Starting phenix.real_space_refine
on Mon Jul 28 16:54:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uvk_26812/07_2025/7uvk_26812.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uvk_26812/07_2025/7uvk_26812.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uvk_26812/07_2025/7uvk_26812.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uvk_26812/07_2025/7uvk_26812.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uvk_26812/07_2025/7uvk_26812.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uvk_26812/07_2025/7uvk_26812.cif"
  }
  resolution = 3.28
  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=   0.045
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      19      5.16       5
     C    6536      2.51       5
     N    1750      2.21       5
     O    2045      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10350
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1295, 10350
          Classifications: {'peptide': 1295}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 1264}
  Time building chain proxies: 6.68, per 1000 atoms: 0.65
  Number of scatterers: 10350
  At special positions: 0
  Unit cell: (87.15, 110.39, 144.42, 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      19     16.00
     O    2045      8.00
     N    1750      7.00
     C    6536      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.52
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2440

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 16 sheets defined
      34.3% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1025 through 1036
    Processing helix  chain 'A' and resid 1253 through 1257
    Processing helix  chain 'A' and resid 1318 through 1323
    Processing helix  chain 'A' and resid 1324 through 1326
      No H-bonds generated for 'chain 'A' and resid 1324 through 1326'
    Processing helix  chain 'A' and resid 1359 through 1361
      No H-bonds generated for 'chain 'A' and resid 1359 through 1361'
    Processing helix  chain 'A' and resid 1362 through 1373
      removed outlier: 4.176A  pdb=" N   LYS A1371 " --> pdb=" O   LYS A1367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1387
    Processing helix  chain 'A' and resid 1392 through 1396
      removed outlier: 3.775A  pdb=" N   TYR A1395 " --> pdb=" O   ASN A1392 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR A1396 " --> pdb=" O   THR A1393 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1392 through 1396'
    Processing helix  chain 'A' and resid 1412 through 1417
    Processing helix  chain 'A' and resid 1468 through 1481
      removed outlier: 4.688A  pdb=" N   ASN A1477 " --> pdb=" O   LYS A1473 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   ASP A1478 " --> pdb=" O   ALA A1474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1493
      removed outlier: 3.632A  pdb=" N   ARG A1490 " --> pdb=" O   SER A1486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1500 through 1505
      removed outlier: 4.393A  pdb=" N   GLU A1503 " --> pdb=" O   LYS A1500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1506 through 1516
      removed outlier: 4.350A  pdb=" N   THR A1511 " --> pdb=" O   ASP A1507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1516 through 1529
      removed outlier: 3.924A  pdb=" N   SER A1520 " --> pdb=" O   ASN A1516 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA A1529 " --> pdb=" O   LEU A1525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1537 through 1550
      removed outlier: 3.833A  pdb=" N   TYR A1542 " --> pdb=" O   ILE A1538 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A1550 " --> pdb=" O   LYS A1546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1550 through 1565
      removed outlier: 3.502A  pdb=" N   TYR A1565 " --> pdb=" O   LEU A1561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1573 through 1580
      removed outlier: 3.848A  pdb=" N   LEU A1577 " --> pdb=" O   SER A1573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1581 through 1586
      removed outlier: 4.269A  pdb=" N   PHE A1585 " --> pdb=" O   LEU A1582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1591 through 1601
    Processing helix  chain 'A' and resid 1608 through 1610
      No H-bonds generated for 'chain 'A' and resid 1608 through 1610'
    Processing helix  chain 'A' and resid 1611 through 1619
    Processing helix  chain 'A' and resid 1628 through 1640
    Processing helix  chain 'A' and resid 1645 through 1654
    Processing helix  chain 'A' and resid 1665 through 1673
    Processing helix  chain 'A' and resid 1682 through 1688
    Processing helix  chain 'A' and resid 1694 through 1696
      No H-bonds generated for 'chain 'A' and resid 1694 through 1696'
    Processing helix  chain 'A' and resid 1697 through 1703
    Processing helix  chain 'A' and resid 1723 through 1727
    Processing helix  chain 'A' and resid 1737 through 1764
    Processing helix  chain 'A' and resid 1768 through 1772
    Processing helix  chain 'A' and resid 1801 through 1807
    Processing helix  chain 'A' and resid 1838 through 1853
      removed outlier: 3.920A  pdb=" N   ALA A1842 " --> pdb=" O   ASP A1838 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL A1843 " --> pdb=" O   LYS A1839 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1869 through 1875
      removed outlier: 4.216A  pdb=" N   TYR A1873 " --> pdb=" O   GLY A1869 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA A1874 " --> pdb=" O   PRO A1870 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LYS A1875 " --> pdb=" O   GLU A1871 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1869 through 1875'
    Processing helix  chain 'A' and resid 1910 through 1915
      removed outlier: 3.780A  pdb=" N   PHE A1915 " --> pdb=" O   PRO A1911 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1917 through 1944
      removed outlier: 3.553A  pdb=" N   ALA A1942 " --> pdb=" O   LEU A1938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1947 through 1954
    Processing helix  chain 'A' and resid 1981 through 1988
    Processing helix  chain 'A' and resid 1990 through 1997
      removed outlier: 3.714A  pdb=" N   LEU A1994 " --> pdb=" O   SER A1990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2039 through 2052
    Processing helix  chain 'A' and resid 2066 through 2073
    Processing helix  chain 'A' and resid 2088 through 2097
    Processing helix  chain 'A' and resid 2103 through 2120
    Processing helix  chain 'A' and resid 2144 through 2161
      removed outlier: 4.091A  pdb=" N   LEU A2148 " --> pdb=" O   ASN A2144 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A2161 " --> pdb=" O   ARG A2157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2173 through 2190
      removed outlier: 3.506A  pdb=" N   LYS A2177 " --> pdb=" O   SER A2173 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 923 through 924
      removed outlier: 6.419A  pdb=" N   LEU A 923 " --> pdb=" O   ILE A 997 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   HIS A 999 " --> pdb=" O   LEU A 923 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 942 through 944
      removed outlier: 3.548A  pdb=" N   ARG A 942 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LEU A 933 " --> pdb=" O   VAL A 944 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   PHE A 958 " --> pdb=" O   TYR A 934 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   VAL A 990 " --> pdb=" O   LYS A 974 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 978 through 980
      removed outlier: 7.330A  pdb=" N   VAL A 990 " --> pdb=" O   LYS A 974 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1047 through 1048
      removed outlier: 6.963A  pdb=" N   MET A1047 " --> pdb=" O   TYR A1082 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1105 through 1109
      removed outlier: 5.719A  pdb=" N   ALA A1105 " --> pdb=" O   VAL A1134 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ALA A1136 " --> pdb=" O   ALA A1105 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   VAL A1107 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   PHE A1158 " --> pdb=" O   SER A1194 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   ASP A1196 " --> pdb=" O   PHE A1158 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   GLY A1160 " --> pdb=" O   ASP A1196 " (cutoff:3.500A)
      removed outlier: 8.277A  pdb=" N   ALA A1198 " --> pdb=" O   GLY A1160 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ILE A1162 " --> pdb=" O   ALA A1198 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1113 through 1114
      removed outlier: 6.389A  pdb=" N   ALA A1113 " --> pdb=" O   GLY A1142 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1120
      removed outlier: 6.949A  pdb=" N   LYS A1118 " --> pdb=" O   ILE A1145 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1152 through 1154
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1178 through 1181
      removed outlier: 6.846A  pdb=" N   GLY A1179 " --> pdb=" O   ALA A1212 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL A1214 " --> pdb=" O   GLY A1179 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLY A1213 " --> pdb=" O   VAL A1243 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASN A1245 " --> pdb=" O   GLY A1213 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1220 through 1222
      removed outlier: 6.023A  pdb=" N   ILE A1221 " --> pdb=" O   THR A1261 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1299 through 1300
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1424 through 1427
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1438 through 1442
      removed outlier: 7.513A  pdb=" N   GLU A1449 " --> pdb=" O   LEU A1441 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1657 through 1660
      removed outlier: 3.690A  pdb=" N   THR A1718 " --> pdb=" O   ASN A1715 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1973 through 1978
    Processing sheet with id=AB7, first strand: chain 'A' and resid 2076 through 2079

    321 hydrogen bonds defined for protein.
