Starting phenix.real_space_refine
on Fri Oct 23 22:13:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rf3_53939/10_2026/9rf3_53939.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rf3_53939/10_2026/9rf3_53939.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rf3_53939/10_2026/9rf3_53939.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rf3_53939/10_2026/9rf3_53939.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rf3_53939/10_2026/9rf3_53939.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rf3_53939/10_2026/9rf3_53939.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.012
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      58      5.16       5
     C    7018      2.51       5
     N    1884      2.21       5
     O    2118      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11078
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1392, 11078
          Classifications: {'peptide': 1392}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 64, 'TRANS': 1324}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 2.80, per 1000 atoms: 0.25
  Number of scatterers: 11078
  At special positions: 0
  Unit cell: (106.272, 147.744, 141.264, 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      58     16.00
     O    2118      8.00
     N    1884      7.00
     C    7018      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 671 " - pdb=" SG  CYS A 698 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 672 " - pdb=" SG  CYS A 705 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 685 " - pdb=" SG  CYS A 706 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 851 " - pdb=" SG  CYS A1491 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1079 " - pdb=" SG  CYS A1136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1336 " - pdb=" SG  CYS A1467 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1367 " - pdb=" SG  CYS A1436 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1484 " - pdb=" SG  CYS A1489 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1496 " - pdb=" SG  CYS A1568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1515 " - pdb=" SG  CYS A1639 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1615 " - pdb=" SG  CYS A1624 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 760.0 milliseconds
  

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2628

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      17.2% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 668 through 676
      removed outlier: 4.385A  pdb=" N   CYS A 672 " --> pdb=" O   LEU A 668 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   MET A 676 " --> pdb=" O   CYS A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 974
      removed outlier: 3.687A  pdb=" N   ASP A 971 " --> pdb=" O   GLN A 967 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ALA A 972 " --> pdb=" O   MET A 968 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASP A 974 " --> pdb=" O   GLU A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 981
    Processing helix  chain 'A' and resid 991 through 995
      removed outlier: 3.810A  pdb=" N   GLY A 995 " --> pdb=" O   ASN A 992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1009
      removed outlier: 3.540A  pdb=" N   LEU A1006 " --> pdb=" O   ALA A1002 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASP A1007 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1030
      removed outlier: 3.997A  pdb=" N   LYS A1019 " --> pdb=" O   PHE A1015 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ARG A1020 " --> pdb=" O   GLY A1016 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN A1021 " --> pdb=" O   LEU A1017 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLY A1022 " --> pdb=" O   GLU A1018 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY A1030 " --> pdb=" O   LEU A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1037
      removed outlier: 3.593A  pdb=" N   GLN A1034 " --> pdb=" O   GLY A1030 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   PHE A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1064
      removed outlier: 3.803A  pdb=" N   VAL A1061 " --> pdb=" O   THR A1057 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LYS A1062 " --> pdb=" O   ALA A1058 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   VAL A1063 " --> pdb=" O   TYR A1059 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   PHE A1064 " --> pdb=" O   VAL A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1067
      No H-bonds generated for 'chain 'A' and resid 1065 through 1067'
    Processing helix  chain 'A' and resid 1077 through 1085
    Processing helix  chain 'A' and resid 1117 through 1132
      removed outlier: 4.203A  pdb=" N   LEU A1121 " --> pdb=" O   LYS A1117 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLN A1130 " --> pdb=" O   LEU A1126 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLU A1131 " --> pdb=" O   ILE A1127 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA A1132 " --> pdb=" O   SER A1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1142 through 1157
      removed outlier: 3.580A  pdb=" N   THR A1148 " --> pdb=" O   PRO A1144 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLU A1155 " --> pdb=" O   GLY A1151 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA A1156 " --> pdb=" O   ASP A1152 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ASN A1157 " --> pdb=" O   PHE A1153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1175
      removed outlier: 3.731A  pdb=" N   TYR A1172 " --> pdb=" O   ALA A1168 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA A1173 " --> pdb=" O   ILE A1169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1182 through 1190
    Processing helix  chain 'A' and resid 1192 through 1196
      removed outlier: 3.539A  pdb=" N   ASN A1196 " --> pdb=" O   LYS A1193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1221
      removed outlier: 3.661A  pdb=" N   VAL A1208 " --> pdb=" O   GLN A1204 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU A1209 " --> pdb=" O   LEU A1205 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU A1219 " --> pdb=" O   LEU A1215 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   GLN A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   LEU A1221 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1227 through 1235
      removed outlier: 3.737A  pdb=" N   TRP A1233 " --> pdb=" O   PRO A1229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1264
      removed outlier: 4.281A  pdb=" N   VAL A1253 " --> pdb=" O   ALA A1249 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE A1254 " --> pdb=" O   THR A1250 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU A1257 " --> pdb=" O   VAL A1253 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   GLN A1261 " --> pdb=" O   LEU A1257 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LYS A1262 " --> pdb=" O   ALA A1258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1392 through 1401
      removed outlier: 3.915A  pdb=" N   GLN A1398 " --> pdb=" O   ASP A1394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1490 through 1494
      removed outlier: 3.632A  pdb=" N   GLU A1494 " --> pdb=" O   CYS A1491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1506 through 1513
      removed outlier: 4.325A  pdb=" N   LYS A1513 " --> pdb=" O   GLU A1509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1567 through 1569
      No H-bonds generated for 'chain 'A' and resid 1567 through 1569'
