Starting phenix.real_space_refine
on Wed Feb  4 17:21:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qx5_53435/02_2026/9qx5_53435.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qx5_53435/02_2026/9qx5_53435.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qx5_53435/02_2026/9qx5_53435.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qx5_53435/02_2026/9qx5_53435.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qx5_53435/02_2026/9qx5_53435.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qx5_53435/02_2026/9qx5_53435.cif"
  }
  resolution = 3.5
  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=   0.001
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      66      5.16       5
     C    7416      2.51       5
     N    1956      2.21       5
     O    2116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 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: 11554
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1435, 11554
          Classifications: {'peptide': 1435}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1387}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 153
          Unresolved non-hydrogen angles: 189
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 13, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 128
  Time building chain proxies: 2.44, per 1000 atoms: 0.21
  Number of scatterers: 11554
  At special positions: 0
  Unit cell: (111.584, 103.976, 168.644, 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      66     16.00
     O    2116      8.00
     N    1956      7.00
     C    7416      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 528.7 milliseconds
  

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2774

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 9 sheets defined
      59.2% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 657 through 674
    Processing helix  chain 'A' and resid 684 through 686
      No H-bonds generated for 'chain 'A' and resid 684 through 686'
    Processing helix  chain 'A' and resid 687 through 696
      removed outlier: 3.581A  pdb=" N   ILE A 695 " --> pdb=" O   TRP A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 699
      No H-bonds generated for 'chain 'A' and resid 697 through 699'
    Processing helix  chain 'A' and resid 700 through 723
      removed outlier: 4.107A  pdb=" N   THR A 704 " --> pdb=" O   SER A 700 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLU A 705 " --> pdb=" O   PRO A 701 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   LYS A 706 " --> pdb=" O   GLN A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 741
    Processing helix  chain 'A' and resid 744 through 749
      removed outlier: 3.866A  pdb=" N   LEU A 749 " --> pdb=" O   LEU A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 773
    Processing helix  chain 'A' and resid 775 through 785
    Processing helix  chain 'A' and resid 797 through 809
    Processing helix  chain 'A' and resid 810 through 814
      removed outlier: 3.854A  pdb=" N   THR A 814 " --> pdb=" O   GLY A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 823
      removed outlier: 3.532A  pdb=" N   ALA A 822 " --> pdb=" O   GLU A 819 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ASP A 823 " --> pdb=" O   ASP A 820 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 819 through 823'
    Processing helix  chain 'A' and resid 826 through 838
      removed outlier: 3.712A  pdb=" N   SER A 837 " --> pdb=" O   LEU A 833 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLY A 838 " --> pdb=" O   GLY A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 843 through 858
    Processing helix  chain 'A' and resid 861 through 879
    Processing helix  chain 'A' and resid 892 through 907
    Processing helix  chain 'A' and resid 908 through 910
      No H-bonds generated for 'chain 'A' and resid 908 through 910'
    Processing helix  chain 'A' and resid 915 through 923
    Processing helix  chain 'A' and resid 925 through 931
    Processing helix  chain 'A' and resid 934 through 939
    Processing helix  chain 'A' and resid 943 through 965
      removed outlier: 3.734A  pdb=" N   ALA A 965 " --> pdb=" O   GLU A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 988
    Processing helix  chain 'A' and resid 989 through 994
      removed outlier: 5.048A  pdb=" N   THR A 992 " --> pdb=" O   ASP A 989 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE A 993 " --> pdb=" O   LYS A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1000 through 1008
      removed outlier: 3.524A  pdb=" N   TYR A1004 " --> pdb=" O   HIS A1000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1008 through 1017
      removed outlier: 3.585A  pdb=" N   LEU A1012 " --> pdb=" O   PHE A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1018 through 1025
    Processing helix  chain 'A' and resid 1026 through 1042
      removed outlier: 3.907A  pdb=" N   LEU A1040 " --> pdb=" O   LEU A1036 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU A1041 " --> pdb=" O   PHE A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1052
    Processing helix  chain 'A' and resid 1084 through 1096
    Processing helix  chain 'A' and resid 1097 through 1121
      removed outlier: 5.113A  pdb=" N   GLN A1113 " --> pdb=" O   LYS A1109 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   THR A1114 " --> pdb=" O   LYS A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1127
    Processing helix  chain 'A' and resid 1138 through 1162
      removed outlier: 3.941A  pdb=" N   LEU A1146 " --> pdb=" O   CYS A1142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1167 through 1176
    Processing helix  chain 'A' and resid 1179 through 1187
    Processing helix  chain 'A' and resid 1319 through 1321
      No H-bonds generated for 'chain 'A' and resid 1319 through 1321'
    Processing helix  chain 'A' and resid 1322 through 1339
      removed outlier: 4.526A  pdb=" N   LEU A1326 " --> pdb=" O   CYS A1322 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS A1338 " --> pdb=" O   GLN A1334 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLU A1339 " --> pdb=" O   GLU A1335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1358
    Processing helix  chain 'A' and resid 1361 through 1371
    Processing helix  chain 'A' and resid 1372 through 1373
      No H-bonds generated for 'chain 'A' and resid 1372 through 1373'
    Processing helix  chain 'A' and resid 1374 through 1378
      removed outlier: 3.775A  pdb=" N   ASP A1377 " --> pdb=" O   ASP A1374 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL A1378 " --> pdb=" O   MET A1375 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1374 through 1378'
    Processing helix  chain 'A' and resid 1454 through 1461
    Processing helix  chain 'A' and resid 1942 through 1959
    Processing helix  chain 'A' and resid 1959 through 1968
      removed outlier: 3.632A  pdb=" N   LYS A1968 " --> pdb=" O   GLY A1964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1977 through 1992
    Processing helix  chain 'A' and resid 1996 through 2013
      removed outlier: 4.023A  pdb=" N   PHE A2000 " --> pdb=" O   ASP A1996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2014 through 2016
      No H-bonds generated for 'chain 'A' and resid 2014 through 2016'
    Processing helix  chain 'A' and resid 2018 through 2022
      removed outlier: 3.505A  pdb=" N   GLY A2022 " --> pdb=" O   GLU A2019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2024 through 2038