    918 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.88

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2120
        1.33 -     1.45: 2435
        1.45 -     1.57: 5939
        1.57 -     1.69: 1
        1.69 -     1.81: 38
  Bond restraints: 10533
  Sorted by residual:
  bond pdb=" CG  PRO A 954 "
       pdb=" CD  PRO A 954 "
    ideal  model  delta    sigma   weight residual
    1.503  1.208  0.295 3.40e-02 8.65e+02 7.54e+01
  bond pdb=" N   PRO A 954 "
       pdb=" CD  PRO A 954 "
    ideal  model  delta    sigma   weight residual
    1.473  1.545 -0.072 1.40e-02 5.10e+03 2.62e+01
  bond pdb=" CB  PRO A 954 "
       pdb=" CG  PRO A 954 "
    ideal  model  delta    sigma   weight residual
    1.492  1.681 -0.189 5.00e-02 4.00e+02 1.43e+01
  bond pdb=" N   PRO A 954 "
       pdb=" CA  PRO A 954 "
    ideal  model  delta    sigma   weight residual
    1.469  1.443  0.026 1.28e-02 6.10e+03 4.05e+00
  bond pdb=" CA  ILE A1071 "
       pdb=" CB  ILE A1071 "
    ideal  model  delta    sigma   weight residual
    1.528  1.546 -0.018 1.34e-02 5.57e+03 1.77e+00
  ... (remaining 10528 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.27: 14146
        3.27 -     6.55: 70
        6.55 -     9.82: 7
        9.82 -    13.10: 2
       13.10 -    16.37: 3
  Bond angle restraints: 14228
  Sorted by residual:
  angle pdb=" CA  PRO A 954 "
        pdb=" N   PRO A 954 "
        pdb=" CD  PRO A 954 "
      ideal   model   delta    sigma   weight residual
     112.00   96.05   15.95 1.40e+00 5.10e-01 1.30e+02
  angle pdb=" N   PRO A 954 "
        pdb=" CD  PRO A 954 "
        pdb=" CG  PRO A 954 "
      ideal   model   delta    sigma   weight residual
     103.20   86.83   16.37 1.50e+00 4.44e-01 1.19e+02
  angle pdb=" CA  PRO A 954 "
        pdb=" CB  PRO A 954 "
        pdb=" CG  PRO A 954 "
      ideal   model   delta    sigma   weight residual
     104.50   91.55   12.95 1.90e+00 2.77e-01 4.65e+01
  angle pdb=" N   VAL A1318 "
        pdb=" CA  VAL A1318 "
        pdb=" C   VAL A1318 "
      ideal   model   delta    sigma   weight residual
     111.91  106.85    5.06 8.90e-01 1.26e+00 3.23e+01
  angle pdb=" C   ASN A 953 "
        pdb=" N   PRO A 954 "
        pdb=" CD  PRO A 954 "
      ideal   model   delta    sigma   weight residual
     125.00  141.11  -16.11 4.10e+00 5.95e-02 1.54e+01
  ... (remaining 14223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 5716
       17.39 -    34.77: 574
       34.77 -    52.16: 87
       52.16 -    69.54: 10
       69.54 -    86.93: 5
  Dihedral angle restraints: 6392
    sinusoidal: 2582
      harmonic: 3810
  Sorted by residual:
  dihedral pdb=" CA  SER A1055 "
           pdb=" C   SER A1055 "
           pdb=" N   ASP A1056 "
           pdb=" CA  ASP A1056 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.58   34.42     0      5.00e+00 4.00e-02 4.74e+01
  dihedral pdb=" CA  LYS A2191 "
           pdb=" C   LYS A2191 "
           pdb=" N   ASP A2192 "
           pdb=" CA  ASP A2192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.06   23.94     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  PRO A1705 "
           pdb=" C   PRO A1705 "
           pdb=" N   GLU A1706 "
           pdb=" CA  GLU A1706 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.26  -22.74     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 6389 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1323
       0.060 -    0.121: 234
       0.121 -    0.181: 21
       0.181 -    0.241: 2
       0.241 -    0.302: 1
  Chirality restraints: 1581
  Sorted by residual:
  chirality pdb=" CB  ILE A1071 "
            pdb=" CA  ILE A1071 "
            pdb=" CG1 ILE A1071 "
            pdb=" CG2 ILE A1071 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CA  PRO A1966 "
            pdb=" N   PRO A1966 "
            pdb=" C   PRO A1966 "
            pdb=" CB  PRO A1966 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.53e-01
  chirality pdb=" CB  VAL A1475 "
            pdb=" CA  VAL A1475 "
            pdb=" CG1 VAL A1475 "
            pdb=" CG2 VAL A1475 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.19 2.00e-01 2.50e+01 9.48e-01
  ... (remaining 1578 not shown)

  Planarity restraints: 1841
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1829 "   -0.008 2.00e-02 2.50e+03   1.53e-02 4.09e+00
        pdb=" CG  PHE A1829 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1829 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1829 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1829 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1829 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1829 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A1965 "   -0.009 2.00e-02 2.50e+03   1.86e-02 3.47e+00
        pdb=" CG  ASP A1965 "    0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASP A1965 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP A1965 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 953 "   -0.034 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO A 954 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 954 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 954 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1838 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 445
        2.71 -     3.26: 10615
        3.26 -     3.81: 15755
        3.81 -     4.35: 20937
        4.35 -     4.90: 35527
  Nonbonded interactions: 83279
  Sorted by model distance:
  nonbonded pdb=" O   GLY A1204 "
            pdb=" NZ  LYS A1238 "
     model   vdw
     2.168 3.120
  nonbonded pdb=" OG  SER A2031 "
            pdb=" O   GLY A2034 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OE2 GLU A1370 "
            pdb=" NH1 ARG A1378 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   SER A1663 "
            pdb=" OG  SER A1669 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" NH2 ARG A2073 "
            pdb=" OE2 GLU A2094 "
     model   vdw
     2.240 3.120
  ... (remaining 83274 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             2.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     27.160
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.295  10533  Z= 0.197
  Angle     :  0.741  16.372  14228  Z= 0.432
  Chirality :  0.046   0.302   1581
  Planarity :  0.004   0.045   1841
  Dihedral  : 13.598  86.927   3952
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.16 (0.21), residues: 1293
  helix: -0.34 (0.26), residues: 402
  sheet: -3.39 (0.34), residues: 180