    Processing helix  chain 'A' and resid 1585 through 1589
      removed outlier: 3.932A  pdb=" N   ASP A1588 " --> pdb=" O   LEU A1585 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A1589 " --> pdb=" O   SER A1586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1585 through 1589'
    Processing helix  chain 'A' and resid 1623 through 1637
      removed outlier: 3.842A  pdb=" N   LEU A1627 " --> pdb=" O   GLN A1623 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY A1628 " --> pdb=" O   CYS A1624 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA A1629 " --> pdb=" O   GLN A1625 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   PHE A1630 " --> pdb=" O   ASP A1626 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLU A1632 " --> pdb=" O   GLY A1628 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   SER A1633 " --> pdb=" O   ALA A1629 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL A1635 " --> pdb=" O   THR A1631 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL A1636 " --> pdb=" O   GLU A1632 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 811 through 812
      removed outlier: 3.708A  pdb=" N   ARG A 826 " --> pdb=" O   ARG A 812 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 829 through 830
    Processing sheet with id=AA3, first strand: chain 'A' and resid 861 through 864
      removed outlier: 3.819A  pdb=" N   GLN A 862 " --> pdb=" O   VAL A 842 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL A 842 " --> pdb=" O   GLN A 862 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 864 " --> pdb=" O   VAL A 840 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ARG A 841 " --> pdb=" O   ALA A 893 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA A 893 " --> pdb=" O   ARG A 841 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA A 892 " --> pdb=" O   ASP A 901 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   ASP A 901 " --> pdb=" O   ALA A 892 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 915 through 919
      removed outlier: 3.822A  pdb=" N   MET A 916 " --> pdb=" O   TYR A1326 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR A1326 " --> pdb=" O   MET A 916 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER A1321 " --> pdb=" O   LEU A 959 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1038 through 1039
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1285 through 1286
      removed outlier: 3.501A  pdb=" N   SER A1275 " --> pdb=" O   THR A1311 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   THR A1311 " --> pdb=" O   SER A1275 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLN A1277 " --> pdb=" O   THR A1309 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   THR A1309 " --> pdb=" O   GLN A1277 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1339 through 1343
      removed outlier: 3.809A  pdb=" N   ASN A1360 " --> pdb=" O   GLN A1443 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   MET A1362 " --> pdb=" O   VAL A1441 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A1441 " --> pdb=" O   MET A1362 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASP A1435 " --> pdb=" O   THR A1368 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   HIS A1442 " --> pdb=" O   ALA A1390 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA A1390 " --> pdb=" O   HIS A1442 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1421 through 1425
      removed outlier: 3.511A  pdb=" N   LEU A1422 " --> pdb=" O   ILE A1383 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   TYR A1458 " --> pdb=" O   ILE A1380 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1579 through 1584
      removed outlier: 3.961A  pdb=" N   GLY A1584 " --> pdb=" O   TYR A1521 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   TYR A1521 " --> pdb=" O   GLY A1584 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ARG A1526 " --> pdb=" O   ILE A1543 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   ILE A1543 " --> pdb=" O   ARG A1526 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   VAL A1528 " --> pdb=" O   MET A1541 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   MET A1541 " --> pdb=" O   VAL A1528 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL A1530 " --> pdb=" O   TYR A1539 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   TYR A1539 " --> pdb=" O   VAL A1530 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   PHE A1562 " --> pdb=" O   TYR A1539 " (cutoff:3.500A)

    154 hydrogen bonds defined for protein.
    423 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1898
        1.32 -     1.44: 2848
        1.44 -     1.56: 6460
        1.56 -     1.69: 1
        1.69 -     1.81: 90
  Bond restraints: 11297
  Sorted by residual:
  bond pdb=" N   ILE A 127 "
       pdb=" CA  ILE A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.499 -0.041 1.18e-02 7.18e+03 1.20e+01
  bond pdb=" N   TYR A 467 "
       pdb=" CA  TYR A 467 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.041 1.19e-02 7.06e+03 1.17e+01
  bond pdb=" N   VAL A1505 "
       pdb=" CA  VAL A1505 "
    ideal  model  delta    sigma   weight residual
    1.460  1.502 -0.042 1.23e-02 6.61e+03 1.17e+01
  bond pdb=" N   TYR A 468 "
       pdb=" CA  TYR A 468 "
    ideal  model  delta    sigma   weight residual
    1.457  1.500 -0.042 1.29e-02 6.01e+03 1.07e+01
  bond pdb=" N   ASP A 358 "
       pdb=" CA  ASP A 358 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.042 1.28e-02 6.10e+03 1.05e+01
  ... (remaining 11292 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.63: 15256
        6.63 -    13.26: 29
       13.26 -    19.89: 4
       19.89 -    26.52: 1
       26.52 -    33.15: 3
  Bond angle restraints: 15293
  Sorted by residual:
  angle pdb=" N   LYS A1504 "
        pdb=" CA  LYS A1504 "
        pdb=" C   LYS A1504 "
      ideal   model   delta    sigma   weight residual
     113.30  146.45  -33.15 1.34e+00 5.57e-01 6.12e+02
  angle pdb=" C   GLU A 938 "
        pdb=" CA  GLU A 938 "
        pdb=" CB  GLU A 938 "
      ideal   model   delta    sigma   weight residual
     111.85   81.61   30.24 1.47e+00 4.63e-01 4.23e+02
  angle pdb=" C   LYS A1504 "
        pdb=" CA  LYS A1504 "
        pdb=" CB  LYS A1504 "
      ideal   model   delta    sigma   weight residual
     110.17   82.24   27.93 1.69e+00 3.50e-01 2.73e+02
  angle pdb=" N   VAL A1505 "
        pdb=" CA  VAL A1505 "
        pdb=" CB  VAL A1505 "
      ideal   model   delta    sigma   weight residual
     111.66   92.96   18.70 1.14e+00 7.69e-01 2.69e+02
  angle pdb=" N   ASP A 939 "
        pdb=" CA  ASP A 939 "
        pdb=" CB  ASP A 939 "
      ideal   model   delta    sigma   weight residual
     110.49   89.53   20.96 1.69e+00 3.50e-01 1.54e+02
  ... (remaining 15288 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.87: 6259
       14.87 -    29.75: 485
       29.75 -    44.62: 131
       44.62 -    59.49: 36
       59.49 -    74.37: 3
  Dihedral angle restraints: 6914
    sinusoidal: 2853
      harmonic: 4061
  Sorted by residual:
  dihedral pdb=" C   GLU A 938 "
           pdb=" N   GLU A 938 "
           pdb=" CA  GLU A 938 "
           pdb=" CB  GLU A 938 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -87.26  -35.34     0      2.50e+00 1.60e-01 2.00e+02
  dihedral pdb=" N   VAL A1505 "
           pdb=" C   VAL A1505 "
           pdb=" CA  VAL A1505 "
           pdb=" CB  VAL A1505 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  100.96   22.44     0      2.50e+00 1.60e-01 8.05e+01