    Processing helix  chain 'A' and resid 2039 through 2043
    Processing helix  chain 'A' and resid 2044 through 2057
    Processing helix  chain 'A' and resid 2058 through 2073
      removed outlier: 3.585A  pdb=" N   PHE A2062 " --> pdb=" O   THR A2058 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LYS A2071 " --> pdb=" O   ARG A2067 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ARG A2072 " --> pdb=" O   ASN A2068 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   MET A2073 " --> pdb=" O   GLU A2069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2078 through 2096
    Processing helix  chain 'A' and resid 2099 through 2113
      removed outlier: 4.329A  pdb=" N   PHE A2111 " --> pdb=" O   PHE A2107 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   THR A2112 " --> pdb=" O   LEU A2108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2116 through 2118
      No H-bonds generated for 'chain 'A' and resid 2116 through 2118'
    Processing helix  chain 'A' and resid 2119 through 2148
      removed outlier: 3.578A  pdb=" N   SER A2125 " --> pdb=" O   ASN A2121 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   SER A2132 " --> pdb=" O   GLN A2128 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU A2140 " --> pdb=" O   ASN A2136 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS A2143 " --> pdb=" O   LYS A2139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2152 through 2154
      No H-bonds generated for 'chain 'A' and resid 2152 through 2154'
    Processing helix  chain 'A' and resid 2165 through 2169
    Processing helix  chain 'A' and resid 2177 through 2188
      removed outlier: 3.822A  pdb=" N   ILE A2186 " --> pdb=" O   LEU A2182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2198 through 2215
    Processing helix  chain 'A' and resid 2227 through 2241
    Processing helix  chain 'A' and resid 2244 through 2257
      removed outlier: 3.542A  pdb=" N   HIS A2257 " --> pdb=" O   SER A2253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2270 through 2292
      removed outlier: 3.800A  pdb=" N   SER A2275 " --> pdb=" O   GLU A2271 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLU A2292 " --> pdb=" O   PHE A2288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2293 through 2296
    Processing helix  chain 'A' and resid 2298 through 2316
    Processing helix  chain 'A' and resid 2316 through 2335
      removed outlier: 4.022A  pdb=" N   LEU A2320 " --> pdb=" O   GLY A2316 " (cutoff:3.500A)
      Proline residue:  A2330  - end of helix
    Processing helix  chain 'A' and resid 2375 through 2399
      Proline residue:  A2392  - end of helix
    Processing helix  chain 'A' and resid 2407 through 2421
    Processing helix  chain 'A' and resid 2428 through 2438
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1379 through 1381
      removed outlier: 6.933A  pdb=" N   ILE A1379 " --> pdb=" O   ILE A1709 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   LEU A1711 " --> pdb=" O   ILE A1379 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   SER A1381 " --> pdb=" O   LEU A1711 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   LYS A1713 " --> pdb=" O   SER A1381 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   GLN A1698 " --> pdb=" O   SER A1692 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   SER A1692 " --> pdb=" O   GLN A1698 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ALA A1680 " --> pdb=" O   LEU A1691 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1387 through 1393
      removed outlier: 6.765A  pdb=" N   ILE A1748 " --> pdb=" O   LEU A1390 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   SER A1392 " --> pdb=" O   CYS A1746 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   CYS A1746 " --> pdb=" O   SER A1392 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   VAL A1734 " --> pdb=" O   THR A1751 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1421 through 1425
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1475 through 1479
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1524 through 1529
      removed outlier: 3.676A  pdb=" N   ARG A1526 " --> pdb=" O   ALA A1546 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLU A1565 " --> pdb=" O   ILE A1553 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1576 through 1581
      removed outlier: 3.956A  pdb=" N   ASP A1576 " --> pdb=" O   LEU A1592 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1630 through 1636
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1766 through 1769
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2173 through 2175
      removed outlier: 4.409A  pdb=" N   ARG A2158 " --> pdb=" O   ILE A2190 " (cutoff:3.500A)

    653 hydrogen bonds defined for protein.
    1899 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: 2.13

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3736
        1.34 -     1.46: 2678
        1.46 -     1.58: 5277
        1.58 -     1.70: 0
        1.70 -     1.82: 103
  Bond restraints: 11794
  Sorted by residual:
  bond pdb=" CB  GLU A 752 "
       pdb=" CG  GLU A 752 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.14e+00
  bond pdb=" CB  GLN A 769 "
       pdb=" CG  GLN A 769 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.52e+00
  bond pdb=" C   HIS A1703 "
       pdb=" N   PRO A1704 "
    ideal  model  delta    sigma   weight residual
    1.334  1.322  0.012 1.11e-02 8.12e+03 1.16e+00
  bond pdb=" CB  VAL A1678 "
       pdb=" CG2 VAL A1678 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.04e+00
  bond pdb=" CB  MET A2269 "
       pdb=" CG  MET A2269 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.78e-01
  ... (remaining 11789 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 15796
        2.57 -     5.14: 137
        5.14 -     7.72: 18
        7.72 -    10.29: 4
       10.29 -    12.86: 2
  Bond angle restraints: 15957
  Sorted by residual:
  angle pdb=" CB  MET A1107 "
        pdb=" CG  MET A1107 "
        pdb=" SD  MET A1107 "
      ideal   model   delta    sigma   weight residual
     112.70  125.56  -12.86 3.00e+00 1.11e-01 1.84e+01
  angle pdb=" CB  MET A2269 "
        pdb=" CG  MET A2269 "
        pdb=" SD  MET A2269 "
      ideal   model   delta    sigma   weight residual
     112.70  125.51  -12.81 3.00e+00 1.11e-01 1.82e+01
  angle pdb=" CB  GLU A 752 "
        pdb=" CG  GLU A 752 "
        pdb=" CD  GLU A 752 "
      ideal   model   delta    sigma   weight residual
     112.60  118.66   -6.06 1.70e+00 3.46e-01 1.27e+01
  angle pdb=" N   GLY A 838 "
        pdb=" CA  GLY A 838 "
        pdb=" C   GLY A 838 "
      ideal   model   delta    sigma   weight residual
     113.18  120.95   -7.77 2.37e+00 1.78e-01 1.07e+01
  angle pdb=" CA  GLU A 752 "
        pdb=" CB  GLU A 752 "
        pdb=" CG  GLU A 752 "
      ideal   model   delta    sigma   weight residual
     114.10  120.58   -6.48 2.00e+00 2.50e-01 1.05e+01
  ... (remaining 15952 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 6120
       17.87 -    35.74: 772
       35.74 -    53.61: 204
       53.61 -    71.48: 29
       71.48 -    89.34: 13
  Dihedral angle restraints: 7138
    sinusoidal: 2894
      harmonic: 4244
  Sorted by residual:
  dihedral pdb=" CA  PHE A2267 "
           pdb=" C   PHE A2267 "
           pdb=" N   PRO A2268 "
           pdb=" CA  PRO A2268 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  THR A1684 "
           pdb=" C   THR A1684 "
           pdb=" N   SER A1685 "