  loop : -2.91 (0.19), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1247 
 HIS   0.008   0.001   HIS A1847 
 PHE   0.032   0.002   PHE A1829 
 TYR   0.024   0.001   TYR A1172 
 ARG   0.010   0.000   ARG A1139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17953 (  320)
  hydrogen bonds       : angle       7.07764 (  918)
  covalent geometry    : bond        0.00494 (10533)
  covalent geometry    : angle       0.74124 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.257 
Fit side-chains
REVERT: A  922 LYS cc_start: 0.7116 (mmtp) cc_final: 0.6678 (mmtm)
REVERT: A  939 ASN cc_start: 0.6680 (t0) cc_final: 0.6247 (t0)
REVERT: A  940 LYS cc_start: 0.7893 (ptmm) cc_final: 0.7631 (ptmm)
REVERT: A 1034 ASN cc_start: 0.7371 (m-40) cc_final: 0.7128 (m-40)
REVERT: A 1050 ARG cc_start: 0.7375 (ptp-170) cc_final: 0.6883 (mtt180)
REVERT: A 1077 LYS cc_start: 0.6487 (ttpt) cc_final: 0.6217 (ptpp)
REVERT: A 1195 ILE cc_start: 0.8254 (pt) cc_final: 0.7816 (pt)
REVERT: A 1266 ASP cc_start: 0.7104 (t0) cc_final: 0.6844 (t0)
REVERT: A 1294 ASN cc_start: 0.7379 (m-40) cc_final: 0.7087 (m-40)
REVERT: A 1406 LYS cc_start: 0.7331 (mttt) cc_final: 0.6763 (mtmm)
REVERT: A 1407 ASP cc_start: 0.6877 (m-30) cc_final: 0.6633 (m-30)
REVERT: A 1473 LYS cc_start: 0.7569 (ptmm) cc_final: 0.7350 (pttt)
REVERT: A 1478 ASP cc_start: 0.7380 (m-30) cc_final: 0.7140 (m-30)
REVERT: A 1498 ASN cc_start: 0.7990 (t0) cc_final: 0.7703 (p0)
REVERT: A 1546 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7733 (ttmm)
REVERT: A 1583 ASP cc_start: 0.8350 (p0) cc_final: 0.8108 (p0)
REVERT: A 1594 ASP cc_start: 0.7509 (m-30) cc_final: 0.7182 (m-30)
REVERT: A 1646 ASN cc_start: 0.7837 (p0) cc_final: 0.7474 (p0)
REVERT: A 1662 LYS cc_start: 0.8613 (mttp) cc_final: 0.8404 (mtmt)
REVERT: A 1703 THR cc_start: 0.8526 (m) cc_final: 0.8040 (p)
REVERT: A 1725 ASP cc_start: 0.7397 (m-30) cc_final: 0.7142 (t0)
REVERT: A 1832 MET cc_start: 0.8452 (mmm) cc_final: 0.8236 (mmt)
REVERT: A 1855 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6936 (mtm180)
REVERT: A 1856 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7480 (mm-30)
REVERT: A 1953 ASP cc_start: 0.6904 (t0) cc_final: 0.6538 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.2818
  time to fit residues: 99.6079
Evaluate side-chains
  157 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0970
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0030
   chunk 65 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A1007 ASN
A1368 ASN
A1415 ASN
** A1715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1987 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.144457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.126168 restraints weight = 12240.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.36
r_work: 0.3179 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  10533  Z= 0.127
  Angle     :  0.596   7.562  14228  Z= 0.324
  Chirality :  0.044   0.183   1581
  Planarity :  0.004   0.046   1841
  Dihedral  :  5.467  32.280   1419
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  8.62 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.77 (0.22), residues: 1293
  helix: -0.04 (0.26), residues: 411
  sheet: -3.03 (0.33), residues: 205
  loop : -2.67 (0.20), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1247 
 HIS   0.007   0.001   HIS A1847 
 PHE   0.029   0.002   PHE A2119 
 TYR   0.021   0.001   TYR A1831 
 ARG   0.005   0.000   ARG A1139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  320)
  hydrogen bonds       : angle       5.10796 (  918)
  covalent geometry    : bond        0.00291 (10533)
  covalent geometry    : angle       0.59566 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 1.197 
Fit side-chains
REVERT: A  922 LYS cc_start: 0.8453 (mmtp) cc_final: 0.8197 (mmtt)
REVERT: A  939 ASN cc_start: 0.7095 (t0) cc_final: 0.6753 (t0)
REVERT: A 1050 ARG cc_start: 0.7936 (ptp-170) cc_final: 0.7492 (mtm-85)
REVERT: A 1098 GLN cc_start: 0.8430 (tt0) cc_final: 0.7911 (tt0)
REVERT: A 1266 ASP cc_start: 0.7736 (t0) cc_final: 0.7203 (t0)
REVERT: A 1406 LYS cc_start: 0.7876 (mttt) cc_final: 0.7428 (mtmm)
REVERT: A 1583 ASP cc_start: 0.8521 (p0) cc_final: 0.8294 (p0)
REVERT: A 1757 TYR cc_start: 0.8218 (m-80) cc_final: 0.7514 (m-80)
REVERT: A 1953 ASP cc_start: 0.7536 (t0) cc_final: 0.7330 (m-30)
REVERT: A 2084 ILE cc_start: 0.8248 (tt) cc_final: 0.7983 (tt)
REVERT: A 2124 ARG cc_start: 0.6828 (mmp80) cc_final: 0.6174 (mmp80)
REVERT: A 2172 ASN cc_start: 0.8364 (t0) cc_final: 0.7975 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 182
  average time/residue: 0.2663
  time to fit residues: 67.2961
Evaluate side-chains
  143 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 THR
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1267 VAL
Chi-restraints excluded: chain A residue 1588 SER
Chi-restraints excluded: chain A residue 1736 ASP
Chi-restraints excluded: chain A residue 1777 LEU
Chi-restraints excluded: chain A residue 1779 TYR
Chi-restraints excluded: chain A residue 1789 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 115 optimal weight:    2.9990
   chunk 126 optimal weight:    0.8980
   chunk 117 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0870
   chunk 22 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8560

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1415 ASN
** A1715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1817 HIS
A1927 ASN
** A1969 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 = 0.3439 r_free = 0.3439 target = 0.135495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.115412 restraints weight = 12524.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.49
r_work: 0.3081 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10533  Z= 0.152
  Angle     :  0.609  11.043  14228  Z= 0.329
  Chirality :  0.045   0.183   1581
  Planarity :  0.004   0.049   1841
  Dihedral  :  5.517  32.119   1419
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.46 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.72 (0.22), residues: 1293
  helix: -0.00 (0.26), residues: 413
  sheet: -2.87 (0.31), residues: 225
  loop : -2.66 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1247 
 HIS   0.006   0.001   HIS A1847 
 PHE   0.030   0.002   PHE A2119 
 TYR   0.023   0.002   TYR A1831 
 ARG   0.004   0.001   ARG A1774 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  320)
  hydrogen bonds       : angle       4.88751 (  918)
  covalent geometry    : bond        0.00356 (10533)
