Starting phenix.real_space_refine
on Thu Feb  5 02:09:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tdt_25838/02_2026/7tdt_25838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tdt_25838/02_2026/7tdt_25838.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tdt_25838/02_2026/7tdt_25838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tdt_25838/02_2026/7tdt_25838.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tdt_25838/02_2026/7tdt_25838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tdt_25838/02_2026/7tdt_25838.map"
  }
  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=   0.000 sd=   0.004
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      84      5.16       5
     C    9352      2.51       5
     N    2403      2.21       5
     O    2605      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14444
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 14444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1818, 14444
          Classifications: {'peptide': 1818}
          Link IDs: {'PTRANS': 87, 'TRANS': 1730}
          Chain breaks: 10
  Time building chain proxies: 2.47, per 1000 atoms: 0.17
  Number of scatterers: 14444
  At special positions: 0
  Unit cell: (124, 219.48, 93, 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      84     16.00
     O    2605      8.00
     N    2403      7.00
     C    9352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  81 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 355 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1465 " - pdb=" SG  CYS A1477 " 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: 1.06
  Conformation dependent library (CDL) restraints added in 455.5 milliseconds
  

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3420

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 11 sheets defined
      60.3% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 21
      removed outlier: 4.120A  pdb=" N   GLN A  21 " --> pdb=" O   PHE A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 46
      removed outlier: 3.525A  pdb=" N   LEU A  27 " --> pdb=" O   CYS A  23 " (cutoff:3.500A)
      Proline residue:  A  32  - end of helix
    Processing helix  chain 'A' and resid 65 through 75
    Processing helix  chain 'A' and resid 86 through 90
    Processing helix  chain 'A' and resid 100 through 117
      removed outlier: 3.722A  pdb=" N   GLN A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 135
    Processing helix  chain 'A' and resid 200 through 210
    Processing helix  chain 'A' and resid 215 through 222
    Processing helix  chain 'A' and resid 230 through 242
      removed outlier: 3.671A  pdb=" N   ASP A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      Proline residue:  A 238  - end of helix
    Processing helix  chain 'A' and resid 243 through 245
      No H-bonds generated for 'chain 'A' and resid 243 through 245'
    Processing helix  chain 'A' and resid 251 through 276
      removed outlier: 4.218A  pdb=" N   ARG A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 289
      removed outlier: 4.164A  pdb=" N   ASP A 280 " --> pdb=" O   ARG A 276 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 309
    Processing helix  chain 'A' and resid 352 through 365
    Processing helix  chain 'A' and resid 368 through 380
      Proline residue:  A 377  - end of helix
    Processing helix  chain 'A' and resid 389 through 405
    Processing helix  chain 'A' and resid 408 through 429
      Proline residue:  A 421  - end of helix
    Processing helix  chain 'A' and resid 430 through 440
    Processing helix  chain 'A' and resid 444 through 454
    Processing helix  chain 'A' and resid 461 through 467
    Processing helix  chain 'A' and resid 483 through 504
      removed outlier: 4.049A  pdb=" N   CYS A 504 " --> pdb=" O   ARG A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'A' and resid 559 through 563
    Processing helix  chain 'A' and resid 586 through 591
      removed outlier: 4.429A  pdb=" N   TRP A 590 " --> pdb=" O   MET A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 610
    Processing helix  chain 'A' and resid 630 through 665
      Proline residue:  A 641  - end of helix
    Processing helix  chain 'A' and resid 666 through 674
    Processing helix  chain 'A' and resid 677 through 706
      Proline residue:  A 692  - end of helix
    Processing helix  chain 'A' and resid 714 through 737
    Processing helix  chain 'A' and resid 742 through 759
    Processing helix  chain 'A' and resid 759 through 768
      removed outlier: 4.298A  pdb=" N   LEU A 763 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 780
      removed outlier: 3.838A  pdb=" N   LYS A 776 " --> pdb=" O   GLY A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 800
      removed outlier: 4.006A  pdb=" N   ALA A 786 " --> pdb=" O   LEU A 782 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLU A 799 " --> pdb=" O   ALA A 795 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN A 800 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 845
    Processing helix  chain 'A' and resid 939 through 948
    Processing helix  chain 'A' and resid 968 through 975
    Processing helix  chain 'A' and resid 991 through 1002
    Processing helix  chain 'A' and resid 1005 through 1019
      removed outlier: 4.141A  pdb=" N   GLU A1011 " --> pdb=" O   HIS A1007 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   MET A1012 " --> pdb=" O   VAL A1008 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLU A1013 " --> pdb=" O   LYS A1009 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1021 through 1028
    Processing helix  chain 'A' and resid 1037 through 1047
    Processing helix  chain 'A' and resid 1063 through 1079
      removed outlier: 3.865A  pdb=" N   SER A1067 " --> pdb=" O   VAL A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1097
      removed outlier: 4.131A  pdb=" N   ASP A1095 " --> pdb=" O   MET A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1114 through 1123
      removed outlier: 4.147A  pdb=" N   GLN A1121 " --> pdb=" O   PHE A1117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1180 through 1191
      removed outlier: 3.661A  pdb=" N   HIS A1190 " --> pdb=" O   LEU A1186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1214 through 1232
      removed outlier: 4.588A  pdb=" N   HIS A1223 " --> pdb=" O   VAL A1219 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   GLU A1224 " --> pdb=" O   GLU A1220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1243 through 1252
      removed outlier: 3.879A  pdb=" N   ILE A1247 " --> pdb=" O   THR A1243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1323 through 1342
    Processing helix  chain 'A' and resid 1343 through 1368