  dihedral pdb=" N   ASP A 939 "
           pdb=" C   ASP A 939 "
           pdb=" CA  ASP A 939 "
           pdb=" CB  ASP A 939 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  100.85   21.95     0      2.50e+00 1.60e-01 7.71e+01
  ... (remaining 6911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.185: 1692
       0.185 -    0.370: 16
       0.370 -    0.555: 2
       0.555 -    0.740: 3
       0.740 -    0.925: 2
  Chirality restraints: 1715
  Sorted by residual:
  chirality pdb=" CA  PRO A 357 "
            pdb=" N   PRO A 357 "
            pdb=" C   PRO A 357 "
            pdb=" CB  PRO A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    1.79    0.92 2.00e-01 2.50e+01 2.14e+01
  chirality pdb=" CA  LYS A1504 "
            pdb=" N   LYS A1504 "
            pdb=" C   LYS A1504 "
            pdb=" CB  LYS A1504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.75    0.76 2.00e-01 2.50e+01 1.45e+01
  chirality pdb=" CA  VAL A1505 "
            pdb=" N   VAL A1505 "
            pdb=" C   VAL A1505 "
            pdb=" CB  VAL A1505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    3.09   -0.65 2.00e-01 2.50e+01 1.06e+01
  ... (remaining 1712 not shown)

  Planarity restraints: 1979
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 466 "   -1.066 9.50e-02 1.11e+02   4.78e-01 1.38e+02
        pdb=" NE  ARG A 466 "    0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 466 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 466 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 466 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 936 "    0.024 2.00e-02 2.50e+03   4.68e-02 2.19e+01
        pdb=" C   GLN A 936 "   -0.081 2.00e-02 2.50e+03
        pdb=" O   GLN A 936 "    0.031 2.00e-02 2.50e+03
        pdb=" N   LYS A 937 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 360 "   -0.075 5.00e-02 4.00e+02   1.13e-01 2.06e+01
        pdb=" N   PRO A 361 "    0.196 5.00e-02 4.00e+02
        pdb=" CA  PRO A 361 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 361 "   -0.059 5.00e-02 4.00e+02
  ... (remaining 1976 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 12
        2.51 -     3.11: 7950
        3.11 -     3.71: 15668
        3.71 -     4.30: 20940
        4.30 -     4.90: 33778
  Nonbonded interactions: 78348
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 938 "
            pdb=" CB  GLU A 938 "
     model   vdw
     1.915 2.752
  nonbonded pdb=" N   ILE A 127 "
            pdb=" O   LYS A 544 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" O   LYS A1504 "
            pdb=" CB  LYS A1504 "
     model   vdw
     2.359 2.752
  nonbonded pdb=" O   PRO A 361 "
            pdb=" N   GLN A 380 "
     model   vdw
     2.411 3.120
  nonbonded pdb=" O   SER A 160 "
            pdb=" OG  SER A 160 "
     model   vdw
     2.412 3.040
  ... (remaining 78343 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.370
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2578
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      :  0.004   0.076  11308  Z= 0.269
  Angle     :  1.013  33.147  15315  Z= 0.646
  Chirality :  0.066   0.925   1715
  Planarity :  0.012   0.478   1979
  Dihedral  : 11.816  74.366   4253
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.96 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  :  9.41 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.68 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.21), residues: 1376
  helix: -1.36 (0.37), residues: 182
  sheet: -0.65 (0.41), residues: 173
  loop : -2.74 (0.17), residues: 1021

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1560 
 TYR   0.011   0.001   TYR A1172 
 PHE   0.014   0.001   PHE A 353 
 TRP   0.006   0.001   TRP A1233 
 HIS   0.002   0.000   HIS A1104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.27 (11297)
  covalent geometry    : angle       1.01339 /  0.65 (15293)
  SS BOND              : bond        0.00115 /  0.07 (   11)
  SS BOND              : angle       0.55721 /  0.34 (   22)
  hydrogen bonds       : bond        0.25040 / 17.25 (  154)
  hydrogen bonds       : angle       8.48052 /  6.00 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 121
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 60
  outliers final: 24
  residues processed: 178
  average time/residue: 0.1032
  time to fit residues: 26.1411
Evaluate side-chains
  94 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  161 GLN
Chi-restraints excluded: chain A residue  162 ASN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  547 GLN
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  938 GLU
Chi-restraints excluded: chain A residue  965 VAL
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1208 VAL
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1253 VAL
Chi-restraints excluded: chain A residue 1445 PHE
Chi-restraints excluded: chain A residue 1465 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55]
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  60 HIS
A 144 ASN
A 161 GLN
A 557 GLN
A 805 GLN
A 820 ASN
A 886 GLN
A 961 GLN
** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1261 GLN
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1333 GLN
** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1451 GLN
A1555 GLN
A1579 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4887 r_free = 0.4887 target = 0.153090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.127181 restraints weight = 91870.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.129189 restraints weight = 67868.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.130264 restraints weight = 54202.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.131647 restraints weight = 46873.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.132218 restraints weight = 42230.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.4492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6782
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096  11308  Z= 0.171
  Angle     :  0.709  13.733  15315  Z= 0.350
  Chirality :  0.045   0.327   1715
  Planarity :  0.005   0.140   1979
  Dihedral  :  6.702  57.586   1546
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.08 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 12.33 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.21), residues: 1376
  helix: -1.06 (0.35), residues: 189
  sheet: -0.63 (0.41), residues: 161
  loop : -2.64 (0.18), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1038 
 TYR   0.016   0.002   TYR A1260 
 PHE   0.018   0.001   PHE A1124 
 TRP   0.021   0.002   TRP A 182 
 HIS   0.008   0.001   HIS A1104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.17 (11297)
  covalent geometry    : angle       0.70909 /  0.35 (15293)
  SS BOND              : bond        0.00611 /  0.36 (   11)
  SS BOND              : angle       0.81512 /  0.49 (   22)
  hydrogen bonds       : bond        0.04236 /  2.92 (  154)
  hydrogen bonds       : angle       6.26341 /  4.36 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 77
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.9420 (ppp) cc_final: 0.9212 (ppp)
REVERT: A  419 MET cc_start: 0.6681 (mpp) cc_final: 0.5658 (mpp)
REVERT: A  468 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8930 (m-80)
REVERT: A  492 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7569 (mt)
REVERT: A 1024 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7378 (pp)