  covalent geometry    : angle       0.60897 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 1.275 
Fit side-chains
REVERT: A  922 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8458 (mmtm)
REVERT: A 1050 ARG cc_start: 0.8086 (ptp-170) cc_final: 0.7609 (mtm-85)
REVERT: A 1266 ASP cc_start: 0.7754 (t0) cc_final: 0.7241 (t0)
REVERT: A 1298 LYS cc_start: 0.8020 (tptm) cc_final: 0.7427 (mmtm)
REVERT: A 1406 LYS cc_start: 0.7842 (mttt) cc_final: 0.7402 (mtmm)
REVERT: A 1757 TYR cc_start: 0.8709 (m-80) cc_final: 0.8045 (m-80)
REVERT: A 1770 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7594 (mm-30)
REVERT: A 2032 LYS cc_start: 0.8445 (mttm) cc_final: 0.8085 (mptt)
REVERT: A 2124 ARG cc_start: 0.6931 (mmp80) cc_final: 0.6716 (mmp80)
REVERT: A 2172 ASN cc_start: 0.8334 (t0) cc_final: 0.8035 (t0)
  outliers start: 29
  outliers final: 23
  residues processed: 166
  average time/residue: 0.3569
  time to fit residues: 85.3306
Evaluate side-chains
  149 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 2.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 THR
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1003 ILE
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1255 SER
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1267 VAL
Chi-restraints excluded: chain A residue 1286 THR
Chi-restraints excluded: chain A residue 1299 VAL
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1430 ASP
Chi-restraints excluded: chain A residue 1500 LYS
Chi-restraints excluded: chain A residue 1588 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1646 ASN
Chi-restraints excluded: chain A residue 1709 MET
Chi-restraints excluded: chain A residue 1777 LEU
Chi-restraints excluded: chain A residue 1779 TYR
Chi-restraints excluded: chain A residue 1789 ASN
Chi-restraints excluded: chain A residue 1894 VAL
Chi-restraints excluded: chain A residue 1965 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 69 optimal weight:    0.4980
   chunk 83 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 122 optimal weight:    0.2980
   chunk 66 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1262 ASN
A1415 ASN
A1817 HIS
** A1969 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 = 0.3441 r_free = 0.3441 target = 0.135767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.115768 restraints weight = 12315.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.47
r_work: 0.3093 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10533  Z= 0.121
  Angle     :  0.563   9.904  14228  Z= 0.305
  Chirality :  0.044   0.203   1581
  Planarity :  0.004   0.045   1841
  Dihedral  :  5.285  29.915   1419
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 13.50 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.22), residues: 1293
  helix:  0.17 (0.26), residues: 409
  sheet: -2.64 (0.31), residues: 227
  loop : -2.62 (0.20), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1247 
 HIS   0.006   0.001   HIS A1847 
 PHE   0.028   0.002   PHE A2119 
 TYR   0.021   0.001   TYR A1831 
 ARG   0.007   0.000   ARG A2157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03540 (  320)
  hydrogen bonds       : angle       4.70722 (  918)
  covalent geometry    : bond        0.00274 (10533)
  covalent geometry    : angle       0.56348 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 1.269 
Fit side-chains
REVERT: A 1050 ARG cc_start: 0.8104 (ptp-170) cc_final: 0.7593 (mtm-85)
REVERT: A 1100 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7193 (mt)
REVERT: A 1119 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8048 (tt0)
REVERT: A 1266 ASP cc_start: 0.7764 (t0) cc_final: 0.7271 (t0)
REVERT: A 1298 LYS cc_start: 0.8055 (tptm) cc_final: 0.7470 (mmtm)
REVERT: A 1406 LYS cc_start: 0.7823 (mttt) cc_final: 0.7376 (mtmm)
REVERT: A 1416 LYS cc_start: 0.7298 (mttm) cc_final: 0.6825 (mttt)
REVERT: A 1770 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7608 (mm-30)
REVERT: A 1829 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8620 (t80)
REVERT: A 1988 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7310 (mp)
REVERT: A 2032 LYS cc_start: 0.8427 (mttm) cc_final: 0.8113 (mptt)
  outliers start: 38
  outliers final: 27
  residues processed: 165
  average time/residue: 0.3093
  time to fit residues: 72.7395
Evaluate side-chains
  153 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 THR
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1003 ILE
Chi-restraints excluded: chain A residue 1009 THR
Chi-restraints excluded: chain A residue 1100 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1220 THR
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1267 VAL
Chi-restraints excluded: chain A residue 1286 THR
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1430 ASP
Chi-restraints excluded: chain A residue 1500 LYS
Chi-restraints excluded: chain A residue 1580 TYR
Chi-restraints excluded: chain A residue 1588 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1646 ASN
Chi-restraints excluded: chain A residue 1709 MET
Chi-restraints excluded: chain A residue 1718 THR
Chi-restraints excluded: chain A residue 1777 LEU
Chi-restraints excluded: chain A residue 1779 TYR
Chi-restraints excluded: chain A residue 1789 ASN
Chi-restraints excluded: chain A residue 1829 PHE
Chi-restraints excluded: chain A residue 1862 TYR
Chi-restraints excluded: chain A residue 1894 VAL
Chi-restraints excluded: chain A residue 1920 ASP
Chi-restraints excluded: chain A residue 1965 ASP
Chi-restraints excluded: chain A residue 1988 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 125 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 128 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 126 optimal weight:    3.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1001 ASN
A1415 ASN
A1768 ASN
** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1907 GLN
** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2189 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 = 0.3343 r_free = 0.3343 target = 0.127801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.107522 restraints weight = 12354.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.47
r_work: 0.2973 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10533  Z= 0.209
  Angle     :  0.670  12.636  14228  Z= 0.359
  Chirality :  0.048   0.186   1581
  Planarity :  0.005   0.052   1841
  Dihedral  :  5.837  31.319   1419
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 14.11 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.71 (0.21), residues: 1293