      removed outlier: 4.634A  pdb=" N   ALA A1349 " --> pdb=" O   LYS A1345 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   GLN A1350 " --> pdb=" O   GLY A1346 " (cutoff:3.500A)
      Proline residue:  A1354  - end of helix
    Processing helix  chain 'A' and resid 1400 through 1409
    Processing helix  chain 'A' and resid 1446 through 1451
    Processing helix  chain 'A' and resid 1505 through 1524
    Processing helix  chain 'A' and resid 1547 through 1561
    Processing helix  chain 'A' and resid 1569 through 1584
      removed outlier: 3.524A  pdb=" N   PHE A1573 " --> pdb=" O   SER A1569 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A1584 " --> pdb=" O   PHE A1580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1600 through 1618
    Processing helix  chain 'A' and resid 1639 through 1648
    Processing helix  chain 'A' and resid 1651 through 1666
    Processing helix  chain 'A' and resid 1667 through 1681
      removed outlier: 3.537A  pdb=" N   VAL A1681 " --> pdb=" O   ILE A1677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1684 through 1691
    Processing helix  chain 'A' and resid 1694 through 1724
      removed outlier: 4.160A  pdb=" N   TYR A1698 " --> pdb=" O   LYS A1694 " (cutoff:3.500A)
      Proline residue:  A1713  - end of helix
      removed outlier: 3.861A  pdb=" N   PHE A1724 " --> pdb=" O   ILE A1720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1734 through 1753
      removed outlier: 3.649A  pdb=" N   THR A1750 " --> pdb=" O   GLY A1746 " (cutoff:3.500A)
      Proline residue:  A1751  - end of helix
    Processing helix  chain 'A' and resid 1755 through 1760
      removed outlier: 3.668A  pdb=" N   VAL A1759 " --> pdb=" O   PRO A1755 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A1760 " --> pdb=" O   ALA A1756 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1755 through 1760'
    Processing helix  chain 'A' and resid 1765 through 1788
      removed outlier: 4.230A  pdb=" N   LEU A1788 " --> pdb=" O   ALA A1784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1805 through 1809
      removed outlier: 3.920A  pdb=" N   ILE A1809 " --> pdb=" O   VAL A1806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1812 through 1838
    Processing helix  chain 'A' and resid 1849 through 1874
      removed outlier: 3.585A  pdb=" N   LEU A1853 " --> pdb=" O   VAL A1849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2002 through 2013
    Processing helix  chain 'A' and resid 2020 through 2033
      removed outlier: 4.105A  pdb=" N   GLY A2025 " --> pdb=" O   VAL A2021 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   GLU A2026 " --> pdb=" O   GLY A2022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2046 through 2059
      removed outlier: 3.654A  pdb=" N   LYS A2050 " --> pdb=" O   SER A2046 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU A2059 " --> pdb=" O   THR A2055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2078 through 2094
    Processing helix  chain 'A' and resid 2103 through 2111
    Processing helix  chain 'A' and resid 2127 through 2135
    Processing helix  chain 'A' and resid 2148 through 2150
      No H-bonds generated for 'chain 'A' and resid 2148 through 2150'
    Processing helix  chain 'A' and resid 2151 through 2163
      removed outlier: 3.664A  pdb=" N   VAL A2155 " --> pdb=" O   ASP A2151 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLN A2156 " --> pdb=" O   LEU A2152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2185 through 2202
      removed outlier: 4.079A  pdb=" N   ARG A2189 " --> pdb=" O   SER A2185 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ILE A2190 " --> pdb=" O   SER A2186 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ARG A2200 " --> pdb=" O   GLN A2196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2214 through 2220
      removed outlier: 3.599A  pdb=" N   PHE A2220 " --> pdb=" O   VAL A2216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60
      removed outlier: 5.857A  pdb=" N   GLY A 616 " --> pdb=" O   VAL A1590 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   VAL A1592 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   TYR A 618 " --> pdb=" O   VAL A1592 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   PHE A1594 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   GLN A 620 " --> pdb=" O   PHE A1594 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   PHE A1390 " --> pdb=" O   PHE A1535 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASN A1492 " --> pdb=" O   ASP A1495 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142
    Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 161
      removed outlier: 3.631A  pdb=" N   HIS A 160 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LYS A 166 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 383 through 385
      removed outlier: 6.319A  pdb=" N   LEU A 384 " --> pdb=" O   ILE A 536 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   VAL A 552 " --> pdb=" O   THR A1630 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906
    Processing sheet with id=AA7, first strand: chain 'A' and resid 928 through 929
      removed outlier: 6.324A  pdb=" N   THR A 929 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   VAL A1054 " --> pdb=" O   ILE A1085 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   SER A1087 " --> pdb=" O   VAL A1054 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU A1056 " --> pdb=" O   SER A1087 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   CYS A 978 " --> pdb=" O   ASP A1057 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 932 through 933
      removed outlier: 6.529A  pdb=" N   ILE A1101 " --> pdb=" O   VAL A1112 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   VAL A1112 " --> pdb=" O   ILE A1101 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ILE A1103 " --> pdb=" O   CYS A1110 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1195 through 1200
      removed outlier: 4.143A  pdb=" N   VAL A1197 " --> pdb=" O   THR A1205 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   THR A1205 " --> pdb=" O   VAL A1197 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   ASP A1199 " --> pdb=" O   GLU A1203 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   GLU A1203 " --> pdb=" O   ASP A1199 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2067 through 2068
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2171 through 2172
      removed outlier: 3.993A  pdb=" N   LEU A2176 " --> pdb=" O   VAL A2143 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL A2143 " --> pdb=" O   LEU A2176 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ASP A2205 " --> pdb=" O   ARG A2144 " (cutoff:3.500A)

    782 hydrogen bonds defined for protein.