           pdb=" CA  SER A1685 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.75  -18.25     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  MET A 747 "
           pdb=" C   MET A 747 "
           pdb=" N   ASP A 748 "
           pdb=" CA  ASP A 748 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.87   17.13     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 7135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1124
       0.036 -    0.071: 500
       0.071 -    0.107: 146
       0.107 -    0.142: 39
       0.142 -    0.178: 5
  Chirality restraints: 1814
  Sorted by residual:
  chirality pdb=" CA  ILE A1551 "
            pdb=" N   ILE A1551 "
            pdb=" C   ILE A1551 "
            pdb=" CB  ILE A1551 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.89e-01
  chirality pdb=" CG  LEU A 854 "
            pdb=" CB  LEU A 854 "
            pdb=" CD1 LEU A 854 "
            pdb=" CD2 LEU A 854 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.06e-01
  chirality pdb=" CB  ILE A 987 "
            pdb=" CA  ILE A 987 "
            pdb=" CG1 ILE A 987 "
            pdb=" CG2 ILE A 987 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 1811 not shown)

  Planarity restraints: 2014
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A2244 "   -0.038 5.00e-02 4.00e+02   5.85e-02 5.48e+00
        pdb=" N   PRO A2245 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A2245 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A2245 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A1977 "   -0.037 5.00e-02 4.00e+02   5.60e-02 5.03e+00
        pdb=" N   PRO A1978 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A1978 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A1978 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A1150 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.56e+00
        pdb=" C   PHE A1150 "    0.037 2.00e-02 2.50e+03
        pdb=" O   PHE A1150 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A1151 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2011 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.00: 6417
        3.00 -     3.48: 11837
        3.48 -     3.95: 17525
        3.95 -     4.43: 21008
        4.43 -     4.90: 33273
  Nonbonded interactions: 90060
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 752 "
            pdb=" OE1 GLU A 752 "
     model   vdw
     2.531 3.120
  nonbonded pdb=" O   GLN A2302 "
            pdb=" OD2 ASP A2306 "
     model   vdw
     2.552 3.040
  nonbonded pdb=" N   GLU A 686 "
            pdb=" OE1 GLU A 686 "
     model   vdw
     2.573 3.120
  nonbonded pdb=" O   GLU A2397 "
            pdb=" OE1 GLU A2397 "
     model   vdw
     2.578 3.040
  nonbonded pdb=" O   GLU A 768 "
            pdb=" OD1 ASP A 771 "
     model   vdw
     2.590 3.040
  ... (remaining 90055 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:             3.520
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.520
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11794  Z= 0.184
  Angle     :  0.662  12.859  15957  Z= 0.349
  Chirality :  0.044   0.178   1814
  Planarity :  0.005   0.059   2014
  Dihedral  : 17.116  89.345   4364
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.24 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.31 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.61 (0.23), residues: 1415
  helix:  1.22 (0.19), residues: 774
  sheet:  0.16 (0.37), residues: 171
  loop : -0.79 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A2027 
 TYR   0.017   0.002   TYR A1667 
 PHE   0.021   0.002   PHE A 895 
 TRP   0.011   0.002   TRP A1681 
 HIS   0.008   0.001   HIS A2030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (11794)
  covalent geometry    : angle       0.66223 (15957)
  hydrogen bonds       : bond        0.12578 (  653)
  hydrogen bonds       : angle       5.78827 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  733 TRP cc_start: 0.7552 (m-90) cc_final: 0.6891 (m-10)
REVERT: A  748 ASP cc_start: 0.7286 (t0) cc_final: 0.7085 (t0)
REVERT: A  843 LYS cc_start: 0.7471 (mmmt) cc_final: 0.7020 (mtpp)
REVERT: A  915 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7426 (p)
REVERT: A  944 PHE cc_start: 0.6973 (m-80) cc_final: 0.6688 (m-80)
REVERT: A 1120 LEU cc_start: 0.8830 (tp) cc_final: 0.8339 (mt)
REVERT: A 1624 MET cc_start: 0.6938 (pmm) cc_final: 0.6118 (mmp)
REVERT: A 1626 MET cc_start: 0.5610 (tmm) cc_final: 0.5346 (ppp)
REVERT: A 1742 ASN cc_start: 0.7448 (m-40) cc_final: 0.7064 (p0)
REVERT: A 2026 MET cc_start: 0.8522 (ttp) cc_final: 0.8224 (ttp)
REVERT: A 2240 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8315 (mm)
REVERT: A 2252 PHE cc_start: 0.8518 (t80) cc_final: 0.8011 (t80)
REVERT: A 2269 MET cc_start: 0.5156 (tpp) cc_final: 0.4184 (ptm)
  outliers start: 37
  outliers final: 25
  residues processed: 155
  average time/residue: 0.0957
  time to fit residues: 21.7844
Evaluate side-chains
  145 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1067 SER
Chi-restraints excluded: chain A residue 1085 VAL
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1430 THR
Chi-restraints excluded: chain A residue 1604 SER
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1676 ASN
Chi-restraints excluded: chain A residue 1692 SER
Chi-restraints excluded: chain A residue 1693 THR
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2073 MET
Chi-restraints excluded: chain A residue 2075 LEU
Chi-restraints excluded: chain A residue 2081 MET
Chi-restraints excluded: chain A residue 2192 ILE
Chi-restraints excluded: chain A residue 2210 GLU
Chi-restraints excluded: chain A residue 2224 LEU
Chi-restraints excluded: chain A residue 2240 LEU
Chi-restraints excluded: chain A residue 2259 ILE
Chi-restraints excluded: chain A residue 2322 LEU
Chi-restraints excluded: chain A residue 2384 CYS
Chi-restraints excluded: chain A residue 2395 LEU
Chi-restraints excluded: chain A residue 2428 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 724 GLN
A 892 HIS
** A1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.118044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.092125 restraints weight = 20472.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.094156 restraints weight = 11595.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.095539 restraints weight = 8480.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.096020 restraints weight = 6660.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.096414 restraints weight = 6506.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.0749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11794  Z= 0.133
  Angle     :  0.537   7.972  15957  Z= 0.280
  Chirality :  0.041   0.170   1814
  Planarity :  0.004   0.057   2014
  Dihedral  :  6.522  56.051   1580
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.03 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.21 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.09 (0.23), residues: 1415
  helix:  1.73 (0.19), residues: 774
  sheet:  0.14 (0.37), residues: 166
  loop : -0.71 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2294 
 TYR   0.011   0.001   TYR A 842 
 PHE   0.015   0.002   PHE A 741 
 TRP   0.017   0.001   TRP A 798 
 HIS   0.006   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (11794)
  covalent geometry    : angle       0.53735 (15957)
  hydrogen bonds       : bond        0.04432 (  653)
  hydrogen bonds       : angle       4.41261 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 130
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  662 MET cc_start: 0.6533 (mtt) cc_final: 0.6222 (ttm)