  helix: -0.19 (0.25), residues: 420
  sheet: -2.74 (0.36), residues: 178
  loop : -2.64 (0.19), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A1247 
 HIS   0.005   0.001   HIS A1847 
 PHE   0.031   0.002   PHE A2119 
 TYR   0.024   0.002   TYR A1172 
 ARG   0.006   0.001   ARG A2124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04297 (  320)
  hydrogen bonds       : angle       4.99299 (  918)
  covalent geometry    : bond        0.00502 (10533)
  covalent geometry    : angle       0.67037 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 132
  time to evaluate  : 1.174 
Fit side-chains
REVERT: A 1098 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8302 (pt0)
REVERT: A 1225 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6984 (t80)
REVERT: A 1266 ASP cc_start: 0.7906 (t0) cc_final: 0.7637 (t0)
REVERT: A 1298 LYS cc_start: 0.8024 (tptm) cc_final: 0.7371 (mmtm)
REVERT: A 1338 LYS cc_start: 0.6039 (ptmm) cc_final: 0.5245 (mmtm)
REVERT: A 1406 LYS cc_start: 0.7905 (mttt) cc_final: 0.7451 (mtmm)
REVERT: A 1416 LYS cc_start: 0.7553 (mttm) cc_final: 0.7003 (mttt)
REVERT: A 1422 ASN cc_start: 0.8449 (m-40) cc_final: 0.8110 (m110)
REVERT: A 1583 ASP cc_start: 0.8511 (p0) cc_final: 0.8269 (p0)
REVERT: A 1757 TYR cc_start: 0.8857 (m-80) cc_final: 0.8163 (m-80)
REVERT: A 1829 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8816 (t80)
REVERT: A 2124 ARG cc_start: 0.6946 (mmp80) cc_final: 0.6701 (mmt-90)
REVERT: A 2153 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8087 (tt0)
  outliers start: 47
  outliers final: 32
  residues processed: 165
  average time/residue: 0.2192
  time to fit residues: 52.4178
Evaluate side-chains
  154 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 THR
Chi-restraints excluded: chain A residue  953 ASN
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1003 ILE
Chi-restraints excluded: chain A residue 1009 THR
Chi-restraints excluded: chain A residue 1098 GLN
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1134 VAL
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1220 THR
Chi-restraints excluded: chain A residue 1225 TYR
Chi-restraints excluded: chain A residue 1255 SER
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1269 VAL
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1430 ASP
Chi-restraints excluded: chain A residue 1500 LYS
Chi-restraints excluded: chain A residue 1580 TYR
Chi-restraints excluded: chain A residue 1588 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1646 ASN
Chi-restraints excluded: chain A residue 1659 VAL
Chi-restraints excluded: chain A residue 1709 MET
Chi-restraints excluded: chain A residue 1718 THR
Chi-restraints excluded: chain A residue 1776 VAL
Chi-restraints excluded: chain A residue 1777 LEU
Chi-restraints excluded: chain A residue 1779 TYR
Chi-restraints excluded: chain A residue 1789 ASN
Chi-restraints excluded: chain A residue 1827 ASP
Chi-restraints excluded: chain A residue 1829 PHE
Chi-restraints excluded: chain A residue 1862 TYR
Chi-restraints excluded: chain A residue 1918 VAL
Chi-restraints excluded: chain A residue 1950 GLU
Chi-restraints excluded: chain A residue 1965 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1028 ASN
A1415 ASN
** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1969 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 = 0.3344 r_free = 0.3344 target = 0.128027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.108117 restraints weight = 12411.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 1.41
r_work: 0.3015 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.4353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10533  Z= 0.193
  Angle     :  0.649  11.391  14228  Z= 0.349
  Chirality :  0.047   0.188   1581
  Planarity :  0.004   0.057   1841
  Dihedral  :  5.814  30.713   1419
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 15.24 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.70 (0.21), residues: 1293
  helix: -0.21 (0.25), residues: 420
  sheet: -2.75 (0.36), residues: 179
  loop : -2.62 (0.20), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1247 
 HIS   0.005   0.001   HIS A1847 
 PHE   0.030   0.002   PHE A2119 
 TYR   0.021   0.002   TYR A1172 
 ARG   0.006   0.001   ARG A2124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04142 (  320)
  hydrogen bonds       : angle       4.93114 (  918)
  covalent geometry    : bond        0.00461 (10533)
  covalent geometry    : angle       0.64906 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 125
  time to evaluate  : 2.667 
Fit side-chains
REVERT: A  929 SER cc_start: 0.9183 (t) cc_final: 0.8950 (p)
REVERT: A 1225 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.6933 (t80)
REVERT: A 1266 ASP cc_start: 0.7919 (t0) cc_final: 0.7356 (t0)
REVERT: A 1298 LYS cc_start: 0.7973 (tptm) cc_final: 0.7345 (mmtm)
REVERT: A 1338 LYS cc_start: 0.5994 (ptmm) cc_final: 0.5305 (mmtm)
REVERT: A 1416 LYS cc_start: 0.7580 (mttm) cc_final: 0.7030 (mttt)
REVERT: A 1422 ASN cc_start: 0.8500 (m-40) cc_final: 0.8153 (m110)
REVERT: A 1757 TYR cc_start: 0.8799 (m-80) cc_final: 0.8108 (m-80)
REVERT: A 1780 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.7817 (t0)
REVERT: A 1829 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8835 (t80)
REVERT: A 2153 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8123 (tt0)
  outliers start: 48
  outliers final: 33
  residues processed: 160
  average time/residue: 0.2764
  time to fit residues: 65.7261
Evaluate side-chains
  158 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 THR
Chi-restraints excluded: chain A residue  953 ASN
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1003 ILE
Chi-restraints excluded: chain A residue 1009 THR
Chi-restraints excluded: chain A residue 1022 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1134 VAL
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1220 THR
Chi-restraints excluded: chain A residue 1225 TYR
Chi-restraints excluded: chain A residue 1255 SER
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1269 VAL
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1430 ASP
Chi-restraints excluded: chain A residue 1500 LYS
Chi-restraints excluded: chain A residue 1580 TYR
Chi-restraints excluded: chain A residue 1588 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1646 ASN
Chi-restraints excluded: chain A residue 1659 VAL
Chi-restraints excluded: chain A residue 1718 THR
Chi-restraints excluded: chain A residue 1776 VAL