    2283 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4563
        1.35 -     1.47: 3542
        1.47 -     1.59: 6540
        1.59 -     1.71: 0
        1.71 -     1.84: 138
  Bond restraints: 14783
  Sorted by residual:
  bond pdb=" CA  PHE A 154 "
       pdb=" CB  PHE A 154 "
    ideal  model  delta    sigma   weight residual
    1.526  1.558 -0.032 1.51e-02 4.39e+03 4.38e+00
  bond pdb=" C   ASN A2149 "
       pdb=" N   PRO A2150 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.046 2.34e-02 1.83e+03 3.93e+00
  bond pdb=" N   GLU A1005 "
       pdb=" CA  GLU A1005 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.23e+00
  bond pdb=" C   THR A 645 "
       pdb=" O   THR A 645 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.32e-02 5.74e+03 9.93e-01
  bond pdb=" N   TYR A1374 "
       pdb=" CA  TYR A1374 "
    ideal  model  delta    sigma   weight residual
    1.463  1.456  0.007 6.90e-03 2.10e+04 9.79e-01
  ... (remaining 14778 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 19429
        1.41 -     2.83: 489
        2.83 -     4.24: 110
        4.24 -     5.66: 14
        5.66 -     7.07: 7
  Bond angle restraints: 20049
  Sorted by residual:
  angle pdb=" C   LYS A 137 "
        pdb=" CA  LYS A 137 "
        pdb=" CB  LYS A 137 "
      ideal   model   delta    sigma   weight residual
     116.34  111.29    5.05 1.40e+00 5.10e-01 1.30e+01
  angle pdb=" N   VAL A1681 "
        pdb=" CA  VAL A1681 "
        pdb=" C   VAL A1681 "
      ideal   model   delta    sigma   weight residual
     106.21  109.65   -3.44 1.07e+00 8.73e-01 1.04e+01
  angle pdb=" CG  ARG A2004 "
        pdb=" CD  ARG A2004 "
        pdb=" NE  ARG A2004 "
      ideal   model   delta    sigma   weight residual
     112.00  119.07   -7.07 2.20e+00 2.07e-01 1.03e+01
  angle pdb=" CA  CYS A  54 "
        pdb=" CB  CYS A  54 "
        pdb=" SG  CYS A  54 "
      ideal   model   delta    sigma   weight residual
     114.40  120.89   -6.49 2.30e+00 1.89e-01 7.97e+00
  angle pdb=" C   GLU A1005 "
        pdb=" CA  GLU A1005 "
        pdb=" CB  GLU A1005 "
      ideal   model   delta    sigma   weight residual
     110.42  115.77   -5.35 1.99e+00 2.53e-01 7.22e+00
  ... (remaining 20044 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 7992
       17.41 -    34.83: 698
       34.83 -    52.24: 121
       52.24 -    69.66: 12
       69.66 -    87.07: 13
  Dihedral angle restraints: 8836
    sinusoidal: 3552
      harmonic: 5284
  Sorted by residual:
  dihedral pdb=" CB  CYS A  54 "
           pdb=" SG  CYS A  54 "
           pdb=" SG  CYS A  81 "
           pdb=" CB  CYS A  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -2.19  -83.81     1      1.00e+01 1.00e-02 8.56e+01
  dihedral pdb=" CA  CYS A  81 "
           pdb=" C   CYS A  81 "
           pdb=" N   PHE A  82 "
           pdb=" CA  PHE A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.44   23.56     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ASP A1064 "
           pdb=" C   ASP A1064 "
           pdb=" N   PRO A1065 "
           pdb=" CA  PRO A1065 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.10  -21.90     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 8833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1525
       0.032 -    0.063: 513
       0.063 -    0.095: 153
       0.095 -    0.126: 75
       0.126 -    0.158: 11
  Chirality restraints: 2277
  Sorted by residual:
  chirality pdb=" CA  TRP A1436 "
            pdb=" N   TRP A1436 "
            pdb=" C   TRP A1436 "
            pdb=" CB  TRP A1436 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.23e-01
  chirality pdb=" CA  ILE A1629 "
            pdb=" N   ILE A1629 "
            pdb=" C   ILE A1629 "
            pdb=" CB  ILE A1629 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 6.00e-01
  chirality pdb=" CA  PHE A1222 "
            pdb=" N   PHE A1222 "
            pdb=" C   PHE A1222 "
            pdb=" CB  PHE A1222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.41e-01
  ... (remaining 2274 not shown)

  Planarity restraints: 2521
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1064 "    0.056 5.00e-02 4.00e+02   8.54e-02 1.17e+01
        pdb=" N   PRO A1065 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A1065 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A1065 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 995 "    0.019 2.00e-02 2.50e+03   1.55e-02 6.02e+00
        pdb=" CG  TRP A 995 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 995 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 995 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 995 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 995 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 995 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 995 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 995 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 995 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  67 "    0.029 5.00e-02 4.00e+02   4.34e-02 3.02e+00
        pdb=" N   PRO A  68 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A  68 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  68 "    0.024 5.00e-02 4.00e+02
  ... (remaining 2518 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 123
        2.51 -     3.10: 12024
        3.10 -     3.70: 22712
        3.70 -     4.30: 30486
        4.30 -     4.90: 49295
  Nonbonded interactions: 114640
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 385 "
            pdb=" OG1 THR A 392 "
     model   vdw
     1.908 3.040
  nonbonded pdb=" OE1 GLN A1498 "
            pdb=" OH  TYR A1508 "
     model   vdw
     1.952 3.040
  nonbonded pdb=" OG1 THR A 483 "
            pdb=" OE1 GLU A 486 "
     model   vdw
     2.004 3.040
  nonbonded pdb=" OE2 GLU A 967 "
            pdb=" OG  SER A 969 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" O   ASN A1734 "
            pdb=" NZ  LYS A1824 "
     model   vdw
     2.099 3.120
  ... (remaining 114635 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:             1.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.440
  Find NCS groups from input model:        0.070
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
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      :  0.002   0.046  14787  Z= 0.119
  Angle     :  0.572   7.069  20057  Z= 0.307
  Chirality :  0.039   0.158   2277
  Planarity :  0.004   0.085   2521
  Dihedral  : 13.402  87.069   5404
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.24 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.20), residues: 1796
  helix:  1.22 (0.17), residues: 992
  sheet: -1.43 (0.47), residues: 121
  loop : -2.64 (0.23), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A2004 
 TYR   0.020   0.001   TYR A1126 
 PHE   0.023   0.001   PHE A2009 
 TRP   0.042   0.001   TRP A 995 
 HIS   0.005   0.001   HIS A2102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (14783)
  covalent geometry    : angle       0.57163 (20049)
  SS BOND              : bond        0.00749 (    4)
  SS BOND              : angle       0.98934 (    8)
  hydrogen bonds       : bond        0.13563 (  782)
  hydrogen bonds       : angle       5.98991 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LEU cc_start: 0.8247 (tp) cc_final: 0.7718 (pt)
REVERT: A  513 ILE cc_start: 0.6339 (pt) cc_final: 0.6120 (pt)
REVERT: A  644 MET cc_start: 0.7379 (ppp) cc_final: 0.6864 (ppp)
REVERT: A 1744 LEU cc_start: 0.7925 (tt) cc_final: 0.7356 (tt)
REVERT: A 1745 TYR cc_start: 0.7171 (t80) cc_final: 0.6825 (t80)
REVERT: A 1833 GLU cc_start: 0.7843 (pp20) cc_final: 0.7454 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.0818
