7564 (tpp)
REVERT: A 1808 LEU cc_start: 0.8736 (tp) cc_final: 0.8125 (tp)
REVERT: A 1818 MET cc_start: 0.8792 (mtp) cc_final: 0.8371 (mmm)
REVERT: L   34 TRP cc_start: 0.6693 (m100) cc_final: 0.5071 (m100)
REVERT: L   87 CYS cc_start: 0.7658 (p) cc_final: 0.7173 (p)
REVERT: H   83 LEU cc_start: 0.8770 (mp) cc_final: 0.8491 (mp)
REVERT: H  104 TYR cc_start: 0.7261 (m-10) cc_final: 0.7044 (m-80)
REVERT: H  183 LEU cc_start: 0.9338 (tt) cc_final: 0.9054 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.2336
  time to fit residues: 76.7568
Evaluate side-chains
  153 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 112 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   chunk 165 optimal weight:   30.0000
   chunk 83 optimal weight:    0.6980
   chunk 126 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 79 optimal weight:   10.0000
   chunk 34 optimal weight:   20.0000
   overall best weight:    5.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 840 ASN
** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 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
** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1379 GLN
** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1612 GLN
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1937 HIS ** 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 = 0.2893 r_free = 0.2893 target = 0.038153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2486 r_free = 0.2486 target = 0.026067 restraints weight = 108296.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.027724 restraints weight = 62001.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.029001 restraints weight = 41321.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5167
moved from start:          0.5258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13597  Z= 0.256
  Angle     :  0.745  10.998  18413  Z= 0.406
  Chirality :  0.045   0.298   2033
  Planarity :  0.005   0.048   2378
  Dihedral  :  6.011  39.564   1852
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 30.14
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.42 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.75 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.19), residues: 1699
  helix: -0.89 (0.22), residues: 434
  sheet: -1.75 (0.27), residues: 339
  loop : -1.78 (0.19), residues: 926

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1448 
 HIS   0.007   0.002   HIS A1937 
 PHE   0.040   0.003   PHE L 117 
 TYR   0.028   0.003   TYR A1861 
 ARG   0.010   0.001   ARG A1052 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04325 (  403)
  hydrogen bonds       : angle       6.85305 ( 1110)
  SS BOND              : bond        0.00411 (    4)
  SS BOND              : angle       1.67507 (    8)
  covalent geometry    : bond        0.00501 (13593)
  covalent geometry    : angle       0.74425 (18405)

*********************** 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
  190 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.442 
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: A  849 LEU cc_start: 0.9437 (mt) cc_final: 0.8980 (mt)
REVERT: A  926 THR cc_start: 0.7284 (p) cc_final: 0.6833 (p)
REVERT: A 1003 LEU cc_start: 0.9390 (mm) cc_final: 0.8907 (tp)
REVERT: A 1133 TYR cc_start: 0.9187 (m-80) cc_final: 0.8921 (m-80)
REVERT: A 1161 MET cc_start: 0.8424 (pmm) cc_final: 0.8081 (pmm)
REVERT: A 1207 TYR cc_start: 0.9451 (m-10) cc_final: 0.9054 (m-80)
REVERT: A 1455 LEU cc_start: 0.8397 (tp) cc_final: 0.8150 (tp)
REVERT: A 1532 LEU cc_start: 0.8606 (pp) cc_final: 0.7725 (pp)
REVERT: A 1534 TYR cc_start: 0.9402 (m-10) cc_final: 0.9172 (m-10)
REVERT: A 1561 MET cc_start: 0.8699 (ppp) cc_final: 0.8444 (ppp)
REVERT: A 1593 MET cc_start: 0.8291 (tmm) cc_final: 0.7938 (tmm)
REVERT: A 1616 LEU cc_start: 0.4259 (mt) cc_final: 0.3838 (mt)
REVERT: A 1800 MET cc_start: 0.8341 (mmm) cc_final: 0.8021 (mmm)
REVERT: L   34 TRP cc_start: 0.7415 (m100) cc_final: 0.5912 (m100)
REVERT: L   87 CYS cc_start: 0.7404 (p) cc_final: 0.6943 (p)
REVERT: H   81 MET cc_start: 0.9117 (tpt) cc_final: 0.8798 (tpt)
REVERT: H  115 VAL cc_start: 0.4599 (t) cc_final: 0.3943 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.2313
  time to fit residues: 67.5682
Evaluate side-chains
  134 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 147 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9980
   chunk 131 optimal weight:   10.0000
   chunk 149 optimal weight:    8.9990
   chunk 78 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 75 optimal weight:    0.0870
   chunk 76 optimal weight:    4.9990
   chunk 125 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    2.5962