Chi-restraints excluded: chain A residue 1777 LEU
Chi-restraints excluded: chain A residue 1779 TYR
Chi-restraints excluded: chain A residue 1780 ASP
Chi-restraints excluded: chain A residue 1789 ASN
Chi-restraints excluded: chain A residue 1827 ASP
Chi-restraints excluded: chain A residue 1829 PHE
Chi-restraints excluded: chain A residue 1862 TYR
Chi-restraints excluded: chain A residue 1918 VAL
Chi-restraints excluded: chain A residue 1950 GLU
Chi-restraints excluded: chain A residue 1965 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 102 optimal weight:    0.7980
   chunk 122 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1415 ASN
A1422 ASN
** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1969 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 = 0.3349 r_free = 0.3349 target = 0.128473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.109955 restraints weight = 12421.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.29
r_work: 0.3006 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10533  Z= 0.168
  Angle     :  0.626  11.306  14228  Z= 0.337
  Chirality :  0.046   0.192   1581
  Planarity :  0.004   0.057   1841
  Dihedral  :  5.679  28.564   1419
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 15.16 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.21), residues: 1293
  helix: -0.03 (0.25), residues: 412
  sheet: -2.61 (0.37), residues: 170
  loop : -2.64 (0.19), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1247 
 HIS   0.005   0.001   HIS A1847 
 PHE   0.028   0.002   PHE A2119 
 TYR   0.019   0.002   TYR A1172 
 ARG   0.005   0.000   ARG A2124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03959 (  320)
  hydrogen bonds       : angle       4.85220 (  918)
  covalent geometry    : bond        0.00396 (10533)
  covalent geometry    : angle       0.62639 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 129
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A  929 SER cc_start: 0.9159 (t) cc_final: 0.8949 (p)
REVERT: A 1047 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8939 (mtt)
REVERT: A 1225 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.6827 (t80)
REVERT: A 1243 VAL cc_start: 0.9117 (t) cc_final: 0.8848 (p)
REVERT: A 1266 ASP cc_start: 0.7819 (t0) cc_final: 0.7330 (t0)
REVERT: A 1298 LYS cc_start: 0.7870 (tptm) cc_final: 0.7262 (mmtm)
REVERT: A 1338 LYS cc_start: 0.5991 (ptmm) cc_final: 0.5359 (mmtm)
REVERT: A 1406 LYS cc_start: 0.7931 (mttt) cc_final: 0.7465 (mtmm)
REVERT: A 1416 LYS cc_start: 0.7519 (mttm) cc_final: 0.7031 (mttt)
REVERT: A 1422 ASN cc_start: 0.8348 (m110) cc_final: 0.7951 (m110)
REVERT: A 1757 TYR cc_start: 0.8747 (m-80) cc_final: 0.8017 (m-80)
REVERT: A 1780 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.7779 (t0)
REVERT: A 1829 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8844 (t80)
REVERT: A 1965 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7295 (t0)
REVERT: A 2084 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8585 (pp)
REVERT: A 2153 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8077 (tt0)
  outliers start: 52
  outliers final: 32
  residues processed: 165
  average time/residue: 0.2545
  time to fit residues: 61.6195
Evaluate side-chains
  160 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 THR
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1003 ILE
Chi-restraints excluded: chain A residue 1009 THR
Chi-restraints excluded: chain A residue 1022 VAL
Chi-restraints excluded: chain A residue 1047 MET
Chi-restraints excluded: chain A residue 1075 LYS
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1134 VAL
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1220 THR
Chi-restraints excluded: chain A residue 1225 TYR
Chi-restraints excluded: chain A residue 1255 SER
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1430 ASP
Chi-restraints excluded: chain A residue 1500 LYS
Chi-restraints excluded: chain A residue 1580 TYR
Chi-restraints excluded: chain A residue 1588 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1646 ASN
Chi-restraints excluded: chain A residue 1659 VAL
Chi-restraints excluded: chain A residue 1776 VAL
Chi-restraints excluded: chain A residue 1777 LEU
Chi-restraints excluded: chain A residue 1779 TYR
Chi-restraints excluded: chain A residue 1780 ASP
Chi-restraints excluded: chain A residue 1789 ASN
Chi-restraints excluded: chain A residue 1827 ASP
Chi-restraints excluded: chain A residue 1829 PHE
Chi-restraints excluded: chain A residue 1840 SER
Chi-restraints excluded: chain A residue 1862 TYR
Chi-restraints excluded: chain A residue 1894 VAL
Chi-restraints excluded: chain A residue 1918 VAL
Chi-restraints excluded: chain A residue 1950 GLU
Chi-restraints excluded: chain A residue 1965 ASP
Chi-restraints excluded: chain A residue 2084 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 84 optimal weight:    0.6980
   chunk 128 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 118 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0470
   chunk 79 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.2882

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1922 HIS
** A1969 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 = 0.3338 r_free = 0.3338 target = 0.127538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.108408 restraints weight = 12267.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.44
r_work: 0.2963 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.4644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10533  Z= 0.191
  Angle     :  0.657  11.845  14228  Z= 0.352
  Chirality :  0.047   0.197   1581
  Planarity :  0.004   0.059   1841
  Dihedral  :  5.818  28.207   1419
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 15.85 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.21), residues: 1293
  helix: -0.16 (0.25), residues: 419
  sheet: -2.51 (0.36), residues: 184
  loop : -2.63 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1247 
 HIS   0.005   0.001   HIS A1847 
 PHE   0.028   0.002   PHE A2119 
 TYR   0.020   0.002   TYR A1172 
 ARG   0.004   0.000   ARG A1774 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04150 (  320)
  hydrogen bonds       : angle       4.91793 (  918)
  covalent geometry    : bond        0.00456 (10533)
  covalent geometry    : angle       0.65675 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 127
  time to evaluate  : 1.229 
Fit side-chains
REVERT: A  939 ASN cc_start: 0.7574 (t0) cc_final: 0.7098 (t0)