  time to fit residues: 37.3623
Evaluate side-chains
  223 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    0.2980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN
A 452 GLN
A1089 HIS
** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1610 ASN
** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1642 GLN
A1686 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.110333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.092985 restraints weight = 52825.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.095091 restraints weight = 33794.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.096527 restraints weight = 24282.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.097448 restraints weight = 19124.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.098158 restraints weight = 16183.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14787  Z= 0.164
  Angle     :  0.713   8.592  20057  Z= 0.360
  Chirality :  0.045   0.217   2277
  Planarity :  0.005   0.083   2521
  Dihedral  :  4.546  25.393   1943
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.13 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.03 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.20), residues: 1796
  helix:  0.93 (0.16), residues: 1029
  sheet: -1.44 (0.46), residues: 128
  loop : -2.72 (0.23), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A2004 
 TYR   0.020   0.002   TYR A1767 
 PHE   0.037   0.002   PHE A2158 
 TRP   0.049   0.002   TRP A 995 
 HIS   0.006   0.001   HIS A2006 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (14783)
  covalent geometry    : angle       0.71303 (20049)
  SS BOND              : bond        0.00393 (    4)
  SS BOND              : angle       0.99383 (    8)
  hydrogen bonds       : bond        0.04369 (  782)
  hydrogen bonds       : angle       5.10825 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 243
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 TRP cc_start: 0.8432 (OUTLIER) cc_final: 0.8117 (t-100)
REVERT: A  382 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8115 (tppt)
REVERT: A  396 MET cc_start: 0.7742 (tmm) cc_final: 0.7471 (tmm)
REVERT: A 2190 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8542 (tp)
REVERT: A 2198 LYS cc_start: 0.8239 (pptt) cc_final: 0.7990 (pptt)
  outliers start: 23
  outliers final: 15
  residues processed: 252
  average time/residue: 0.0858
  time to fit residues: 33.9740
Evaluate side-chains
  238 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 221
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   12 TRP
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  940 THR
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1197 VAL
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1377 LEU
Chi-restraints excluded: chain A residue 1636 LEU
Chi-restraints excluded: chain A residue 1654 ASP
Chi-restraints excluded: chain A residue 1721 PHE
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 2012 LEU
Chi-restraints excluded: chain A residue 2190 ILE
Chi-restraints excluded: chain A residue 2208 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 140 optimal weight:    1.9990
   chunk 115 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 89 optimal weight:    9.9990
   chunk 151 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  96 ASN
A 160 HIS
A 349 ASN
** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1549 GLN
A1595 ASN
A1686 HIS
A2049 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.105535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.087872 restraints weight = 53579.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.089803 restraints weight = 34135.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.091145 restraints weight = 24868.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.091910 restraints weight = 19707.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.092638 restraints weight = 16976.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14787  Z= 0.233
  Angle     :  0.760  12.560  20057  Z= 0.389
  Chirality :  0.046   0.193   2277
  Planarity :  0.005   0.082   2521
  Dihedral  :  4.914  27.160   1943
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.96 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.20), residues: 1796
  helix:  0.53 (0.16), residues: 1036
  sheet: -1.82 (0.44), residues: 138
  loop : -2.88 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 579 
 TYR   0.019   0.002   TYR A1767 
 PHE   0.027   0.002   PHE A2158 
 TRP   0.056   0.002   TRP A 995 
 HIS   0.011   0.001   HIS A 993 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (14783)
  covalent geometry    : angle       0.76007 (20049)
  SS BOND              : bond        0.00446 (    4)
  SS BOND              : angle       1.43521 (    8)
  hydrogen bonds       : bond        0.04554 (  782)
  hydrogen bonds       : angle       5.18010 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 226
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 TRP cc_start: 0.8609 (OUTLIER) cc_final: 0.8350 (t-100)
REVERT: A   25 LEU cc_start: 0.8166 (tp) cc_final: 0.7635 (pt)
REVERT: A  502 MET cc_start: 0.8593 (tmm) cc_final: 0.8332 (tmm)
REVERT: A  619 MET cc_start: 0.8801 (mmm) cc_final: 0.8540 (mmm)
REVERT: A  644 MET cc_start: 0.7743 (ppp) cc_final: 0.7199 (ppp)
REVERT: A  728 VAL cc_start: 0.8789 (t) cc_final: 0.8451 (p)
REVERT: A 1037 MET cc_start: 0.7638 (pmm) cc_final: 0.7426 (pmm)
REVERT: A 2190 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8645 (mm)
  outliers start: 49
  outliers final: 32
  residues processed: 255
  average time/residue: 0.0816
  time to fit residues: 33.3949
Evaluate side-chains
  241 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 207
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   12 TRP
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   36 PHE
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  940 THR
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1247 ILE
Chi-restraints excluded: chain A residue 1358 VAL
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1377 LEU
Chi-restraints excluded: chain A residue 1385 ASN
Chi-restraints excluded: chain A residue 1391 VAL
Chi-restraints excluded: chain A residue 1398 ASP
Chi-restraints excluded: chain A residue 1636 LEU
Chi-restraints excluded: chain A residue 1654 ASP
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1721 PHE
Chi-restraints excluded: chain A residue 1741 LEU
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1858 VAL
Chi-restraints excluded: chain A residue 2190 ILE
Chi-restraints excluded: chain A residue 2208 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 167 optimal weight:   20.0000
   chunk 26 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 102 optimal weight:    0.6980
   chunk 111 optimal weight:    5.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
A1686 HIS
A1774 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.107408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.089782 restraints weight = 52455.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.091829 restraints weight = 32789.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.093137 restraints weight = 23441.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.094190 restraints weight = 18567.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.094809 restraints weight = 15514.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14787  Z= 0.150
  Angle     :  0.717  12.326  20057  Z= 0.356
  Chirality :  0.045   0.182   2277
  Planarity :  0.005   0.081   2521
  Dihedral  :  4.762  27.103   1943