REVERT: A 1025 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8301 (mm-30)
REVERT: A 1089 LYS cc_start: 0.1323 (OUTLIER) cc_final: -0.1067 (pptt)
REVERT: A 1386 MET cc_start: 0.3658 (ttt) cc_final: 0.3264 (tpp)
REVERT: A 1448 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6474 (tt0)
  outliers start: 43
  outliers final: 25
  residues processed: 118
  average time/residue: 0.1022
  time to fit residues: 17.5076
Evaluate side-chains
  101 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  161 GLN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  182 TRP
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  965 VAL
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1035 LEU
Chi-restraints excluded: chain A residue 1089 LYS
Chi-restraints excluded: chain A residue 1136 CYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1208 VAL
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1334 LEU
Chi-restraints excluded: chain A residue 1407 ILE
Chi-restraints excluded: chain A residue 1412 LEU
Chi-restraints excluded: chain A residue 1445 PHE
Chi-restraints excluded: chain A residue 1465 GLU
Chi-restraints excluded: chain A residue 1484 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [80, 40, 1, 76, 111, 106, 11, 49, 18, 126, 45]
   chunk 80 optimal weight:    3.9990
   chunk 40 optimal weight:   20.0000
   chunk 1 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 111 optimal weight:    0.6980
   chunk 106 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 49 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 126 optimal weight:   30.0000
   chunk 45 optimal weight:   10.0000
   overall best weight:    5.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 181 GLN
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 GLN
A 567 HIS
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 820 ASN
** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1443 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 = 0.4736 r_free = 0.4736 target = 0.140171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.114661 restraints weight = 89409.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.114301 restraints weight = 68739.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.115649 restraints weight = 54900.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.117697 restraints weight = 43796.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.117398 restraints weight = 38115.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.4248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.117  11308  Z= 0.344
  Angle     :  0.917  14.949  15315  Z= 0.470
  Chirality :  0.049   0.292   1715
  Planarity :  0.007   0.141   1979
  Dihedral  :  6.494  59.834   1525
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 31.47
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.90 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 14.52 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.34 (0.20), residues: 1376
  helix: -2.10 (0.32), residues: 202
  sheet: -0.63 (0.39), residues: 181
  loop : -2.78 (0.18), residues: 993

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A1526 
 TYR   0.037   0.003   TYR A1172 
 PHE   0.031   0.002   PHE A1562 
 TRP   0.018   0.002   TRP A 182 
 HIS   0.012   0.002   HIS A1004 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00702 /  0.34 (11297)
  covalent geometry    : angle       0.91692 /  0.47 (15293)
  SS BOND              : bond        0.00704 /  0.47 (   11)
  SS BOND              : angle       1.07553 /  0.59 (   22)
  hydrogen bonds       : bond        0.07531 /  4.93 (  154)
  hydrogen bonds       : angle       7.44648 /  5.40 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 69
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8788 (mmm) cc_final: 0.8376 (mmm)
REVERT: A  142 MET cc_start: 0.9636 (ppp) cc_final: 0.9434 (ppp)
REVERT: A  179 MET cc_start: 0.8342 (mmm) cc_final: 0.7976 (mmm)
REVERT: A  468 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8863 (m-80)
REVERT: A  473 MET cc_start: 0.3966 (tpt) cc_final: 0.3615 (tpt)
REVERT: A  492 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7788 (mt)
REVERT: A  930 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5220 (mt)
REVERT: A 1024 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7927 (mp)
REVERT: A 1025 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8653 (mm-30)
REVERT: A 1154 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8505 (mm)
REVERT: A 1337 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.5539 (p0)
REVERT: A 1338 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6444 (mtmt)
REVERT: A 1386 MET cc_start: 0.5941 (ttt) cc_final: 0.5416 (tpp)
REVERT: A 1397 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8403 (mptt)
REVERT: A 1406 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.6260 (t80)
REVERT: A 1448 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6291 (mt-10)
REVERT: A 1465 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.4561 (pt0)
  outliers start: 52
  outliers final: 26
  residues processed: 116
  average time/residue: 0.0889
  time to fit residues: 15.5984
Evaluate side-chains
  99 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 64
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  182 TRP
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  965 VAL
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1035 LEU
Chi-restraints excluded: chain A residue 1038 ARG
Chi-restraints excluded: chain A residue 1079 CYS
Chi-restraints excluded: chain A residue 1118 ASP
Chi-restraints excluded: chain A residue 1119 MET
Chi-restraints excluded: chain A residue 1136 CYS
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1206 TYR
Chi-restraints excluded: chain A residue 1208 VAL
Chi-restraints excluded: chain A residue 1334 LEU
Chi-restraints excluded: chain A residue 1337 ASN
Chi-restraints excluded: chain A residue 1338 LYS
Chi-restraints excluded: chain A residue 1401 ASN
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1407 ILE
Chi-restraints excluded: chain A residue 1412 LEU
Chi-restraints excluded: chain A residue 1445 PHE
Chi-restraints excluded: chain A residue 1465 GLU
Chi-restraints excluded: chain A residue 1484 CYS
Chi-restraints excluded: chain A residue 1630 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [61, 24, 27, 94, 57, 51, 87, 36, 65, 19, 55]
   chunk 61 optimal weight:   10.0000
   chunk 24 optimal weight:   40.0000
   chunk 27 optimal weight:    0.4980
   chunk 94 optimal weight:    0.0770
   chunk 57 optimal weight:    5.9990
   chunk 51 optimal weight:   30.0000
   chunk 87 optimal weight:    0.7980
   chunk 36 optimal weight:    8.9990
   chunk 65 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 55 optimal weight:    0.2980
   overall best weight:    1.5340

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  38 HIS
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 GLN
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 547 GLN
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1130 GLN
A1237 GLN
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1327 HIS
** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1481 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4898 r_free = 0.4898 target = 0.148428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.125189 restraints weight = 104339.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.126893 restraints weight = 71136.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.128012 restraints weight = 54570.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.128904 restraints weight = 45049.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.129808 restraints weight = 39542.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.5328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.105  11308  Z= 0.140
  Angle     :  0.674  12.409  15315  Z= 0.329