REVERT: A 1225 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6844 (t80)
REVERT: A 1243 VAL cc_start: 0.9155 (t) cc_final: 0.8902 (p)
REVERT: A 1266 ASP cc_start: 0.7915 (t0) cc_final: 0.7352 (t0)
REVERT: A 1298 LYS cc_start: 0.7879 (tptm) cc_final: 0.7281 (mmtm)
REVERT: A 1338 LYS cc_start: 0.6077 (ptmm) cc_final: 0.5351 (mmtm)
REVERT: A 1406 LYS cc_start: 0.7830 (mttt) cc_final: 0.7366 (mtmm)
REVERT: A 1416 LYS cc_start: 0.7619 (mttm) cc_final: 0.7148 (mttt)
REVERT: A 1422 ASN cc_start: 0.8420 (m110) cc_final: 0.8089 (m110)
REVERT: A 1757 TYR cc_start: 0.8826 (m-80) cc_final: 0.8107 (m-80)
REVERT: A 1780 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.7890 (t0)
REVERT: A 1829 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8886 (t80)
REVERT: A 1965 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7318 (t0)
REVERT: A 2084 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8604 (pp)
REVERT: A 2153 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8122 (tt0)
  outliers start: 51
  outliers final: 34
  residues processed: 161
  average time/residue: 0.2460
  time to fit residues: 56.8118
Evaluate side-chains
  160 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 THR
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1003 ILE
Chi-restraints excluded: chain A residue 1009 THR
Chi-restraints excluded: chain A residue 1022 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1134 VAL
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1174 ILE
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1220 THR
Chi-restraints excluded: chain A residue 1225 TYR
Chi-restraints excluded: chain A residue 1253 GLU
Chi-restraints excluded: chain A residue 1255 SER
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1269 VAL
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1430 ASP
Chi-restraints excluded: chain A residue 1500 LYS
Chi-restraints excluded: chain A residue 1580 TYR
Chi-restraints excluded: chain A residue 1588 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1646 ASN
Chi-restraints excluded: chain A residue 1659 VAL
Chi-restraints excluded: chain A residue 1776 VAL
Chi-restraints excluded: chain A residue 1777 LEU
Chi-restraints excluded: chain A residue 1779 TYR
Chi-restraints excluded: chain A residue 1780 ASP
Chi-restraints excluded: chain A residue 1789 ASN
Chi-restraints excluded: chain A residue 1827 ASP
Chi-restraints excluded: chain A residue 1829 PHE
Chi-restraints excluded: chain A residue 1840 SER
Chi-restraints excluded: chain A residue 1862 TYR
Chi-restraints excluded: chain A residue 1894 VAL
Chi-restraints excluded: chain A residue 1918 VAL
Chi-restraints excluded: chain A residue 1950 GLU
Chi-restraints excluded: chain A residue 1965 ASP
Chi-restraints excluded: chain A residue 2084 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 128 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0970
   chunk 96 optimal weight:    0.6980
   chunk 125 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0570
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1415 ASN
A1442 GLN
A1605 ASN
A1817 HIS
** A1969 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 = 0.3413 r_free = 0.3413 target = 0.133636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.114669 restraints weight = 12363.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.41
r_work: 0.3086 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.4651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10533  Z= 0.115
  Angle     :  0.576   9.080  14228  Z= 0.311
  Chirality :  0.044   0.208   1581
  Planarity :  0.004   0.055   1841
  Dihedral  :  5.348  25.873   1419
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 17.16 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.21), residues: 1293
  helix:  0.14 (0.26), residues: 407
  sheet: -2.43 (0.38), residues: 173
  loop : -2.55 (0.19), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1760 
 HIS   0.006   0.001   HIS A1847 
 PHE   0.025   0.001   PHE A2119 
 TYR   0.013   0.001   TYR A1172 
 ARG   0.004   0.000   ARG A2157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03461 (  320)
  hydrogen bonds       : angle       4.63962 (  918)
  covalent geometry    : bond        0.00253 (10533)
  covalent geometry    : angle       0.57568 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 133
  time to evaluate  : 1.048 
Fit side-chains
REVERT: A 1050 ARG cc_start: 0.8191 (ptp-170) cc_final: 0.7776 (mtt180)
REVERT: A 1119 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8286 (tt0)
REVERT: A 1225 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.6885 (t80)
REVERT: A 1243 VAL cc_start: 0.9054 (t) cc_final: 0.8779 (p)
REVERT: A 1266 ASP cc_start: 0.7901 (t0) cc_final: 0.7410 (t0)
REVERT: A 1298 LYS cc_start: 0.7905 (tptm) cc_final: 0.7295 (mmtm)
REVERT: A 1338 LYS cc_start: 0.5928 (ptmm) cc_final: 0.5227 (mmtm)
REVERT: A 1406 LYS cc_start: 0.7803 (mttt) cc_final: 0.7357 (mtmm)
REVERT: A 1416 LYS cc_start: 0.7515 (mttm) cc_final: 0.7060 (mttt)
REVERT: A 1422 ASN cc_start: 0.8370 (m110) cc_final: 0.8061 (m-40)
REVERT: A 1757 TYR cc_start: 0.8745 (m-80) cc_final: 0.8003 (m-80)
REVERT: A 1770 GLU cc_start: 0.8494 (tp30) cc_final: 0.8179 (mm-30)
REVERT: A 1780 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7900 (m-30)
REVERT: A 1783 ARG cc_start: 0.8979 (mtt-85) cc_final: 0.8649 (mtt180)
REVERT: A 1829 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8698 (t80)
REVERT: A 1950 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7897 (mt-10)
REVERT: A 2153 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8145 (tt0)
  outliers start: 42
  outliers final: 28
  residues processed: 157
  average time/residue: 0.2622
  time to fit residues: 58.6386
Evaluate side-chains
  154 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 1.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 THR
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1003 ILE
Chi-restraints excluded: chain A residue 1009 THR
Chi-restraints excluded: chain A residue 1022 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1220 THR
Chi-restraints excluded: chain A residue 1225 TYR
Chi-restraints excluded: chain A residue 1255 SER
Chi-restraints excluded: chain A residue 1269 VAL
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1430 ASP
Chi-restraints excluded: chain A residue 1500 LYS
Chi-restraints excluded: chain A residue 1580 TYR
Chi-restraints excluded: chain A residue 1588 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1646 ASN