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.02 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.20), residues: 1796
  helix:  0.60 (0.16), residues: 1029
  sheet: -1.74 (0.47), residues: 126
  loop : -2.86 (0.23), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 972 
 TYR   0.021   0.002   TYR A1126 
 PHE   0.029   0.002   PHE A1222 
 TRP   0.060   0.002   TRP A 995 
 HIS   0.006   0.001   HIS A2006 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (14783)
  covalent geometry    : angle       0.71674 (20049)
  SS BOND              : bond        0.00321 (    4)
  SS BOND              : angle       1.23777 (    8)
  hydrogen bonds       : bond        0.04092 (  782)
  hydrogen bonds       : angle       4.99298 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 233
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 TRP cc_start: 0.8485 (OUTLIER) cc_final: 0.8157 (t-100)
REVERT: A   25 LEU cc_start: 0.7989 (tp) cc_final: 0.7510 (pt)
REVERT: A  396 MET cc_start: 0.7701 (tmm) cc_final: 0.7388 (tmm)
REVERT: A  619 MET cc_start: 0.8838 (mmm) cc_final: 0.8574 (mmm)
REVERT: A  644 MET cc_start: 0.7442 (ppp) cc_final: 0.7094 (ppp)
REVERT: A  728 VAL cc_start: 0.8765 (t) cc_final: 0.8417 (p)
REVERT: A 1037 MET cc_start: 0.7453 (pmm) cc_final: 0.7178 (pmm)
REVERT: A 1239 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8372 (mm)
REVERT: A 1379 LEU cc_start: 0.8286 (tt) cc_final: 0.7794 (mt)
REVERT: A 1436 TRP cc_start: 0.7680 (m100) cc_final: 0.7299 (m100)
REVERT: A 2157 ASP cc_start: 0.8184 (m-30) cc_final: 0.7821 (m-30)
REVERT: A 2190 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8602 (mm)
  outliers start: 41
  outliers final: 22
  residues processed: 259
  average time/residue: 0.0952
  time to fit residues: 39.7913
Evaluate side-chains
  243 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 218
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   12 TRP
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1239 ILE
Chi-restraints excluded: chain A residue 1247 ILE
Chi-restraints excluded: chain A residue 1358 VAL
Chi-restraints excluded: chain A residue 1377 LEU
Chi-restraints excluded: chain A residue 1391 VAL
Chi-restraints excluded: chain A residue 1398 ASP
Chi-restraints excluded: chain A residue 1636 LEU
Chi-restraints excluded: chain A residue 1648 LEU
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1654 ASP
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1721 PHE
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1858 VAL
Chi-restraints excluded: chain A residue 2190 ILE
Chi-restraints excluded: chain A residue 2208 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 137 optimal weight:    0.9990
   chunk 161 optimal weight:    6.9990
   chunk 104 optimal weight:   20.0000
   chunk 162 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 152 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN
** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1327 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.106215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.088883 restraints weight = 54398.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.090887 restraints weight = 34315.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.092233 restraints weight = 24803.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.093154 restraints weight = 19659.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.093738 restraints weight = 16673.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14787  Z= 0.185
  Angle     :  0.735  11.922  20057  Z= 0.370
  Chirality :  0.045   0.167   2277
  Planarity :  0.005   0.080   2521
  Dihedral  :  4.860  28.948   1943
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.77 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.20), residues: 1796
  helix:  0.51 (0.16), residues: 1036
  sheet: -1.78 (0.46), residues: 134
  loop : -2.89 (0.23), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 579 
 TYR   0.019   0.002   TYR A1126 
 PHE   0.021   0.002   PHE A2158 
 TRP   0.058   0.002   TRP A 995 
 HIS   0.005   0.001   HIS A2006 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (14783)
  covalent geometry    : angle       0.73464 (20049)
  SS BOND              : bond        0.00377 (    4)
  SS BOND              : angle       1.38403 (    8)
  hydrogen bonds       : bond        0.04205 (  782)
  hydrogen bonds       : angle       5.02993 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 225
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 TRP cc_start: 0.8455 (OUTLIER) cc_final: 0.8155 (t-100)
REVERT: A   25 LEU cc_start: 0.8085 (tp) cc_final: 0.7593 (pt)
REVERT: A  358 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8270 (mm)
REVERT: A  396 MET cc_start: 0.7570 (tmm) cc_final: 0.7353 (tmm)
REVERT: A  644 MET cc_start: 0.7405 (ppp) cc_final: 0.7180 (ppp)
REVERT: A  649 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7334 (tt)
REVERT: A  728 VAL cc_start: 0.8854 (t) cc_final: 0.8486 (p)
REVERT: A  971 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7825 (tt)
REVERT: A 1037 MET cc_start: 0.7413 (pmm) cc_final: 0.7134 (pmm)
REVERT: A 1379 LEU cc_start: 0.8373 (tt) cc_final: 0.7965 (mt)
REVERT: A 1436 TRP cc_start: 0.7579 (m100) cc_final: 0.7209 (m100)
REVERT: A 2157 ASP cc_start: 0.8163 (m-30) cc_final: 0.7736 (m-30)
REVERT: A 2190 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8444 (tp)
  outliers start: 57
  outliers final: 30
  residues processed: 260
  average time/residue: 0.0965
  time to fit residues: 40.5097
Evaluate side-chains
  255 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 220
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   12 TRP
Chi-restraints excluded: chain A residue   36 PHE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  649 ILE
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  828 MET
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1247 ILE
Chi-restraints excluded: chain A residue 1358 VAL
Chi-restraints excluded: chain A residue 1377 LEU
Chi-restraints excluded: chain A residue 1385 ASN
Chi-restraints excluded: chain A residue 1391 VAL
Chi-restraints excluded: chain A residue 1398 ASP
Chi-restraints excluded: chain A residue 1636 LEU
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1654 ASP
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1721 PHE
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1773 VAL
Chi-restraints excluded: chain A residue 1858 VAL
Chi-restraints excluded: chain A residue 2190 ILE
Chi-restraints excluded: chain A residue 2208 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 164 optimal weight:    0.9990
   chunk 141 optimal weight:    0.6980
   chunk 75 optimal weight:    7.9990
   chunk 103 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 157 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A1549 GLN
A1607 ASN
A1610 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.108986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.091400 restraints weight = 54028.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.093504 restraints weight = 34136.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.094943 restraints weight = 24640.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.095895 restraints weight = 19497.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.096467 restraints weight = 16520.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14787  Z= 0.141
  Angle     :  0.735  13.174  20057  Z= 0.363
  Chirality :  0.045   0.190   2277
  Planarity :  0.005   0.080   2521
  Dihedral  :  4.750  28.207   1943
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.20 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.20), residues: 1796