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

Flipped N/Q/H residues before XYZ refinement:
A 764 ASN
** 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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A1508 GLN
** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.039521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2518 r_free = 0.2518 target = 0.026953 restraints weight = 102848.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.028696 restraints weight = 58290.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.030036 restraints weight = 38586.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5067
moved from start:          0.5420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13597  Z= 0.164
  Angle     :  0.664  10.913  18413  Z= 0.357
  Chirality :  0.044   0.272   2033
  Planarity :  0.005   0.045   2378
  Dihedral  :  5.704  31.857   1852
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 22.03
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.83 %
    Favored  : 93.11 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.19), residues: 1699
  helix: -0.45 (0.23), residues: 430
  sheet: -1.55 (0.28), residues: 321
  loop : -1.87 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1448 
 HIS   0.009   0.002   HIS A 977 
 PHE   0.033   0.002   PHE L 117 
 TYR   0.021   0.002   TYR A1861 
 ARG   0.005   0.001   ARG A1621 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  403)
  hydrogen bonds       : angle       6.50511 ( 1110)
  SS BOND              : bond        0.00459 (    4)
  SS BOND              : angle       1.50747 (    8)
  covalent geometry    : bond        0.00342 (13593)
  covalent geometry    : angle       0.66350 (18405)

*********************** 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
  201 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 1.467 
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: 0.9634 (mt) cc_final: 0.9381 (mt)
REVERT: A  898 VAL cc_start: 0.7412 (t) cc_final: 0.7187 (t)
REVERT: A  926 THR cc_start: 0.7085 (p) cc_final: 0.6653 (p)
REVERT: A 1003 LEU cc_start: 0.9346 (mm) cc_final: 0.8893 (tp)
REVERT: A 1133 TYR cc_start: 0.9160 (m-80) cc_final: 0.8838 (m-80)
REVERT: A 1207 TYR cc_start: 0.9415 (m-10) cc_final: 0.9071 (m-80)
REVERT: A 1455 LEU cc_start: 0.8314 (tp) cc_final: 0.8055 (tp)
REVERT: A 1510 ASP cc_start: 0.9092 (m-30) cc_final: 0.8875 (p0)
REVERT: A 1532 LEU cc_start: 0.8621 (pp) cc_final: 0.7820 (pp)
REVERT: A 1561 MET cc_start: 0.8684 (ppp) cc_final: 0.8446 (ppp)
REVERT: A 1593 MET cc_start: 0.8193 (tmm) cc_final: 0.7894 (tmm)
REVERT: A 1630 PHE cc_start: 0.8384 (m-10) cc_final: 0.8118 (m-10)
REVERT: A 1800 MET cc_start: 0.8214 (mmm) cc_final: 0.7896 (tpp)
REVERT: L   34 TRP cc_start: 0.6730 (m100) cc_final: 0.5286 (m100)
REVERT: L   87 CYS cc_start: 0.7644 (p) cc_final: 0.7215 (p)
REVERT: L   88 PHE cc_start: 0.9111 (t80) cc_final: 0.8820 (t80)
REVERT: H   81 MET cc_start: 0.9127 (tpt) cc_final: 0.8769 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2355
  time to fit residues: 73.6890
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  : 2.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 141 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 148 optimal weight:   20.0000
   chunk 168 optimal weight:    0.7980
   chunk 107 optimal weight:    9.9990
   chunk 156 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 98 optimal weight:    6.9990
   chunk 140 optimal weight:    6.9990
   overall best weight:    3.3586