REVERT: A  733 TRP cc_start: 0.7553 (m-90) cc_final: 0.6811 (m-10)
REVERT: A  748 ASP cc_start: 0.7514 (t0) cc_final: 0.7199 (t0)
REVERT: A  769 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7224 (tm-30)
REVERT: A  778 LYS cc_start: 0.6183 (mmtm) cc_final: 0.5271 (mtmt)
REVERT: A  798 TRP cc_start: 0.6956 (p90) cc_final: 0.6710 (p90)
REVERT: A  843 LYS cc_start: 0.7626 (mmmt) cc_final: 0.6927 (mtpt)
REVERT: A 1120 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8111 (mt)
REVERT: A 1624 MET cc_start: 0.6843 (pmm) cc_final: 0.5989 (mmp)
REVERT: A 1742 ASN cc_start: 0.7551 (m-40) cc_final: 0.7084 (p0)
REVERT: A 2202 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8059 (mm-30)
REVERT: A 2269 MET cc_start: 0.6026 (tpp) cc_final: 0.4919 (ptm)
REVERT: A 2323 LYS cc_start: 0.8289 (mmtp) cc_final: 0.7769 (tppt)
  outliers start: 50
  outliers final: 19
  residues processed: 169
  average time/residue: 0.1031
  time to fit residues: 24.8655
Evaluate side-chains
  142 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1085 VAL
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1161 VAL
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1502 VAL
Chi-restraints excluded: chain A residue 1533 ILE
Chi-restraints excluded: chain A residue 1600 GLU
Chi-restraints excluded: chain A residue 1618 VAL
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1714 THR
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2089 VAL
Chi-restraints excluded: chain A residue 2224 LEU
Chi-restraints excluded: chain A residue 2322 LEU
Chi-restraints excluded: chain A residue 2328 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 104 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 115 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 113 optimal weight:    0.5980
   chunk 130 optimal weight:    2.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 724 GLN
A 801 GLN
A 892 HIS
** A1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.118723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.092528 restraints weight = 20653.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.094844 restraints weight = 11600.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.096154 restraints weight = 8270.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.096393 restraints weight = 6568.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.096731 restraints weight = 6688.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11794  Z= 0.114
  Angle     :  0.511   7.619  15957  Z= 0.264
  Chirality :  0.040   0.158   1814
  Planarity :  0.004   0.054   2014
  Dihedral  :  4.794  51.232   1544
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.96 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.68 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.33 (0.23), residues: 1415
  helix:  1.99 (0.19), residues: 772
  sheet:  0.15 (0.39), residues: 156
  loop : -0.67 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2214 
 TYR   0.009   0.001   TYR A 842 
 PHE   0.019   0.001   PHE A 741 
 TRP   0.014   0.001   TRP A 742 
 HIS   0.005   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (11794)
  covalent geometry    : angle       0.51055 (15957)
  hydrogen bonds       : bond        0.03944 (  653)
  hydrogen bonds       : angle       4.15971 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 139
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  662 MET cc_start: 0.6402 (mtt) cc_final: 0.6115 (ttm)
REVERT: A  733 TRP cc_start: 0.7503 (m-90) cc_final: 0.6786 (m-10)
REVERT: A  748 ASP cc_start: 0.7517 (t0) cc_final: 0.7208 (t0)
REVERT: A  757 LYS cc_start: 0.8847 (tptp) cc_final: 0.8561 (tptp)
REVERT: A  761 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7850 (mmtm)
REVERT: A  843 LYS cc_start: 0.7620 (mmmt) cc_final: 0.6992 (mtpt)
REVERT: A 1120 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8079 (mt)
REVERT: A 1624 MET cc_start: 0.6952 (pmm) cc_final: 0.6003 (mmp)
REVERT: A 1742 ASN cc_start: 0.7428 (m-40) cc_final: 0.7021 (p0)
REVERT: A 2252 PHE cc_start: 0.8713 (t80) cc_final: 0.8242 (t80)
REVERT: A 2323 LYS cc_start: 0.8128 (mmtp) cc_final: 0.7850 (tppt)
  outliers start: 47
  outliers final: 26
  residues processed: 170
  average time/residue: 0.0894
  time to fit residues: 22.2234
Evaluate side-chains
  149 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1027 LYS
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1430 THR
Chi-restraints excluded: chain A residue 1502 VAL
Chi-restraints excluded: chain A residue 1600 GLU
Chi-restraints excluded: chain A residue 1618 VAL
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1693 THR
Chi-restraints excluded: chain A residue 1714 THR
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2041 VAL
Chi-restraints excluded: chain A residue 2075 LEU
Chi-restraints excluded: chain A residue 2192 ILE
Chi-restraints excluded: chain A residue 2210 GLU
Chi-restraints excluded: chain A residue 2224 LEU
Chi-restraints excluded: chain A residue 2259 ILE
Chi-restraints excluded: chain A residue 2263 VAL
Chi-restraints excluded: chain A residue 2322 LEU
Chi-restraints excluded: chain A residue 2328 VAL
Chi-restraints excluded: chain A residue 2395 LEU
Chi-restraints excluded: chain A residue 2428 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   chunk 129 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 123 optimal weight:    0.1980
   chunk 142 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 892 HIS
** A1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.115623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.089417 restraints weight = 20842.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.091155 restraints weight = 12465.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.092461 restraints weight = 9236.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.092963 restraints weight = 7907.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.093217 restraints weight = 7799.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11794  Z= 0.135
  Angle     :  0.531  10.296  15957  Z= 0.274
  Chirality :  0.041   0.157   1814
  Planarity :  0.004   0.063   2014
  Dihedral  :  4.798  50.553   1543
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.89 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.45 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.32 (0.23), residues: 1415
  helix:  1.97 (0.19), residues: 775
  sheet:  0.16 (0.38), residues: 156
  loop : -0.66 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2044 
 TYR   0.010   0.001   TYR A1667 
 PHE   0.018   0.002   PHE A 741 
 TRP   0.014   0.001   TRP A 742 
 HIS   0.005   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (11794)
  covalent geometry    : angle       0.53094 (15957)
  hydrogen bonds       : bond        0.04032 (  653)
  hydrogen bonds       : angle       4.14476 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 131
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
REVERT: A  662 MET cc_start: 0.6430 (mtt) cc_final: 0.6131 (ttm)
REVERT: A  733 TRP cc_start: 0.7484 (m-90) cc_final: 0.6801 (m-10)
REVERT: A  748 ASP cc_start: 0.7571 (t0) cc_final: 0.7251 (t0)
REVERT: A  757 LYS cc_start: 0.8859 (tptp) cc_final: 0.8648 (tptp)
REVERT: A  843 LYS cc_start: 0.7655 (mmmt) cc_final: 0.7040 (mtpt)
REVERT: A  896 MET cc_start: 0.7142 (mtp) cc_final: 0.6747 (mtp)
REVERT: A  947 TYR cc_start: 0.7768 (m-80) cc_final: 0.7524 (m-80)
REVERT: A 1120 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8156 (mt)