  helix:  0.57 (0.16), residues: 1028
  sheet: -1.74 (0.46), residues: 134
  loop : -2.88 (0.23), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A2004 
 TYR   0.022   0.001   TYR A1710 
 PHE   0.056   0.002   PHE A1222 
 TRP   0.064   0.002   TRP A 995 
 HIS   0.004   0.001   HIS A2006 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (14783)
  covalent geometry    : angle       0.73518 (20049)
  SS BOND              : bond        0.00248 (    4)
  SS BOND              : angle       1.11288 (    8)
  hydrogen bonds       : bond        0.03922 (  782)
  hydrogen bonds       : angle       4.95240 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 246
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.8085 (t-100)
REVERT: A   25 LEU cc_start: 0.8004 (tp) cc_final: 0.7560 (pt)
REVERT: A  358 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8196 (mm)
REVERT: A  396 MET cc_start: 0.7518 (tmm) cc_final: 0.7245 (tmm)
REVERT: A  554 TYR cc_start: 0.7911 (p90) cc_final: 0.6976 (p90)
REVERT: A  728 VAL cc_start: 0.8789 (t) cc_final: 0.8446 (p)
REVERT: A  971 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7787 (tt)
REVERT: A 1014 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8561 (pt0)
REVERT: A 1015 MET cc_start: 0.8328 (tmm) cc_final: 0.8073 (tmm)
REVERT: A 1121 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.5089 (pt0)
REVERT: A 1222 PHE cc_start: 0.7557 (m-80) cc_final: 0.7106 (m-80)
REVERT: A 1379 LEU cc_start: 0.8139 (tt) cc_final: 0.7739 (mt)
REVERT: A 1558 MET cc_start: 0.8612 (tmm) cc_final: 0.7954 (tmm)
REVERT: A 1706 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8478 (m-30)
REVERT: A 1709 ASN cc_start: 0.7636 (t0) cc_final: 0.7102 (t0)
REVERT: A 1745 TYR cc_start: 0.7702 (t80) cc_final: 0.7198 (t80)
REVERT: A 1813 PHE cc_start: 0.6264 (m-80) cc_final: 0.5049 (m-10)
REVERT: A 2104 MET cc_start: 0.8442 (ttm) cc_final: 0.8130 (ttt)
REVERT: A 2157 ASP cc_start: 0.8113 (m-30) cc_final: 0.7692 (m-30)
  outliers start: 53
  outliers final: 30
  residues processed: 276
  average time/residue: 0.0903
  time to fit residues: 40.0022
Evaluate side-chains
  265 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 229
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   12 TRP
Chi-restraints excluded: chain A residue   36 PHE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  828 MET
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1014 GLN
Chi-restraints excluded: chain A residue 1121 GLN
Chi-restraints excluded: chain A residue 1197 VAL
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1247 ILE
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1356 VAL
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1377 LEU
Chi-restraints excluded: chain A residue 1385 ASN
Chi-restraints excluded: chain A residue 1398 ASP
Chi-restraints excluded: chain A residue 1636 LEU
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1654 ASP
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1706 ASP
Chi-restraints excluded: chain A residue 1721 PHE
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1858 VAL
Chi-restraints excluded: chain A residue 2039 GLU
Chi-restraints excluded: chain A residue 2208 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 37 optimal weight:   10.0000
   chunk 76 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 98 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 176 optimal weight:    6.9990
   chunk 129 optimal weight:    0.9980
   chunk 41 optimal weight:   20.0000
   chunk 115 optimal weight:    0.9990
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.108957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.091472 restraints weight = 53675.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.093510 restraints weight = 34187.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.094916 restraints weight = 24815.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.095860 restraints weight = 19735.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.096406 restraints weight = 16761.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14787  Z= 0.145
  Angle     :  0.755  13.155  20057  Z= 0.372
  Chirality :  0.045   0.190   2277
  Planarity :  0.005   0.078   2521
  Dihedral  :  4.729  29.541   1943
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.57 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.20), residues: 1796
  helix:  0.49 (0.16), residues: 1028
  sheet: -1.70 (0.46), residues: 135
  loop : -2.93 (0.23), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1579 
 TYR   0.036   0.001   TYR A1710 
 PHE   0.037   0.001   PHE A1222 
 TRP   0.066   0.002   TRP A 995 
 HIS   0.004   0.001   HIS A2006 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (14783)
  covalent geometry    : angle       0.75454 (20049)
  SS BOND              : bond        0.00258 (    4)
  SS BOND              : angle       1.06225 (    8)
  hydrogen bonds       : bond        0.03934 (  782)
  hydrogen bonds       : angle       4.94383 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 234
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 TRP cc_start: 0.8423 (OUTLIER) cc_final: 0.8139 (t-100)
REVERT: A   25 LEU cc_start: 0.8038 (tp) cc_final: 0.7573 (pt)
REVERT: A  358 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8200 (mm)
REVERT: A  396 MET cc_start: 0.7613 (tmm) cc_final: 0.7351 (tmm)
REVERT: A  502 MET cc_start: 0.8086 (tmm) cc_final: 0.7725 (tmm)
REVERT: A  728 VAL cc_start: 0.8774 (t) cc_final: 0.8415 (p)
REVERT: A  971 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7795 (tt)
REVERT: A 1014 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8559 (pt0)
REVERT: A 1015 MET cc_start: 0.8330 (tmm) cc_final: 0.8062 (tmm)
REVERT: A 1121 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.5257 (pt0)
REVERT: A 1379 LEU cc_start: 0.8130 (tt) cc_final: 0.7790 (mt)
REVERT: A 1709 ASN cc_start: 0.7591 (t0) cc_final: 0.7130 (t0)
REVERT: A 1813 PHE cc_start: 0.6239 (m-80) cc_final: 0.5022 (m-10)
REVERT: A 2157 ASP cc_start: 0.8125 (m-30) cc_final: 0.7676 (m-30)
REVERT: A 2190 ILE cc_start: 0.9069 (mm) cc_final: 0.8737 (pt)
  outliers start: 54
  outliers final: 37
  residues processed: 267
  average time/residue: 0.0867
  time to fit residues: 37.8995
Evaluate side-chains
  265 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 223
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   12 TRP
Chi-restraints excluded: chain A residue   36 PHE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  828 MET
Chi-restraints excluded: chain A residue  942 THR
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1014 GLN
Chi-restraints excluded: chain A residue 1121 GLN
Chi-restraints excluded: chain A residue 1197 VAL
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1247 ILE
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1356 VAL
Chi-restraints excluded: chain A residue 1358 VAL
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1377 LEU
Chi-restraints excluded: chain A residue 1385 ASN
Chi-restraints excluded: chain A residue 1391 VAL
Chi-restraints excluded: chain A residue 1402 LEU
Chi-restraints excluded: chain A residue 1542 THR
Chi-restraints excluded: chain A residue 1636 LEU
Chi-restraints excluded: chain A residue 1648 LEU
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1654 ASP
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1706 ASP
Chi-restraints excluded: chain A residue 1721 PHE
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 2013 LEU
Chi-restraints excluded: chain A residue 2039 GLU