-------------------------------------------------------------------------------
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**
** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.038576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2491 r_free = 0.2491 target = 0.026325 restraints weight = 105718.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.028012 restraints weight = 60050.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.029296 restraints weight = 39893.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5204
moved from start:          0.5671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13597  Z= 0.187
  Angle     :  0.685  11.620  18413  Z= 0.368
  Chirality :  0.044   0.249   2033
  Planarity :  0.005   0.046   2378
  Dihedral  :  5.778  24.934   1852
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 25.53
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.59 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.19), residues: 1699
  helix: -0.54 (0.23), residues: 425
  sheet: -1.61 (0.28), residues: 327
  loop : -1.92 (0.19), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP H 109 
 HIS   0.009   0.002   HIS A1604 
 PHE   0.035   0.002   PHE L 117 
 TYR   0.025   0.002   TYR A1861 
 ARG   0.003   0.001   ARG A1507 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03891 (  403)
  hydrogen bonds       : angle       6.57781 ( 1110)
  SS BOND              : bond        0.00471 (    4)
  SS BOND              : angle       1.51567 (    8)
  covalent geometry    : bond        0.00379 (13593)
  covalent geometry    : angle       0.68394 (18405)

*********************** 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
  194 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  680 LEU cc_start: 0.9659 (mt) cc_final: 0.9444 (mt)
REVERT: A  926 THR cc_start: 0.6953 (p) cc_final: 0.6520 (p)
REVERT: A 1003 LEU cc_start: 0.9328 (mm) cc_final: 0.8868 (tp)
REVERT: A 1020 VAL cc_start: 0.8452 (m) cc_final: 0.7861 (t)
REVERT: A 1133 TYR cc_start: 0.9203 (m-80) cc_final: 0.8879 (m-80)
REVERT: A 1161 MET cc_start: 0.8623 (pmm) cc_final: 0.8418 (pmm)
REVERT: A 1207 TYR cc_start: 0.9352 (m-10) cc_final: 0.8941 (m-80)
REVERT: A 1455 LEU cc_start: 0.8427 (tp) cc_final: 0.8149 (tp)
REVERT: A 1532 LEU cc_start: 0.8589 (pp) cc_final: 0.7872 (pp)
REVERT: A 1561 MET cc_start: 0.8745 (ppp) cc_final: 0.8494 (ppp)
REVERT: A 1593 MET cc_start: 0.8178 (tmm) cc_final: 0.7914 (tmm)
REVERT: A 1630 PHE cc_start: 0.8497 (m-10) cc_final: 0.8295 (m-10)
REVERT: A 1925 TRP cc_start: 0.6608 (t-100) cc_final: 0.6391 (t-100)
REVERT: L   21 MET cc_start: 0.5948 (pmm) cc_final: 0.5731 (pmm)
REVERT: L   34 TRP cc_start: 0.6633 (m100) cc_final: 0.5932 (m100)
REVERT: L   87 CYS cc_start: 0.7398 (p) cc_final: 0.7133 (p)
REVERT: H   81 MET cc_start: 0.9199 (tpt) cc_final: 0.8692 (tpt)
REVERT: H  130 LEU cc_start: 0.9375 (mt) cc_final: 0.9131 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2269
  time to fit residues: 68.2566
Evaluate side-chains
  135 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0030
   chunk 73 optimal weight:    9.9990
   chunk 109 optimal weight:    0.6980
   chunk 96 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 146 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 167 optimal weight:    3.9990
   overall best weight:    2.7396

-------------------------------------------------------------------------------
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**
** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1508 GLN
** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.039098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2505 r_free = 0.2505 target = 0.026656 restraints weight = 103175.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2568 r_free = 0.2568 target = 0.028357 restraints weight = 58335.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.029686 restraints weight = 38646.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5127
moved from start:          0.5842

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= 0.163
  Angle     :  0.665  11.992  18413  Z= 0.358
  Chirality :  0.044   0.258   2033
  Planarity :  0.004   0.046   2378
  Dihedral  :  5.675  26.588   1852
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 22.60
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.47 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.19), residues: 1699
  helix: -0.52 (0.23), residues: 427
  sheet: -1.56 (0.28), residues: 319
  loop : -1.91 (0.19), residues: 953