  Chirality :  0.044   0.314   1715
  Planarity :  0.005   0.140   1979
  Dihedral  :  5.329  57.788   1517
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.65 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.11 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.10 (0.21), residues: 1376
  helix: -1.50 (0.33), residues: 212
  sheet: -0.50 (0.38), residues: 178
  loop : -2.71 (0.18), residues: 986

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 826 
 TYR   0.017   0.001   TYR A1260 
 PHE   0.017   0.001   PHE A1562 
 TRP   0.017   0.001   TRP A 182 
 HIS   0.004   0.001   HIS A1104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 (11297)
  covalent geometry    : angle       0.67436 /  0.33 (15293)
  SS BOND              : bond        0.00173 /  0.12 (   11)
  SS BOND              : angle       0.57018 /  0.35 (   22)
  hydrogen bonds       : bond        0.03972 /  2.74 (  154)
  hydrogen bonds       : angle       6.02222 /  4.28 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 72
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.9538 (ppp) cc_final: 0.9305 (ppp)
REVERT: A  179 MET cc_start: 0.8344 (mmm) cc_final: 0.7823 (mmm)
REVERT: A  419 MET cc_start: 0.7150 (mpp) cc_final: 0.6667 (pmm)
REVERT: A  457 MET cc_start: 0.3665 (mpp) cc_final: 0.3095 (mpp)
REVERT: A  473 MET cc_start: 0.4390 (tpt) cc_final: 0.4176 (tpt)
REVERT: A  832 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.6674 (p90)
REVERT: A 1021 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8504 (mm-40)
REVERT: A 1025 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8580 (mm-30)
REVERT: A 1039 GLN cc_start: 0.8584 (mp10) cc_final: 0.8287 (pm20)
REVERT: A 1154 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8587 (mt)
REVERT: A 1177 MET cc_start: 0.7143 (ptt) cc_final: 0.5887 (pmm)
REVERT: A 1325 MET cc_start: 0.8641 (tpt) cc_final: 0.7829 (mpp)
REVERT: A 1337 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6230 (p0)
REVERT: A 1345 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5140 (mm)
REVERT: A 1378 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8211 (tmm)
  outliers start: 33
  outliers final: 17
  residues processed: 99
  average time/residue: 0.0910
  time to fit residues: 13.5896
Evaluate side-chains
  87 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  182 TRP
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  832 TYR
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1035 LEU
Chi-restraints excluded: chain A residue 1119 MET
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1136 CYS
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1208 VAL
Chi-restraints excluded: chain A residue 1334 LEU
Chi-restraints excluded: chain A residue 1337 ASN
Chi-restraints excluded: chain A residue 1345 ILE
Chi-restraints excluded: chain A residue 1378 MET
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1484 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [94, 20, 43, 138, 19, 71, 108, 101, 137, 65, 12]
   chunk 94 optimal weight:    0.5980
   chunk 20 optimal weight:   50.0000
   chunk 43 optimal weight:    6.9990
   chunk 138 optimal weight:    9.9990
   chunk 19 optimal weight:    0.5980
   chunk 71 optimal weight:    9.9990
   chunk 108 optimal weight:    0.6980
   chunk 101 optimal weight:    4.9990
   chunk 137 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 474 ASN
** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1620 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 = 0.4921 r_free = 0.4921 target = 0.155117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.131013 restraints weight = 105949.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.132380 restraints weight = 72357.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.133476 restraints weight = 56863.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.134437 restraints weight = 48562.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.134604 restraints weight = 43289.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.4447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.5361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.102  11308  Z= 0.113
  Angle     :  0.655  14.164  15315  Z= 0.312
  Chirality :  0.043   0.307   1715
  Planarity :  0.005   0.140   1979
  Dihedral  :  4.664  51.648   1507
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.94 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.00 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.21), residues: 1376
  helix: -0.90 (0.34), residues: 209
  sheet: -0.33 (0.37), residues: 177
  loop : -2.65 (0.18), residues: 990

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 483 
 TYR   0.015   0.001   TYR A 832 
 PHE   0.009   0.001   PHE A1153 
 TRP   0.015   0.001   TRP A 182 
 HIS   0.005   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.11 (11297)
  covalent geometry    : angle       0.65484 /  0.31 (15293)
  SS BOND              : bond        0.00124 /  0.08 (   11)
  SS BOND              : angle       0.51418 /  0.31 (   22)
  hydrogen bonds       : bond        0.03175 /  2.24 (  154)
  hydrogen bonds       : angle       5.42198 /  3.83 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 70
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.8485 (mmm) cc_final: 0.8075 (mmm)
REVERT: A  419 MET cc_start: 0.7540 (mpp) cc_final: 0.7162 (pmm)
REVERT: A  832 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7192 (p90)
REVERT: A  968 MET cc_start: 0.7833 (ptt) cc_final: 0.7538 (ptt)
REVERT: A 1021 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8750 (mm-40)
REVERT: A 1025 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8807 (mm-30)
REVERT: A 1177 MET cc_start: 0.8455 (ptt) cc_final: 0.7623 (pmm)
REVERT: A 1337 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.6795 (p0)
REVERT: A 1345 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.5877 (mm)
REVERT: A 1378 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8545 (tmm)
REVERT: A 1385 MET cc_start: 0.3593 (ttp) cc_final: 0.2918 (tmm)
REVERT: A 1386 MET cc_start: 0.7442 (tpt) cc_final: 0.6720 (tpp)
  outliers start: 33
  outliers final: 18
  residues processed: 99
  average time/residue: 0.0989
  time to fit residues: 14.5942
Evaluate side-chains
  84 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  182 TRP
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  832 TYR
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  965 VAL
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1119 MET
Chi-restraints excluded: chain A residue 1136 CYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1197 ARG
Chi-restraints excluded: chain A residue 1334 LEU
Chi-restraints excluded: chain A residue 1337 ASN
Chi-restraints excluded: chain A residue 1345 ILE
Chi-restraints excluded: chain A residue 1378 MET
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1484 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [19, 22, 75, 78, 58, 80, 37, 90, 83, 77, 97]
   chunk 19 optimal weight:    0.0570
   chunk 22 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0980
   chunk 77 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.0102