Chi-restraints excluded: chain A residue 2208 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 56 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 170 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 172 optimal weight:    8.9990
   chunk 111 optimal weight:    0.6980
   chunk 17 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0040
   chunk 153 optimal weight:    0.0970
   overall best weight:    2.3594

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

Flipped N/Q/H residues before XYZ refinement:
A 445 ASN
** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.106906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.089560 restraints weight = 54568.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.091568 restraints weight = 34914.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.092930 restraints weight = 25372.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.093758 restraints weight = 20156.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.094430 restraints weight = 17321.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14787  Z= 0.177
  Angle     :  0.776  13.855  20057  Z= 0.385
  Chirality :  0.046   0.199   2277
  Planarity :  0.005   0.078   2521
  Dihedral  :  4.852  30.326   1943
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.19 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.15 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.20), residues: 1796
  helix:  0.47 (0.16), residues: 1025
  sheet: -1.87 (0.45), residues: 136
  loop : -2.87 (0.23), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A2200 
 TYR   0.026   0.002   TYR A1710 
 PHE   0.018   0.002   PHE A1329 
 TRP   0.071   0.002   TRP A 995 
 HIS   0.004   0.001   HIS A1634 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (14783)
  covalent geometry    : angle       0.77565 (20049)
  SS BOND              : bond        0.00408 (    4)
  SS BOND              : angle       1.00710 (    8)
  hydrogen bonds       : bond        0.04194 (  782)
  hydrogen bonds       : angle       5.00770 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 231
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.8145 (t-100)
REVERT: A   25 LEU cc_start: 0.8084 (tp) cc_final: 0.7597 (pt)
REVERT: A  358 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8204 (mm)
REVERT: A  502 MET cc_start: 0.8096 (tmm) cc_final: 0.7759 (tmm)
REVERT: A  945 ILE cc_start: 0.7617 (pt) cc_final: 0.7198 (tp)
REVERT: A  971 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7792 (tt)
REVERT: A 1014 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8540 (pt0)
REVERT: A 1015 MET cc_start: 0.8397 (tmm) cc_final: 0.8110 (tmm)
REVERT: A 1121 GLN cc_start: 0.5931 (OUTLIER) cc_final: 0.4769 (tt0)
REVERT: A 1379 LEU cc_start: 0.8237 (tt) cc_final: 0.7865 (mt)
REVERT: A 1383 MET cc_start: 0.7899 (mpp) cc_final: 0.7519 (mpp)
REVERT: A 1419 MET cc_start: 0.6095 (mmp) cc_final: 0.5458 (mmp)
REVERT: A 1665 MET cc_start: 0.8910 (tpp) cc_final: 0.8553 (tpp)
REVERT: A 1709 ASN cc_start: 0.7688 (t0) cc_final: 0.7225 (t0)
REVERT: A 1813 PHE cc_start: 0.6359 (m-80) cc_final: 0.5199 (m-10)
REVERT: A 1864 PHE cc_start: 0.6878 (m-10) cc_final: 0.6143 (m-10)
REVERT: A 2157 ASP cc_start: 0.8177 (m-30) cc_final: 0.7701 (m-30)
REVERT: A 2180 LEU cc_start: 0.8654 (mt) cc_final: 0.8162 (tt)
REVERT: A 2190 ILE cc_start: 0.9059 (mm) cc_final: 0.8650 (pt)
  outliers start: 55
  outliers final: 43
  residues processed: 260
  average time/residue: 0.0955
  time to fit residues: 40.3193
Evaluate side-chains
  273 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 225
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   12 TRP
Chi-restraints excluded: chain A residue   36 PHE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  828 MET
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1014 GLN
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1121 GLN
Chi-restraints excluded: chain A residue 1197 VAL
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1247 ILE
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1356 VAL
Chi-restraints excluded: chain A residue 1358 VAL
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1377 LEU
Chi-restraints excluded: chain A residue 1385 ASN
Chi-restraints excluded: chain A residue 1391 VAL
Chi-restraints excluded: chain A residue 1398 ASP
Chi-restraints excluded: chain A residue 1402 LEU
Chi-restraints excluded: chain A residue 1542 THR
Chi-restraints excluded: chain A residue 1636 LEU
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1654 ASP
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1668 VAL
Chi-restraints excluded: chain A residue 1706 ASP
Chi-restraints excluded: chain A residue 1721 PHE
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1858 VAL
Chi-restraints excluded: chain A residue 2013 LEU
Chi-restraints excluded: chain A residue 2176 LEU
Chi-restraints excluded: chain A residue 2208 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0060
   chunk 67 optimal weight:    0.7980
   chunk 98 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 0 optimal weight:    8.9990
   chunk 81 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.109680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.092094 restraints weight = 54241.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.094214 restraints weight = 34264.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.095651 restraints weight = 24745.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.096625 restraints weight = 19585.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.097206 restraints weight = 16610.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14787  Z= 0.139
  Angle     :  0.777  13.688  20057  Z= 0.378
  Chirality :  0.045   0.225   2277
  Planarity :  0.005   0.079   2521
  Dihedral  :  4.755  28.984   1943
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.19 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 23.00 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.20), residues: 1796
  helix:  0.47 (0.16), residues: 1027
  sheet: -1.72 (0.43), residues: 148
  loop : -2.99 (0.22), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1579 
 TYR   0.022   0.001   TYR A 758 
 PHE   0.033   0.001   PHE A1703 
 TRP   0.076   0.002   TRP A 995 
 HIS   0.005   0.001   HIS A 993 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (14783)
  covalent geometry    : angle       0.77713 (20049)
  SS BOND              : bond        0.00316 (    4)
  SS BOND              : angle       0.87474 (    8)
  hydrogen bonds       : bond        0.03930 (  782)
  hydrogen bonds       : angle       4.90849 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 239
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LEU cc_start: 0.8029 (tp) cc_final: 0.7557 (pt)
REVERT: A  358 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8190 (mm)
REVERT: A  945 ILE cc_start: 0.7605 (pt) cc_final: 0.7208 (tp)
REVERT: A  971 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7668 (tt)
REVERT: A 1014 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8541 (pt0)
REVERT: A 1015 MET cc_start: 0.8353 (tmm) cc_final: 0.8094 (tmm)
REVERT: A 1121 GLN cc_start: 0.5981 (OUTLIER) cc_final: 0.4762 (tt0)
REVERT: A 1379 LEU cc_start: 0.7997 (tt) cc_final: 0.7683 (mt)
REVERT: A 1383 MET cc_start: 0.7839 (mpp) cc_final: 0.7438 (mpp)
REVERT: A 1558 MET cc_start: 0.8683 (tmm) cc_final: 0.8155 (tmm)
REVERT: A 1665 MET cc_start: 0.8781 (tpp) cc_final: 0.8388 (tpp)
REVERT: A 1709 ASN cc_start: 0.7620 (t0) cc_final: 0.7148 (t0)
REVERT: A 1745 TYR cc_start: 0.7513 (t80) cc_final: 0.6956 (t80)
REVERT: A 1813 PHE cc_start: 0.6207 (m-80) cc_final: 0.5040 (m-10)
REVERT: A 1864 PHE cc_start: 0.6805 (m-10) cc_final: 0.6165 (m-10)