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP H 109 
 HIS   0.009   0.001   HIS A 977 
 PHE   0.035   0.002   PHE L 117 
 TYR   0.038   0.002   TYR A1392 
 ARG   0.005   0.001   ARG A1803 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  403)
  hydrogen bonds       : angle       6.46073 ( 1110)
  SS BOND              : bond        0.00432 (    4)
  SS BOND              : angle       1.43911 (    8)
  covalent geometry    : bond        0.00336 (13593)
  covalent geometry    : angle       0.66462 (18405)

*********************** 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
  195 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  680 LEU cc_start: 0.9655 (mt) cc_final: 0.9410 (mt)
REVERT: A  926 THR cc_start: 0.6727 (p) cc_final: 0.5057 (p)
REVERT: A  980 ASN cc_start: 0.9342 (m-40) cc_final: 0.8723 (t0)
REVERT: A 1003 LEU cc_start: 0.9298 (mm) cc_final: 0.8830 (tp)
REVERT: A 1020 VAL cc_start: 0.8418 (m) cc_final: 0.7916 (t)
REVERT: A 1133 TYR cc_start: 0.9171 (m-80) cc_final: 0.8836 (m-80)
REVERT: A 1207 TYR cc_start: 0.9323 (m-10) cc_final: 0.8928 (m-80)
REVERT: A 1455 LEU cc_start: 0.8418 (tp) cc_final: 0.8148 (tp)
REVERT: A 1532 LEU cc_start: 0.8525 (pp) cc_final: 0.7809 (pp)
REVERT: A 1561 MET cc_start: 0.8710 (ppp) cc_final: 0.8481 (ppp)
REVERT: A 1568 VAL cc_start: 0.8309 (p) cc_final: 0.7952 (m)
REVERT: A 1593 MET cc_start: 0.8096 (tmm) cc_final: 0.7812 (tmm)
REVERT: L   34 TRP cc_start: 0.6865 (m100) cc_final: 0.6418 (m100)
REVERT: L   45 LEU cc_start: 0.8786 (tp) cc_final: 0.8257 (tp)
REVERT: H   81 MET cc_start: 0.8992 (tpt) cc_final: 0.8462 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.2145
  time to fit residues: 65.5854
Evaluate side-chains
  141 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 115 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 147 optimal weight:    5.9990
   chunk 123 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   chunk 151 optimal weight:   10.0000
   chunk 152 optimal weight:    7.9990
   chunk 77 optimal weight:    0.3980
   chunk 103 optimal weight:    0.0770
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.0542

-------------------------------------------------------------------------------
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**
A1176 GLN
** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1345 ASN
A1508 GLN
** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1835 GLN ** 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 = 0.2961 r_free = 0.2961 target = 0.040331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2536 r_free = 0.2536 target = 0.027412 restraints weight = 99670.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.029170 restraints weight = 57004.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.030545 restraints weight = 38140.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5169
moved from start:          0.6038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13597  Z= 0.128
  Angle     :  0.661  12.526  18413  Z= 0.350
  Chirality :  0.044   0.239   2033
  Planarity :  0.004   0.044   2378
  Dihedral  :  5.435  22.885   1852
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 18.57
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.77 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.20), residues: 1699
  helix: -0.16 (0.24), residues: 426
  sheet: -1.45 (0.29), residues: 321
  loop : -1.89 (0.19), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP H 109 
 HIS   0.007   0.001   HIS A 977 
 PHE   0.033   0.002   PHE L 208 
 TYR   0.023   0.001   TYR A1692 
 ARG   0.014   0.001   ARG A1052 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03467 (  403)
  hydrogen bonds       : angle       6.19801 ( 1110)
  SS BOND              : bond        0.00544 (    4)
  SS BOND              : angle       1.15915 (    8)
  covalent geometry    : bond        0.00268 (13593)
  covalent geometry    : angle       0.66060 (18405)