REVERT: A 1624 MET cc_start: 0.6794 (pmm) cc_final: 0.6324 (mmp)
REVERT: A 1742 ASN cc_start: 0.7435 (m-40) cc_final: 0.6944 (p0)
REVERT: A 2123 MET cc_start: 0.8300 (mtp) cc_final: 0.7944 (mtp)
REVERT: A 2255 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7721 (tp)
REVERT: A 2269 MET cc_start: 0.6188 (tpp) cc_final: 0.5158 (ptm)
REVERT: A 2322 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.6722 (tm)
  outliers start: 50
  outliers final: 30
  residues processed: 165
  average time/residue: 0.0908
  time to fit residues: 21.9286
Evaluate side-chains
  157 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  737 MET
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1027 LYS
Chi-restraints excluded: chain A residue 1049 LEU
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1085 VAL
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1161 VAL
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1430 THR
Chi-restraints excluded: chain A residue 1502 VAL
Chi-restraints excluded: chain A residue 1533 ILE
Chi-restraints excluded: chain A residue 1600 GLU
Chi-restraints excluded: chain A residue 1618 VAL
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1714 THR
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2041 VAL
Chi-restraints excluded: chain A residue 2075 LEU
Chi-restraints excluded: chain A residue 2210 GLU
Chi-restraints excluded: chain A residue 2255 LEU
Chi-restraints excluded: chain A residue 2259 ILE
Chi-restraints excluded: chain A residue 2263 VAL
Chi-restraints excluded: chain A residue 2322 LEU
Chi-restraints excluded: chain A residue 2328 VAL
Chi-restraints excluded: chain A residue 2331 HIS
Chi-restraints excluded: chain A residue 2350 VAL
Chi-restraints excluded: chain A residue 2428 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 109 optimal weight:    0.7980
   chunk 137 optimal weight:    2.9990
   chunk 126 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 46 optimal weight:    0.4980
   chunk 97 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 121 optimal weight:    0.8980
   chunk 135 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.116654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.090017 restraints weight = 20710.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.092458 restraints weight = 11861.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.093581 restraints weight = 8712.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.093796 restraints weight = 6900.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.094425 restraints weight = 6849.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11794  Z= 0.113
  Angle     :  0.513   9.151  15957  Z= 0.263
  Chirality :  0.040   0.153   1814
  Planarity :  0.004   0.063   2014
  Dihedral  :  4.518  50.372   1541
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.03 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 18.39 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.45 (0.23), residues: 1415
  helix:  2.09 (0.19), residues: 769
  sheet:  0.24 (0.39), residues: 157
  loop : -0.61 (0.30), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2172 
 TYR   0.008   0.001   TYR A1083 
 PHE   0.020   0.001   PHE A 741 
 TRP   0.015   0.001   TRP A 742 
 HIS   0.005   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (11794)
  covalent geometry    : angle       0.51274 (15957)
  hydrogen bonds       : bond        0.03712 (  653)
  hydrogen bonds       : angle       4.04407 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 136
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  662 MET cc_start: 0.6359 (mtt) cc_final: 0.6075 (ttm)
REVERT: A  733 TRP cc_start: 0.7411 (m-90) cc_final: 0.6725 (m-10)
REVERT: A  748 ASP cc_start: 0.7546 (t0) cc_final: 0.7260 (t0)
REVERT: A  843 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7151 (mtpt)
REVERT: A  896 MET cc_start: 0.7118 (mtp) cc_final: 0.6731 (mtp)
REVERT: A  947 TYR cc_start: 0.7876 (m-80) cc_final: 0.7533 (m-80)
REVERT: A 1120 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8082 (mt)
REVERT: A 1624 MET cc_start: 0.6699 (pmm) cc_final: 0.6222 (mmp)
REVERT: A 1742 ASN cc_start: 0.7350 (m-40) cc_final: 0.6869 (p0)
REVERT: A 2099 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7228 (mt-10)
REVERT: A 2255 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7704 (tp)
  outliers start: 48
  outliers final: 28
  residues processed: 169
  average time/residue: 0.0861
  time to fit residues: 21.5969
Evaluate side-chains
  156 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  737 MET
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1027 LYS
Chi-restraints excluded: chain A residue 1049 LEU
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1085 VAL
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1161 VAL
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1430 THR
Chi-restraints excluded: chain A residue 1502 VAL
Chi-restraints excluded: chain A residue 1600 GLU
Chi-restraints excluded: chain A residue 1618 VAL
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1693 THR
Chi-restraints excluded: chain A residue 1714 THR
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2041 VAL
Chi-restraints excluded: chain A residue 2075 LEU
Chi-restraints excluded: chain A residue 2099 GLU
Chi-restraints excluded: chain A residue 2164 PHE
Chi-restraints excluded: chain A residue 2210 GLU
Chi-restraints excluded: chain A residue 2224 LEU
Chi-restraints excluded: chain A residue 2255 LEU
Chi-restraints excluded: chain A residue 2259 ILE
Chi-restraints excluded: chain A residue 2328 VAL
Chi-restraints excluded: chain A residue 2331 HIS
Chi-restraints excluded: chain A residue 2395 LEU
Chi-restraints excluded: chain A residue 2428 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 136 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A1562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2095 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.114089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.087832 restraints weight = 20692.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.089428 restraints weight = 12777.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.090677 restraints weight = 9824.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.090850 restraints weight = 7744.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.091068 restraints weight = 7762.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11794  Z= 0.165
  Angle     :  0.568  11.724  15957  Z= 0.290
  Chirality :  0.042   0.160   1814
  Planarity :  0.004   0.063   2014
  Dihedral  :  4.618  49.570   1539
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.31 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 19.33 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.29 (0.23), residues: 1415
  helix:  1.98 (0.19), residues: 769
  sheet:  0.21 (0.38), residues: 156
  loop : -0.73 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2294 
 TYR   0.012   0.001   TYR A1667 
 PHE   0.018   0.002   PHE A1491 
 TRP   0.014   0.001   TRP A1681 
 HIS   0.006   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (11794)
  covalent geometry    : angle       0.56822 (15957)
  hydrogen bonds       : bond        0.04276 (  653)
  hydrogen bonds       : angle       4.18704 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 125
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  662 MET cc_start: 0.6535 (mtt) cc_final: 0.6193 (ttm)
REVERT: A  733 TRP cc_start: 0.7446 (m-90) cc_final: 0.7026 (m-10)