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 547 GLN
** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1472 HIS
** A1620 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 = 0.4917 r_free = 0.4917 target = 0.149720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.126578 restraints weight = 104939.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.128577 restraints weight = 70814.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4786 r_free = 0.4786 target = 0.129669 restraints weight = 53336.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.130398 restraints weight = 45257.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.131099 restraints weight = 40766.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.4387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.5539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.101  11308  Z= 0.113
  Angle     :  0.659  15.447  15315  Z= 0.311
  Chirality :  0.043   0.296   1715
  Planarity :  0.005   0.139   1979
  Dihedral  :  4.598  52.947   1506
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.94 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.00 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.21), residues: 1376
  helix: -0.69 (0.35), residues: 209
  sheet: -0.31 (0.37), residues: 180
  loop : -2.62 (0.18), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 477 
 TYR   0.014   0.001   TYR A 832 
 PHE   0.011   0.001   PHE A1153 
 TRP   0.013   0.001   TRP A 182 
 HIS   0.004   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.11 (11297)
  covalent geometry    : angle       0.65888 /  0.31 (15293)
  SS BOND              : bond        0.00130 /  0.09 (   11)
  SS BOND              : angle       0.57060 /  0.42 (   22)
  hydrogen bonds       : bond        0.03049 /  2.10 (  154)
  hydrogen bonds       : angle       5.24920 /  3.72 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 63
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.8668 (mmm) cc_final: 0.8222 (mmm)
REVERT: A  419 MET cc_start: 0.7388 (mpp) cc_final: 0.6946 (pmm)
REVERT: A  457 MET cc_start: 0.4907 (mpp) cc_final: 0.4674 (mmt)
REVERT: A  832 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.6758 (p90)
REVERT: A  968 MET cc_start: 0.7938 (ptt) cc_final: 0.6711 (ptt)
REVERT: A 1021 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8658 (mm-40)
REVERT: A 1025 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8696 (mm-30)
REVERT: A 1054 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7939 (t)
REVERT: A 1122 THR cc_start: 0.5996 (OUTLIER) cc_final: 0.4591 (t)
REVERT: A 1177 MET cc_start: 0.8036 (ptt) cc_final: 0.7120 (pmm)
REVERT: A 1325 MET cc_start: 0.8883 (tpt) cc_final: 0.7888 (mpp)
REVERT: A 1337 ASN cc_start: 0.6785 (OUTLIER) cc_final: 0.6301 (p0)
REVERT: A 1345 ILE cc_start: 0.6371 (OUTLIER) cc_final: 0.5612 (mm)
REVERT: A 1378 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8373 (tmm)
REVERT: A 1385 MET cc_start: 0.3380 (ttp) cc_final: 0.2709 (tmm)
REVERT: A 1386 MET cc_start: 0.7161 (tpt) cc_final: 0.6405 (tpp)
REVERT: A 1449 LEU cc_start: 0.9310 (tt) cc_final: 0.9040 (pp)
REVERT: A 1541 MET cc_start: 0.7093 (tpp) cc_final: 0.6707 (tpp)
  outliers start: 30
  outliers final: 18
  residues processed: 90
  average time/residue: 0.0930
  time to fit residues: 12.4538
Evaluate side-chains
  86 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  182 TRP
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  832 TYR
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1054 THR
Chi-restraints excluded: chain A residue 1119 MET
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1136 CYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1197 ARG
Chi-restraints excluded: chain A residue 1334 LEU
Chi-restraints excluded: chain A residue 1337 ASN
Chi-restraints excluded: chain A residue 1345 ILE
Chi-restraints excluded: chain A residue 1378 MET
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1484 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [11, 26, 92, 123, 117, 98, 78, 41, 103, 64, 8]
   chunk 11 optimal weight:    0.0970
   chunk 26 optimal weight:    2.9990
   chunk 92 optimal weight:   10.0000
   chunk 123 optimal weight:   10.0000
   chunk 117 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9980
   chunk 78 optimal weight:    0.2980
   chunk 41 optimal weight:    6.9990
   chunk 103 optimal weight:   20.0000
   chunk 64 optimal weight:    0.0070
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.4196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 356 ASN
A1011 GLN
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1620 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 = 0.4836 r_free = 0.4836 target = 0.146463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.120347 restraints weight = 90849.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.122443 restraints weight = 63611.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.123322 restraints weight = 50711.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.124459 restraints weight = 44436.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.125063 restraints weight = 39810.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.4427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6977
moved from start:          0.5555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.102  11308  Z= 0.101
  Angle     :  0.642  15.768  15315  Z= 0.301
  Chirality :  0.043   0.304   1715
  Planarity :  0.005   0.137   1979
  Dihedral  :  4.250  52.750   1504
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.50 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 18.65 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.70 (0.21), residues: 1376
  helix: -0.51 (0.35), residues: 208
  sheet: -0.40 (0.37), residues: 180
  loop : -2.57 (0.18), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1197 
 TYR   0.014   0.001   TYR A 468 
 PHE   0.010   0.001   PHE A1153 
 TRP   0.011   0.001   TRP A 182 
 HIS   0.004   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.10 (11297)
  covalent geometry    : angle       0.64235 /  0.30 (15293)
  SS BOND              : bond        0.00107 /  0.07 (   11)
  SS BOND              : angle       0.43948 /  0.27 (   22)
  hydrogen bonds       : bond        0.02716 /  1.87 (  154)
  hydrogen bonds       : angle       4.91967 /  3.48 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.8705 (mmm) cc_final: 0.8244 (mmm)
REVERT: A  419 MET cc_start: 0.7074 (mpp) cc_final: 0.5849 (pmm)
REVERT: A  457 MET cc_start: 0.3808 (mpp) cc_final: 0.3132 (mmt)
REVERT: A  559 MET cc_start: 0.6059 (mmt) cc_final: 0.5715 (mmm)
REVERT: A  832 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6095 (p90)
REVERT: A  968 MET cc_start: 0.7599 (ptt) cc_final: 0.6450 (ptt)
REVERT: A 1025 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8531 (mm-30)
REVERT: A 1177 MET cc_start: 0.6338 (ptt) cc_final: 0.5959 (pmm)
REVERT: A 1325 MET cc_start: 0.8535 (tpt) cc_final: 0.7686 (mpp)
REVERT: A 1326 TYR cc_start: 0.7329 (p90) cc_final: 0.5206 (p90)
REVERT: A 1337 ASN cc_start: 0.5065 (OUTLIER) cc_final: 0.4600 (p0)
REVERT: A 1345 ILE cc_start: 0.5882 (OUTLIER) cc_final: 0.5107 (mm)
REVERT: A 1385 MET cc_start: 0.2889 (ttp) cc_final: 0.2448 (tmm)
REVERT: A 1386 MET cc_start: 0.6047 (tpt) cc_final: 0.5629 (tpp)
REVERT: A 1449 LEU cc_start: 0.8977 (tt) cc_final: 0.8746 (pp)
REVERT: A 1541 MET cc_start: 0.6684 (tpp) cc_final: 0.6311 (tpp)
  outliers start: 23