REVERT: A 2005 GLU cc_start: 0.4766 (pt0) cc_final: 0.4397 (mt-10)
REVERT: A 2050 LYS cc_start: 0.9082 (mttp) cc_final: 0.8862 (mmpt)
REVERT: A 2157 ASP cc_start: 0.8071 (m-30) cc_final: 0.7584 (m-30)
REVERT: A 2190 ILE cc_start: 0.9015 (mm) cc_final: 0.8811 (mp)
  outliers start: 45
  outliers final: 34
  residues processed: 265
  average time/residue: 0.0939
  time to fit residues: 40.6533
Evaluate side-chains
  269 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 231
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   36 PHE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  828 MET
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1014 GLN
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1121 GLN
Chi-restraints excluded: chain A residue 1197 VAL
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1247 ILE
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1356 VAL
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1377 LEU
Chi-restraints excluded: chain A residue 1385 ASN
Chi-restraints excluded: chain A residue 1391 VAL
Chi-restraints excluded: chain A residue 1402 LEU
Chi-restraints excluded: chain A residue 1542 THR
Chi-restraints excluded: chain A residue 1636 LEU
Chi-restraints excluded: chain A residue 1648 LEU
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1654 ASP
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1721 PHE
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 2176 LEU
Chi-restraints excluded: chain A residue 2208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 159 optimal weight:    0.5980
   chunk 174 optimal weight:    5.9990
   chunk 134 optimal weight:    1.9990
   chunk 157 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 153 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2102 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.107331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.089964 restraints weight = 54078.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.091981 restraints weight = 34280.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.093356 restraints weight = 24858.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.094212 restraints weight = 19694.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.094908 restraints weight = 16861.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14787  Z= 0.163
  Angle     :  0.787  12.400  20057  Z= 0.384
  Chirality :  0.046   0.209   2277
  Planarity :  0.005   0.081   2521
  Dihedral  :  4.821  29.181   1943
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 23.50 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.20), residues: 1796
  helix:  0.44 (0.16), residues: 1034
  sheet: -1.88 (0.45), residues: 136
  loop : -2.83 (0.23), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1579 
 TYR   0.019   0.001   TYR A1710 
 PHE   0.028   0.002   PHE A1703 
 TRP   0.079   0.002   TRP A 995 
 HIS   0.005   0.001   HIS A2102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (14783)
  covalent geometry    : angle       0.78654 (20049)
  SS BOND              : bond        0.00314 (    4)
  SS BOND              : angle       1.17883 (    8)
  hydrogen bonds       : bond        0.04046 (  782)
  hydrogen bonds       : angle       4.94564 ( 2283)

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

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

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3592 Ramachandran restraints generated.
    1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 231
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LEU cc_start: 0.8082 (tp) cc_final: 0.7592 (pt)
REVERT: A  275 MET cc_start: 0.8503 (ppp) cc_final: 0.8264 (ppp)
REVERT: A  358 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8208 (mm)
REVERT: A  971 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7784 (tt)
REVERT: A 1014 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8524 (pt0)
REVERT: A 1015 MET cc_start: 0.8297 (tmm) cc_final: 0.8061 (tmm)
REVERT: A 1121 GLN cc_start: 0.6045 (OUTLIER) cc_final: 0.4861 (tt0)
REVERT: A 1379 LEU cc_start: 0.8137 (tt) cc_final: 0.7801 (mt)
REVERT: A 1383 MET cc_start: 0.7883 (mpp) cc_final: 0.7618 (mpp)
REVERT: A 1419 MET cc_start: 0.6145 (mmp) cc_final: 0.5502 (mmp)
REVERT: A 1709 ASN cc_start: 0.7717 (t0) cc_final: 0.7238 (t0)
REVERT: A 1744 LEU cc_start: 0.8367 (tp) cc_final: 0.7991 (tt)
REVERT: A 1813 PHE cc_start: 0.6366 (m-80) cc_final: 0.5122 (m-10)
REVERT: A 1864 PHE cc_start: 0.6817 (m-10) cc_final: 0.6092 (m-10)
REVERT: A 2005 GLU cc_start: 0.4924 (pt0) cc_final: 0.4561 (mt-10)
REVERT: A 2180 LEU cc_start: 0.8579 (mt) cc_final: 0.8170 (tt)
REVERT: A 2190 ILE cc_start: 0.9061 (mm) cc_final: 0.8847 (mp)
  outliers start: 39
  outliers final: 32
  residues processed: 253
  average time/residue: 0.0959
  time to fit residues: 39.3096
Evaluate side-chains
  263 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 227
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   36 PHE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  828 MET
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1014 GLN
Chi-restraints excluded: chain A residue 1121 GLN
Chi-restraints excluded: chain A residue 1197 VAL
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1247 ILE
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1356 VAL
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1377 LEU
Chi-restraints excluded: chain A residue 1385 ASN
Chi-restraints excluded: chain A residue 1391 VAL
Chi-restraints excluded: chain A residue 1402 LEU
Chi-restraints excluded: chain A residue 1542 THR
Chi-restraints excluded: chain A residue 1636 LEU
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1654 ASP
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1721 PHE
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 2176 LEU
Chi-restraints excluded: chain A residue 2208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 133 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 134 optimal weight:    1.9990
   chunk 112 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.108219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.091022 restraints weight = 53015.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.093121 restraints weight = 33070.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.094551 restraints weight = 23635.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.095422 restraints weight = 18504.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.096113 restraints weight = 15705.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  14787  Z= 0.149
  Angle     :  0.789  12.789  20057  Z= 0.383
  Chirality :  0.045   0.220   2277
  Planarity :  0.005   0.081   2521
  Dihedral  :  4.781  28.680   1943
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 23.38 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.20), residues: 1796
  helix:  0.44 (0.16), residues: 1030
  sheet: -1.84 (0.45), residues: 137
  loop : -2.89 (0.23), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1579 
 TYR   0.021   0.001   TYR A 758 
 PHE   0.033   0.001   PHE A1703 
 TRP   0.077   0.002   TRP A 995 
 HIS   0.004   0.001   HIS A 993 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (14783)
  covalent geometry    : angle       0.78864 (20049)
  SS BOND              : bond        0.00356 (    4)
  SS BOND              : angle       1.06721 (    8)
  hydrogen bonds       : bond        0.03968 (  782)
  hydrogen bonds       : angle       4.91694 ( 2283)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2334.45 seconds
wall clock time: 41 minutes 32.78 seconds (2492.78 seconds total)