REVERT: A  748 ASP cc_start: 0.7584 (t0) cc_final: 0.7339 (t0)
REVERT: A  843 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7411 (mtpt)
REVERT: A  896 MET cc_start: 0.7295 (mtp) cc_final: 0.6910 (mtp)
REVERT: A  947 TYR cc_start: 0.7903 (m-80) cc_final: 0.7600 (m-80)
REVERT: A 1120 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8304 (mt)
REVERT: A 1422 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8291 (m-30)
REVERT: A 1624 MET cc_start: 0.6828 (pmm) cc_final: 0.6237 (mmp)
REVERT: A 1742 ASN cc_start: 0.7429 (m-40) cc_final: 0.6882 (p0)
REVERT: A 2099 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7412 (mt-10)
REVERT: A 2216 ASN cc_start: 0.7537 (t0) cc_final: 0.7193 (p0)
REVERT: A 2255 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7765 (tp)
REVERT: A 2269 MET cc_start: 0.6274 (tpp) cc_final: 0.5263 (ptm)
REVERT: A 2420 LEU cc_start: 0.7849 (mp) cc_final: 0.7601 (tt)
  outliers start: 53
  outliers final: 38
  residues processed: 163
  average time/residue: 0.0917
  time to fit residues: 21.9069
Evaluate side-chains
  161 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 119
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  687 ASN
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  737 MET
Chi-restraints excluded: chain A residue  840 MET
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1027 LYS
Chi-restraints excluded: chain A residue 1049 LEU
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1085 VAL
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1161 VAL
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1422 ASP
Chi-restraints excluded: chain A residue 1430 THR
Chi-restraints excluded: chain A residue 1502 VAL
Chi-restraints excluded: chain A residue 1600 GLU
Chi-restraints excluded: chain A residue 1618 VAL
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1693 THR
Chi-restraints excluded: chain A residue 1714 THR
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2075 LEU
Chi-restraints excluded: chain A residue 2099 GLU
Chi-restraints excluded: chain A residue 2112 THR
Chi-restraints excluded: chain A residue 2164 PHE
Chi-restraints excluded: chain A residue 2210 GLU
Chi-restraints excluded: chain A residue 2224 LEU
Chi-restraints excluded: chain A residue 2255 LEU
Chi-restraints excluded: chain A residue 2259 ILE
Chi-restraints excluded: chain A residue 2286 LEU
Chi-restraints excluded: chain A residue 2289 VAL
Chi-restraints excluded: chain A residue 2328 VAL
Chi-restraints excluded: chain A residue 2331 HIS
Chi-restraints excluded: chain A residue 2350 VAL
Chi-restraints excluded: chain A residue 2395 LEU
Chi-restraints excluded: chain A residue 2428 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 110 optimal weight:    0.0970
   chunk 131 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0670
   chunk 96 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 112 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1562 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.116422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.090225 restraints weight = 20583.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.091580 restraints weight = 12749.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.092648 restraints weight = 10220.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.093621 restraints weight = 8140.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.093750 restraints weight = 7892.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11794  Z= 0.109
  Angle     :  0.520  10.927  15957  Z= 0.265
  Chirality :  0.040   0.152   1814
  Planarity :  0.004   0.063   2014
  Dihedral  :  4.446  49.418   1539
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.17 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.34 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.43 (0.23), residues: 1415
  helix:  2.12 (0.19), residues: 769
  sheet:  0.26 (0.39), residues: 157
  loop : -0.72 (0.30), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2172 
 TYR   0.009   0.001   TYR A1083 
 PHE   0.018   0.001   PHE A 741 
 TRP   0.013   0.001   TRP A 742 
 HIS   0.006   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (11794)
  covalent geometry    : angle       0.51976 (15957)
  hydrogen bonds       : bond        0.03635 (  653)
  hydrogen bonds       : angle       4.02281 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 134
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: A  662 MET cc_start: 0.6432 (mtt) cc_final: 0.6152 (ttm)
REVERT: A  733 TRP cc_start: 0.7395 (m-90) cc_final: 0.6975 (m-10)
REVERT: A  747 MET cc_start: 0.5431 (ttp) cc_final: 0.5133 (mmt)
REVERT: A  748 ASP cc_start: 0.7687 (t0) cc_final: 0.7422 (t0)
REVERT: A  809 ILE cc_start: 0.7153 (mm) cc_final: 0.6859 (tp)
REVERT: A  843 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7360 (mtpt)
REVERT: A  896 MET cc_start: 0.7054 (mtp) cc_final: 0.6649 (mtp)
REVERT: A  947 TYR cc_start: 0.7670 (m-80) cc_final: 0.7333 (m-80)
REVERT: A 1120 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8091 (mt)
REVERT: A 1624 MET cc_start: 0.6492 (pmm) cc_final: 0.6156 (mmp)
REVERT: A 2255 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7829 (tp)
REVERT: A 2269 MET cc_start: 0.6238 (tpp) cc_final: 0.5258 (ptm)
REVERT: A 2294 ARG cc_start: 0.6674 (mmm160) cc_final: 0.6337 (mmm160)
  outliers start: 44
  outliers final: 29
  residues processed: 168
  average time/residue: 0.0899
  time to fit residues: 22.1350
Evaluate side-chains
  154 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  687 ASN
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  737 MET
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1027 LYS
Chi-restraints excluded: chain A residue 1049 LEU
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1085 VAL
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1161 VAL
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1430 THR
Chi-restraints excluded: chain A residue 1502 VAL
Chi-restraints excluded: chain A residue 1600 GLU
Chi-restraints excluded: chain A residue 1618 VAL
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1693 THR
Chi-restraints excluded: chain A residue 1714 THR
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2041 VAL
Chi-restraints excluded: chain A residue 2075 LEU
Chi-restraints excluded: chain A residue 2174 ILE
Chi-restraints excluded: chain A residue 2210 GLU
Chi-restraints excluded: chain A residue 2255 LEU
Chi-restraints excluded: chain A residue 2259 ILE
Chi-restraints excluded: chain A residue 2286 LEU
Chi-restraints excluded: chain A residue 2328 VAL
Chi-restraints excluded: chain A residue 2331 HIS
Chi-restraints excluded: chain A residue 2350 VAL
Chi-restraints excluded: chain A residue 2395 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 120 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0670
   chunk 32 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 114 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 118 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.116113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.090018 restraints weight = 20589.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.091309 restraints weight = 12847.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.092410 restraints weight = 10281.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.092779 restraints weight = 8148.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.092987 restraints weight = 8039.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11794  Z= 0.116