  outliers final: 14
  residues processed: 86
  average time/residue: 0.1056
  time to fit residues: 13.2247
Evaluate side-chains
  79 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  182 TRP
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  832 TYR
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1136 CYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1197 ARG
Chi-restraints excluded: chain A residue 1334 LEU
Chi-restraints excluded: chain A residue 1337 ASN
Chi-restraints excluded: chain A residue 1345 ILE
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1484 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [114, 137, 65, 98, 17, 120, 135, 74, 62, 82, 101]
   chunk 114 optimal weight:    0.3980
   chunk 137 optimal weight:   30.0000
   chunk 65 optimal weight:    6.9990
   chunk 98 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   chunk 120 optimal weight:    0.5980
   chunk 135 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 82 optimal weight:    0.1980
   chunk 101 optimal weight:    0.6980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 356 ASN
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1620 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 = 0.4834 r_free = 0.4834 target = 0.146507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.121637 restraints weight = 91040.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.123506 restraints weight = 63834.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.124714 restraints weight = 50100.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.125507 restraints weight = 42401.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.126210 restraints weight = 37895.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.4435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.5618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.106  11308  Z= 0.101
  Angle     :  0.639  15.657  15315  Z= 0.301
  Chirality :  0.043   0.315   1715
  Planarity :  0.005   0.132   1979
  Dihedral  :  4.196  53.972   1504
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.72 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.57 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.21), residues: 1376
  helix: -0.47 (0.35), residues: 207
  sheet: -0.18 (0.37), residues: 181
  loop : -2.50 (0.19), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 915 
 TYR   0.011   0.001   TYR A1539 
 PHE   0.011   0.001   PHE A1637 
 TRP   0.010   0.001   TRP A 182 
 HIS   0.003   0.000   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.10 (11297)
  covalent geometry    : angle       0.63972 /  0.30 (15293)
  SS BOND              : bond        0.00103 /  0.07 (   11)
  SS BOND              : angle       0.41026 /  0.24 (   22)
  hydrogen bonds       : bond        0.02750 /  1.86 (  154)
  hydrogen bonds       : angle       4.87418 /  3.44 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.8704 (mmm) cc_final: 0.8253 (mmm)
REVERT: A  419 MET cc_start: 0.6197 (mpp) cc_final: 0.4263 (pmm)
REVERT: A  968 MET cc_start: 0.7641 (ptt) cc_final: 0.6497 (ptt)
REVERT: A 1025 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8574 (mm-30)
REVERT: A 1177 MET cc_start: 0.6359 (ptt) cc_final: 0.5911 (pmm)
REVERT: A 1325 MET cc_start: 0.8502 (tpt) cc_final: 0.8023 (mpp)
REVERT: A 1326 TYR cc_start: 0.7368 (p90) cc_final: 0.7081 (p90)
REVERT: A 1337 ASN cc_start: 0.5269 (OUTLIER) cc_final: 0.4726 (p0)
REVERT: A 1345 ILE cc_start: 0.5799 (OUTLIER) cc_final: 0.5066 (mm)
REVERT: A 1378 MET cc_start: 0.8885 (ppp) cc_final: 0.8270 (ppp)
REVERT: A 1386 MET cc_start: 0.5853 (tpt) cc_final: 0.5635 (tpt)
REVERT: A 1449 LEU cc_start: 0.8903 (tt) cc_final: 0.8683 (pp)
REVERT: A 1541 MET cc_start: 0.5854 (tpp) cc_final: 0.5362 (tpp)
  outliers start: 27
  outliers final: 21
  residues processed: 90
  average time/residue: 0.0893
  time to fit residues: 11.9118
Evaluate side-chains
  86 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  182 TRP
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  832 TYR
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1119 MET
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1136 CYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1197 ARG
Chi-restraints excluded: chain A residue 1334 LEU
Chi-restraints excluded: chain A residue 1337 ASN
Chi-restraints excluded: chain A residue 1342 LYS
Chi-restraints excluded: chain A residue 1345 ILE
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1484 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [14, 133, 20, 101, 67, 98, 26, 130, 135, 95, 47]
   chunk 14 optimal weight:    9.9990
   chunk 133 optimal weight:   40.0000
   chunk 20 optimal weight:   20.0000
   chunk 101 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 130 optimal weight:    2.9990
   chunk 135 optimal weight:    8.9990
   chunk 95 optimal weight:    4.9990
   chunk 47 optimal weight:   40.0000
   overall best weight:    3.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 897 HIS
** A1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1237 GLN
** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1620 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 = 0.4838 r_free = 0.4838 target = 0.148719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.123183 restraints weight = 104902.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.124603 restraints weight = 70387.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4740 r_free = 0.4740 target = 0.125747 restraints weight = 54194.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.126210 restraints weight = 45567.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.126760 restraints weight = 42007.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.6797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  11308  Z= 0.235
  Angle     :  0.794  16.875  15315  Z= 0.397
  Chirality :  0.046   0.335   1715
  Planarity :  0.006   0.133   1979
  Dihedral  :  4.846  53.979   1504
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 25.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.32 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.73 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.87 (0.21), residues: 1376
  helix: -1.36 (0.32), residues: 212
  sheet: -0.51 (0.35), residues: 201
  loop : -2.53 (0.19), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 915 
 TYR   0.032   0.002   TYR A1172 
 PHE   0.021   0.002   PHE A1226 
 TRP   0.028   0.002   TRP A1012 
 HIS   0.009   0.002   HIS A1267 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00489 /  0.23 (11297)
  covalent geometry    : angle       0.79390 /  0.40 (15293)
  SS BOND              : bond        0.00381 /  0.19 (   11)
  SS BOND              : angle       0.60894 /  0.36 (   22)
  hydrogen bonds       : bond        0.05123 /  3.46 (  154)
  hydrogen bonds       : angle       5.82693 /  4.19 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 69
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.8701 (mmm) cc_final: 0.8238 (mmm)
REVERT: A  419 MET cc_start: 0.7231 (mpp) cc_final: 0.6744 (pmm)
REVERT: A  820 ASN cc_start: 0.7610 (m-40) cc_final: 0.7198 (p0)
REVERT: A  968 MET cc_start: 0.8072 (ptt) cc_final: 0.6852 (ptt)
REVERT: A 1021 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8497 (mm-40)
REVERT: A 1025 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8580 (mm-30)
REVERT: A 1177 MET cc_start: 0.7706 (ptt) cc_final: 0.6839 (pmm)
REVERT: A 1325 MET cc_start: 0.8482 (tpt) cc_final: 0.8149 (mpp)