********************** 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
  204 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.562 
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  680 LEU cc_start: 0.9664 (mt) cc_final: 0.9421 (mt)
REVERT: A  892 LEU cc_start: 0.7922 (tp) cc_final: 0.7719 (tp)
REVERT: A  980 ASN cc_start: 0.9388 (m-40) cc_final: 0.8807 (t0)
REVERT: A 1003 LEU cc_start: 0.9280 (mm) cc_final: 0.8787 (tp)
REVERT: A 1133 TYR cc_start: 0.9176 (m-80) cc_final: 0.8810 (m-80)
REVERT: A 1207 TYR cc_start: 0.9333 (m-10) cc_final: 0.8915 (m-80)
REVERT: A 1288 LEU cc_start: 0.8163 (mm) cc_final: 0.7899 (mm)
REVERT: A 1455 LEU cc_start: 0.8443 (tp) cc_final: 0.8219 (tp)
REVERT: A 1468 ILE cc_start: 0.9529 (pt) cc_final: 0.9223 (mt)
REVERT: A 1532 LEU cc_start: 0.8544 (pp) cc_final: 0.7835 (pp)
REVERT: A 1561 MET cc_start: 0.8707 (ppp) cc_final: 0.8447 (ppp)
REVERT: A 1568 VAL cc_start: 0.7950 (p) cc_final: 0.7571 (m)
REVERT: A 1594 LEU cc_start: 0.7338 (tp) cc_final: 0.6842 (tp)
REVERT: A 1799 LEU cc_start: 0.8114 (mm) cc_final: 0.7886 (mm)
REVERT: A 1806 TYR cc_start: 0.8903 (m-80) cc_final: 0.8650 (m-10)
REVERT: A 1944 PHE cc_start: 0.9780 (t80) cc_final: 0.9575 (t80)
REVERT: A 1947 TYR cc_start: 0.8918 (t80) cc_final: 0.8703 (t80)
REVERT: L   21 MET cc_start: 0.5869 (pmm) cc_final: 0.5636 (pmm)
REVERT: L   34 TRP cc_start: 0.6315 (m100) cc_final: 0.6091 (m100)
REVERT: L   45 LEU cc_start: 0.8827 (tp) cc_final: 0.8296 (tp)
REVERT: H   81 MET cc_start: 0.8893 (tpt) cc_final: 0.8171 (tpt)
REVERT: H  103 VAL cc_start: 0.6950 (t) cc_final: 0.6614 (t)
REVERT: H  130 LEU cc_start: 0.9413 (mt) cc_final: 0.9094 (mt)
REVERT: H  183 LEU cc_start: 0.9447 (tt) cc_final: 0.9215 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.2199
  time to fit residues: 69.8595
Evaluate side-chains
  156 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 29 optimal weight:    0.0010
   chunk 134 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 60 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 79 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 41 optimal weight:    0.6980
   chunk 118 optimal weight:    5.9990
   overall best weight:    1.8990

-------------------------------------------------------------------------------
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**
** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1166 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
A1508 GLN
** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1937 HIS ** 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 = 0.2941 r_free = 0.2941 target = 0.039677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2520 r_free = 0.2520 target = 0.026927 restraints weight = 101620.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.028679 restraints weight = 57848.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.030035 restraints weight = 38482.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5177
moved from start:          0.6174

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= 0.136
  Angle     :  0.661  14.044  18413  Z= 0.348
  Chirality :  0.043   0.229   2033
  Planarity :  0.004   0.051   2378
  Dihedral  :  5.402  23.455   1852
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 19.94
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.83 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.20), residues: 1699
  helix: -0.17 (0.24), residues: 426
  sheet: -1.44 (0.29), residues: 319
  loop : -1.89 (0.19), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP H 109 
 HIS   0.008   0.001   HIS A 977 
 PHE   0.028   0.002   PHE A1814 
 TYR   0.024   0.002   TYR A1692 
 ARG   0.010   0.001   ARG A1621 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03537 (  403)
  hydrogen bonds       : angle       6.15976 ( 1110)
  SS BOND              : bond        0.00418 (    4)
  SS BOND              : angle       1.15313 (    8)
  covalent geometry    : bond        0.00287 (13593)
  covalent geometry    : angle       0.66070 (18405)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4425.97 seconds
wall clock time: 78 minutes 40.26 seconds (4720.26 seconds total)