  Angle     :  0.537  11.454  15957  Z= 0.271
  Chirality :  0.040   0.151   1814
  Planarity :  0.004   0.063   2014
  Dihedral  :  4.419  47.584   1539
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.24 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.95 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.41 (0.23), residues: 1415
  helix:  2.10 (0.19), residues: 769
  sheet:  0.27 (0.39), residues: 157
  loop : -0.72 (0.30), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2172 
 TYR   0.017   0.001   TYR A2047 
 PHE   0.017   0.001   PHE A 741 
 TRP   0.013   0.001   TRP A 742 
 HIS   0.006   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (11794)
  covalent geometry    : angle       0.53672 (15957)
  hydrogen bonds       : bond        0.03708 (  653)
  hydrogen bonds       : angle       4.03062 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 131
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  662 MET cc_start: 0.6454 (mtt) cc_final: 0.6173 (ttm)
REVERT: A  733 TRP cc_start: 0.7410 (m-90) cc_final: 0.6967 (m-10)
REVERT: A  809 ILE cc_start: 0.7104 (mm) cc_final: 0.6898 (tp)
REVERT: A  843 LYS cc_start: 0.7784 (mmmt) cc_final: 0.7344 (mtpt)
REVERT: A  894 LEU cc_start: 0.7504 (pp) cc_final: 0.7026 (tt)
REVERT: A  896 MET cc_start: 0.7103 (mtp) cc_final: 0.6675 (mtp)
REVERT: A  947 TYR cc_start: 0.7709 (m-80) cc_final: 0.7376 (m-80)
REVERT: A 1120 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8103 (mt)
REVERT: A 1531 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.5139 (mtp-110)
REVERT: A 1624 MET cc_start: 0.6602 (pmm) cc_final: 0.6197 (mmp)
REVERT: A 1742 ASN cc_start: 0.7325 (m-40) cc_final: 0.6820 (p0)
REVERT: A 2099 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7282 (mt-10)
REVERT: A 2123 MET cc_start: 0.8291 (mtp) cc_final: 0.8009 (mtp)
REVERT: A 2255 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7756 (tp)
REVERT: A 2269 MET cc_start: 0.6331 (tpp) cc_final: 0.5264 (ptm)
REVERT: A 2294 ARG cc_start: 0.6073 (mmm160) cc_final: 0.5850 (mmm160)
  outliers start: 47
  outliers final: 34
  residues processed: 162
  average time/residue: 0.0947
  time to fit residues: 22.6984
Evaluate side-chains
  165 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 127
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  687 ASN
Chi-restraints excluded: chain A residue  710 ILE
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1027 LYS
Chi-restraints excluded: chain A residue 1049 LEU
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1085 VAL
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1161 VAL
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1392 SER
Chi-restraints excluded: chain A residue 1430 THR
Chi-restraints excluded: chain A residue 1502 VAL
Chi-restraints excluded: chain A residue 1531 ARG
Chi-restraints excluded: chain A residue 1600 GLU
Chi-restraints excluded: chain A residue 1618 VAL
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1693 THR
Chi-restraints excluded: chain A residue 1714 THR
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2041 VAL
Chi-restraints excluded: chain A residue 2075 LEU
Chi-restraints excluded: chain A residue 2099 GLU
Chi-restraints excluded: chain A residue 2112 THR
Chi-restraints excluded: chain A residue 2210 GLU
Chi-restraints excluded: chain A residue 2224 LEU
Chi-restraints excluded: chain A residue 2255 LEU
Chi-restraints excluded: chain A residue 2259 ILE
Chi-restraints excluded: chain A residue 2286 LEU
Chi-restraints excluded: chain A residue 2328 VAL
Chi-restraints excluded: chain A residue 2331 HIS
Chi-restraints excluded: chain A residue 2350 VAL
Chi-restraints excluded: chain A residue 2395 LEU
Chi-restraints excluded: chain A residue 2419 SER
Chi-restraints excluded: chain A residue 2428 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 142 optimal weight:    0.6980
   chunk 128 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 870 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.115733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.089570 restraints weight = 20291.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.090856 restraints weight = 12598.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.091990 restraints weight = 9859.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.092439 restraints weight = 7945.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.092712 restraints weight = 7905.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11794  Z= 0.124
  Angle     :  0.552  12.498  15957  Z= 0.276
  Chirality :  0.041   0.153   1814
  Planarity :  0.004   0.062   2014
  Dihedral  :  4.426  46.057   1539
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.24 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.50 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.43 (0.23), residues: 1415
  helix:  2.13 (0.19), residues: 762
  sheet:  0.24 (0.39), residues: 158
  loop : -0.70 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 921 
 TYR   0.012   0.001   TYR A1083 
 PHE   0.016   0.001   PHE A 741 
 TRP   0.013   0.001   TRP A 742 
 HIS   0.006   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (11794)
  covalent geometry    : angle       0.55211 (15957)
  hydrogen bonds       : bond        0.03776 (  653)
  hydrogen bonds       : angle       4.03952 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 131
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  662 MET cc_start: 0.6470 (mtt) cc_final: 0.6189 (ttm)
REVERT: A  733 TRP cc_start: 0.7382 (m-90) cc_final: 0.7132 (m-10)
REVERT: A  843 LYS cc_start: 0.7794 (mmmt) cc_final: 0.7370 (mtpt)
REVERT: A  894 LEU cc_start: 0.7463 (pp) cc_final: 0.6834 (tt)
REVERT: A  896 MET cc_start: 0.7183 (mtp) cc_final: 0.6809 (mtp)
REVERT: A  947 TYR cc_start: 0.7728 (m-80) cc_final: 0.7375 (m-80)
REVERT: A 1120 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8137 (mt)
REVERT: A 1422 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8255 (m-30)
REVERT: A 1531 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5198 (mtp-110)
REVERT: A 1624 MET cc_start: 0.6540 (pmm) cc_final: 0.6187 (mmp)
REVERT: A 1742 ASN cc_start: 0.7343 (m-40) cc_final: 0.6866 (p0)
REVERT: A 2099 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7288 (mt-10)
REVERT: A 2123 MET cc_start: 0.8289 (mtp) cc_final: 0.8060 (mtp)
REVERT: A 2255 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7750 (tp)
REVERT: A 2269 MET cc_start: 0.6392 (tpp) cc_final: 0.5345 (ptm)
  outliers start: 46
  outliers final: 33
  residues processed: 165
  average time/residue: 0.0991
  time to fit residues: 23.7469
Evaluate side-chains
  164 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 126
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  687 ASN
Chi-restraints excluded: chain A residue  710 ILE
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1027 LYS
Chi-restraints excluded: chain A residue 1049 LEU
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1085 VAL
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1161 VAL
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1392 SER
Chi-restraints excluded: chain A residue 1422 ASP
Chi-restraints excluded: chain A residue 1430 THR
Chi-restraints excluded: chain A residue 1502 VAL
Chi-restraints excluded: chain A residue 1531 ARG
Chi-restraints excluded: chain A residue 1600 GLU
Chi-restraints excluded: chain A residue 1618 VAL
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1693 THR
Chi-restraints excluded: chain A residue 1714 THR