REVERT: A 1337 ASN cc_start: 0.6294 (OUTLIER) cc_final: 0.5636 (p0)
REVERT: A 1386 MET cc_start: 0.6917 (tpt) cc_final: 0.6419 (tpp)
REVERT: A 1541 MET cc_start: 0.7982 (tpp) cc_final: 0.7267 (tpp)
  outliers start: 26
  outliers final: 23
  residues processed: 93
  average time/residue: 0.1006
  time to fit residues: 13.6093
Evaluate side-chains
  85 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 61
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  182 TRP
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  832 TYR
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  965 VAL
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1032 THR
Chi-restraints excluded: chain A residue 1035 LEU
Chi-restraints excluded: chain A residue 1119 MET
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1136 CYS
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1197 ARG
Chi-restraints excluded: chain A residue 1334 LEU
Chi-restraints excluded: chain A residue 1337 ASN
Chi-restraints excluded: chain A residue 1342 LYS
Chi-restraints excluded: chain A residue 1345 ILE
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1484 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [77, 80, 24, 22, 57, 135, 2, 55, 134, 47, 138]
   chunk 77 optimal weight:    0.7980
   chunk 80 optimal weight:    0.0980
   chunk 24 optimal weight:    0.8980
   chunk 22 optimal weight:   20.0000
   chunk 57 optimal weight:   20.0000
   chunk 135 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0270
   chunk 134 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 138 optimal weight:   10.0000
   overall best weight:    0.5638

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 356 ASN
** A1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1620 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 = 0.4779 r_free = 0.4779 target = 0.142285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.119377 restraints weight = 73085.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.121767 restraints weight = 51768.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.123575 restraints weight = 39766.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.124819 restraints weight = 32194.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.125953 restraints weight = 27422.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.6647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.096  11308  Z= 0.117
  Angle     :  0.732  16.702  15315  Z= 0.346
  Chirality :  0.045   0.291   1715
  Planarity :  0.005   0.129   1979
  Dihedral  :  4.663  55.313   1504
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.99 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.38 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.21), residues: 1376
  helix: -0.90 (0.34), residues: 217
  sheet: -0.43 (0.36), residues: 191
  loop : -2.45 (0.19), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG A 915 
 TYR   0.015   0.001   TYR A 832 
 PHE   0.018   0.001   PHE A1562 
 TRP   0.012   0.001   TRP A1291 
 HIS   0.003   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 (11297)
  covalent geometry    : angle       0.73217 /  0.35 (15293)
  SS BOND              : bond        0.00149 /  0.09 (   11)
  SS BOND              : angle       0.44197 /  0.24 (   22)
  hydrogen bonds       : bond        0.03168 /  2.22 (  154)
  hydrogen bonds       : angle       5.19958 /  3.68 (  423)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 GLN cc_start: 0.5731 (OUTLIER) cc_final: 0.5262 (mp10)
REVERT: A  179 MET cc_start: 0.8691 (mmm) cc_final: 0.8245 (mmm)
REVERT: A  419 MET cc_start: 0.2363 (mpp) cc_final: 0.1764 (pmm)
REVERT: A  820 ASN cc_start: 0.7549 (m-40) cc_final: 0.7282 (p0)
REVERT: A  968 MET cc_start: 0.8010 (ptt) cc_final: 0.6777 (ptt)
REVERT: A 1021 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8476 (mm-40)
REVERT: A 1025 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8720 (mm-30)
REVERT: A 1177 MET cc_start: 0.7799 (ptt) cc_final: 0.7062 (pmm)
REVERT: A 1337 ASN cc_start: 0.6453 (OUTLIER) cc_final: 0.5785 (p0)
REVERT: A 1378 MET cc_start: 0.9041 (ppp) cc_final: 0.8355 (ppp)
REVERT: A 1386 MET cc_start: 0.7098 (tpt) cc_final: 0.6757 (tpp)
REVERT: A 1449 LEU cc_start: 0.8837 (tt) cc_final: 0.8600 (pp)
REVERT: A 1541 MET cc_start: 0.4965 (tpp) cc_final: 0.4693 (tpp)
  outliers start: 24
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0915
  time to fit residues: 12.2252
Evaluate side-chains
  86 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  161 GLN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  182 TRP
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  832 TYR
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  988 CYS
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1119 MET
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1136 CYS
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1197 ARG
Chi-restraints excluded: chain A residue 1334 LEU
Chi-restraints excluded: chain A residue 1337 ASN
Chi-restraints excluded: chain A residue 1342 LYS
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1484 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks: [95, 37, 54, 97, 59, 29, 128, 64, 35, 48, 98]
   chunk 95 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 29 optimal weight:    0.7980
   chunk 128 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 48 optimal weight:   30.0000
   chunk 98 optimal weight:    0.9980
   overall best weight:    3.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 356 ASN
** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1620 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 = 0.4844 r_free = 0.4844 target = 0.148933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.124811 restraints weight = 105981.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 93)----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.125619 restraints weight = 69934.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.126713 restraints weight = 54063.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.127802 restraints weight = 45387.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.128143 restraints weight = 40267.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.7247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093  11308  Z= 0.197
  Angle     :  0.785  16.961  15315  Z= 0.378
  Chirality :  0.045   0.251   1715
  Planarity :  0.005   0.138   1979
  Dihedral  :  4.852  55.238   1504
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 21.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.39 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.46 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.21), residues: 1376
  helix: -1.10 (0.34), residues: 207
  sheet: -0.59 (0.36), residues: 204
  loop : -2.44 (0.19), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 915 
 TYR   0.020   0.002   TYR A1172 
 PHE   0.014   0.001   PHE A1226 
 TRP   0.022   0.002   TRP A1012 
 HIS   0.006   0.001   HIS A1104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.20 (11297)
  covalent geometry    : angle       0.78480 /  0.38 (15293)
  SS BOND              : bond        0.00270 /  0.15 (   11)
  SS BOND              : angle       0.68726 /  0.41 (   22)
  hydrogen bonds       : bond        0.04582 /  3.07 (  154)
  hydrogen bonds       : angle       5.72123 /  4.09 (  423)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3166.42 seconds
wall clock time: 54 minutes 59.01 seconds (3299.01 seconds total)