Chi-restraints excluded: chain A residue 1659 VAL
Chi-restraints excluded: chain A residue 1776 VAL
Chi-restraints excluded: chain A residue 1777 LEU
Chi-restraints excluded: chain A residue 1779 TYR
Chi-restraints excluded: chain A residue 1780 ASP
Chi-restraints excluded: chain A residue 1827 ASP
Chi-restraints excluded: chain A residue 1829 PHE
Chi-restraints excluded: chain A residue 1862 TYR
Chi-restraints excluded: chain A residue 1894 VAL
Chi-restraints excluded: chain A residue 1918 VAL
Chi-restraints excluded: chain A residue 1950 GLU
Chi-restraints excluded: chain A residue 1965 ASP
Chi-restraints excluded: chain A residue 2032 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0170
   chunk 34 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 90 optimal weight:    0.4980
   chunk 122 optimal weight:    4.9990
   chunk 93 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 109 optimal weight:    4.9990
   chunk 107 optimal weight:    0.4980
   overall best weight:    1.1620

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.128498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.109659 restraints weight = 12297.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.30
r_work: 0.3042 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10533  Z= 0.180
  Angle     :  0.639  11.854  14228  Z= 0.341
  Chirality :  0.046   0.196   1581
  Planarity :  0.004   0.058   1841
  Dihedral  :  5.645  26.286   1419
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.42 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.21), residues: 1293
  helix: -0.03 (0.25), residues: 413
  sheet: -2.39 (0.37), residues: 179
  loop : -2.55 (0.19), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1247 
 HIS   0.006   0.001   HIS A1847 
 PHE   0.027   0.002   PHE A2119 
 TYR   0.020   0.002   TYR A1172 
 ARG   0.005   0.000   ARG A1774 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03994 (  320)
  hydrogen bonds       : angle       4.79979 (  918)
  covalent geometry    : bond        0.00425 (10533)
  covalent geometry    : angle       0.63943 (14228)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 124
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A 1050 ARG cc_start: 0.8211 (ptp-170) cc_final: 0.7779 (mtt180)
REVERT: A 1119 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8229 (tt0)
REVERT: A 1225 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6902 (t80)
REVERT: A 1243 VAL cc_start: 0.9133 (t) cc_final: 0.8863 (p)
REVERT: A 1266 ASP cc_start: 0.7933 (t0) cc_final: 0.7357 (t0)
REVERT: A 1298 LYS cc_start: 0.7832 (tptm) cc_final: 0.7327 (mmtm)
REVERT: A 1338 LYS cc_start: 0.6075 (ptmm) cc_final: 0.5395 (mmtm)
REVERT: A 1406 LYS cc_start: 0.7852 (mttt) cc_final: 0.7402 (mtmm)
REVERT: A 1416 LYS cc_start: 0.7660 (mttm) cc_final: 0.7203 (mttt)
REVERT: A 1422 ASN cc_start: 0.8377 (m110) cc_final: 0.8043 (m110)
REVERT: A 1757 TYR cc_start: 0.8792 (m-80) cc_final: 0.8158 (m-80)
REVERT: A 1780 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.7803 (t0)
REVERT: A 1783 ARG cc_start: 0.8934 (mtt-85) cc_final: 0.8627 (mtt180)
REVERT: A 1829 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8835 (t80)
REVERT: A 2071 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8271 (ttpt)
REVERT: A 2153 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8145 (tt0)
  outliers start: 38
  outliers final: 31
  residues processed: 151
  average time/residue: 0.2359
  time to fit residues: 50.6347
Evaluate side-chains
  153 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 THR
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1003 ILE
Chi-restraints excluded: chain A residue 1009 THR
Chi-restraints excluded: chain A residue 1022 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1174 ILE
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1220 THR
Chi-restraints excluded: chain A residue 1225 TYR
Chi-restraints excluded: chain A residue 1255 SER
Chi-restraints excluded: chain A residue 1269 VAL
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1430 ASP
Chi-restraints excluded: chain A residue 1500 LYS
Chi-restraints excluded: chain A residue 1580 TYR
Chi-restraints excluded: chain A residue 1588 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1646 ASN
Chi-restraints excluded: chain A residue 1659 VAL
Chi-restraints excluded: chain A residue 1776 VAL
Chi-restraints excluded: chain A residue 1777 LEU
Chi-restraints excluded: chain A residue 1779 TYR
Chi-restraints excluded: chain A residue 1780 ASP
Chi-restraints excluded: chain A residue 1827 ASP
Chi-restraints excluded: chain A residue 1829 PHE
Chi-restraints excluded: chain A residue 1840 SER
Chi-restraints excluded: chain A residue 1862 TYR
Chi-restraints excluded: chain A residue 1894 VAL
Chi-restraints excluded: chain A residue 1918 VAL
Chi-restraints excluded: chain A residue 1950 GLU
Chi-restraints excluded: chain A residue 1965 ASP
Chi-restraints excluded: chain A residue 2032 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 106 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 69 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1415 ASN
** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1969 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 = 0.3346 r_free = 0.3346 target = 0.128177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.109126 restraints weight = 12307.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.33
r_work: 0.2986 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.4861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10533  Z= 0.185
  Angle     :  0.657  11.310  14228  Z= 0.349
  Chirality :  0.047   0.261   1581
  Planarity :  0.004   0.062   1841
  Dihedral  :  5.785  26.526   1419
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 17.42 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.21), residues: 1293
  helix: -0.10 (0.25), residues: 413
  sheet: -2.24 (0.40), residues: 162
  loop : -2.54 (0.19), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1247 
 HIS   0.005   0.001   HIS A1847 
 PHE   0.028   0.002   PHE A2119 
 TYR   0.020   0.002   TYR A1172 
 ARG   0.007   0.001   ARG A2124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04034 (  320)
  hydrogen bonds       : angle       4.84688 (  918)
  covalent geometry    : bond        0.00441 (10533)
  covalent geometry    : angle       0.65742 (14228)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7644.45 seconds
wall clock time: 141 minutes 55.87 seconds (8515.87 seconds total)