Chi-restraints excluded: chain A residue 2041 VAL
Chi-restraints excluded: chain A residue 2075 LEU
Chi-restraints excluded: chain A residue 2099 GLU
Chi-restraints excluded: chain A residue 2112 THR
Chi-restraints excluded: chain A residue 2174 ILE
Chi-restraints excluded: chain A residue 2210 GLU
Chi-restraints excluded: chain A residue 2224 LEU
Chi-restraints excluded: chain A residue 2255 LEU
Chi-restraints excluded: chain A residue 2259 ILE
Chi-restraints excluded: chain A residue 2286 LEU
Chi-restraints excluded: chain A residue 2328 VAL
Chi-restraints excluded: chain A residue 2331 HIS
Chi-restraints excluded: chain A residue 2350 VAL
Chi-restraints excluded: chain A residue 2395 LEU
Chi-restraints excluded: chain A residue 2419 SER
Chi-restraints excluded: chain A residue 2428 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 141 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 121 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3542 r_free = 0.3542 target = 0.115008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.088904 restraints weight = 20687.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.090318 restraints weight = 12817.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.091623 restraints weight = 10165.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.091740 restraints weight = 8065.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.091952 restraints weight = 8061.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11794  Z= 0.137
  Angle     :  0.566  10.367  15957  Z= 0.285
  Chirality :  0.041   0.159   1814
  Planarity :  0.004   0.062   2014
  Dihedral  :  4.249  37.248   1535
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.45 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.74 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.33 (0.23), residues: 1415
  helix:  1.99 (0.18), residues: 770
  sheet:  0.17 (0.38), residues: 165
  loop : -0.68 (0.30), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 921 
 TYR   0.012   0.001   TYR A1083 
 PHE   0.016   0.002   PHE A1491 
 TRP   0.012   0.001   TRP A 742 
 HIS   0.006   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11794)
  covalent geometry    : angle       0.56590 (15957)
  hydrogen bonds       : bond        0.03948 (  653)
  hydrogen bonds       : angle       4.08664 ( 1899)

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

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

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2830 Ramachandran restraints generated.
    1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 121
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  662 MET cc_start: 0.6459 (mtt) cc_final: 0.6174 (ttm)
REVERT: A  733 TRP cc_start: 0.7430 (m-90) cc_final: 0.7029 (m-10)
REVERT: A  747 MET cc_start: 0.5959 (ttp) cc_final: 0.5191 (mmt)
REVERT: A  843 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7378 (mtpt)
REVERT: A  894 LEU cc_start: 0.7530 (pp) cc_final: 0.6991 (tt)
REVERT: A  896 MET cc_start: 0.7186 (mtp) cc_final: 0.6802 (mtp)
REVERT: A  947 TYR cc_start: 0.7733 (m-80) cc_final: 0.7368 (m-80)
REVERT: A 1120 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8236 (mt)
REVERT: A 1422 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8237 (m-30)
REVERT: A 1531 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.5257 (mtp-110)
REVERT: A 1624 MET cc_start: 0.6552 (pmm) cc_final: 0.6179 (mmp)
REVERT: A 1742 ASN cc_start: 0.7317 (m-40) cc_final: 0.6815 (p0)
REVERT: A 2075 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8507 (tt)
REVERT: A 2099 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7209 (mt-10)
REVERT: A 2255 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7826 (tp)
REVERT: A 2269 MET cc_start: 0.6419 (tpp) cc_final: 0.5351 (ptm)
  outliers start: 41
  outliers final: 32
  residues processed: 152
  average time/residue: 0.1018
  time to fit residues: 22.4465
Evaluate side-chains
  158 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 120
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  687 ASN
Chi-restraints excluded: chain A residue  710 ILE
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1027 LYS
Chi-restraints excluded: chain A residue 1049 LEU
Chi-restraints excluded: chain A residue 1063 TYR
Chi-restraints excluded: chain A residue 1085 VAL
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1131 CYS
Chi-restraints excluded: chain A residue 1161 VAL
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain A residue 1392 SER
Chi-restraints excluded: chain A residue 1422 ASP
Chi-restraints excluded: chain A residue 1430 THR
Chi-restraints excluded: chain A residue 1502 VAL
Chi-restraints excluded: chain A residue 1531 ARG
Chi-restraints excluded: chain A residue 1600 GLU
Chi-restraints excluded: chain A residue 1618 VAL
Chi-restraints excluded: chain A residue 1663 THR
Chi-restraints excluded: chain A residue 1693 THR
Chi-restraints excluded: chain A residue 1714 THR
Chi-restraints excluded: chain A residue 2041 VAL
Chi-restraints excluded: chain A residue 2075 LEU
Chi-restraints excluded: chain A residue 2099 GLU
Chi-restraints excluded: chain A residue 2112 THR
Chi-restraints excluded: chain A residue 2174 ILE
Chi-restraints excluded: chain A residue 2210 GLU
Chi-restraints excluded: chain A residue 2224 LEU
Chi-restraints excluded: chain A residue 2255 LEU
Chi-restraints excluded: chain A residue 2259 ILE
Chi-restraints excluded: chain A residue 2286 LEU
Chi-restraints excluded: chain A residue 2328 VAL
Chi-restraints excluded: chain A residue 2331 HIS
Chi-restraints excluded: chain A residue 2350 VAL
Chi-restraints excluded: chain A residue 2395 LEU
Chi-restraints excluded: chain A residue 2419 SER
Chi-restraints excluded: chain A residue 2428 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 117 optimal weight:    1.9990
   chunk 140 optimal weight:    4.9990
   chunk 112 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 142 optimal weight:    4.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.115969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.090052 restraints weight = 20508.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.092005 restraints weight = 12108.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.093496 restraints weight = 8846.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.094013 restraints weight = 7005.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.094242 restraints weight = 7066.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11794  Z= 0.152
  Angle     :  0.589  12.994  15957  Z= 0.295
  Chirality :  0.042   0.163   1814
  Planarity :  0.004   0.062   2014
  Dihedral  :  4.345  37.947   1535
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.38 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.58 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.23 (0.23), residues: 1415
  helix:  1.92 (0.19), residues: 770
  sheet:  0.21 (0.38), residues: 163
  loop : -0.76 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 921 
 TYR   0.013   0.001   TYR A1083 
 PHE   0.017   0.002   PHE A1491 
 TRP   0.012   0.001   TRP A1681 
 HIS   0.004   0.001   HIS A2030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (11794)
  covalent geometry    : angle       0.58923 (15957)
  hydrogen bonds       : bond        0.04142 (  653)
  hydrogen bonds       : angle       4.15175 ( 1899)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1695.37 seconds
wall clock time: 30 minutes 10.34 seconds (1810.34 seconds total)