Starting phenix.real_space_refine
on Thu Jul 31 19:33:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dgj_27427/07_2025/8dgj_27427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dgj_27427/07_2025/8dgj_27427.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dgj_27427/07_2025/8dgj_27427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dgj_27427/07_2025/8dgj_27427.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dgj_27427/07_2025/8dgj_27427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dgj_27427/07_2025/8dgj_27427.cif"
  }
  resolution = 4.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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      73      5.16       5
     C    8605      2.51       5
     N    2383      2.21       5
     O    2513      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13574
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 12727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1581, 12727
          Classifications: {'peptide': 1581}
          Link IDs: {'PCIS': 1, 'PTRANS': 95, 'TRANS': 1484}
          Chain breaks: 9
    Chain: "N"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 847
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 105}
  Time building chain proxies: 8.66, per 1000 atoms: 0.64
  Number of scatterers: 13574
  At special positions: 0
  Unit cell: (153.99, 137.46, 139.2, 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      73     16.00
     O    2513      8.00
     N    2383      7.00
     C    8605      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: 3.18
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3220

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 9 sheets defined
      49.8% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 31
    Processing helix  chain 'A' and resid 39 through 61
      removed outlier: 4.000A  pdb=" N   LYS A  43 " --> pdb=" O   HIS A  39 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   ARG A  57 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   HIS A  61 " --> pdb=" O   ARG A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 87
    Processing helix  chain 'A' and resid 117 through 127
      removed outlier: 3.615A  pdb=" N   THR A 127 " --> pdb=" O   TYR A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 145 through 159
      Proline residue:  A 154  - end of helix
    Processing helix  chain 'A' and resid 177 through 181
      removed outlier: 3.753A  pdb=" N   ALA A 181 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 199
    Processing helix  chain 'A' and resid 207 through 215
    Processing helix  chain 'A' and resid 232 through 251
    Processing helix  chain 'A' and resid 265 through 272
      removed outlier: 4.062A  pdb=" N   LYS A 270 " --> pdb=" O   MET A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 293
    Processing helix  chain 'A' and resid 294 through 316
      removed outlier: 3.902A  pdb=" N   LYS A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 345
    Processing helix  chain 'A' and resid 353 through 361
    Processing helix  chain 'A' and resid 362 through 374
    Processing helix  chain 'A' and resid 501 through 517
    Processing helix  chain 'A' and resid 541 through 559
    Processing helix  chain 'A' and resid 569 through 573
      removed outlier: 3.511A  pdb=" N   GLU A 573 " --> pdb=" O   SER A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 603
      removed outlier: 4.000A  pdb=" N   TYR A 596 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 782
    Processing helix  chain 'A' and resid 783 through 785
      No H-bonds generated for 'chain 'A' and resid 783 through 785'
    Processing helix  chain 'A' and resid 791 through 801
    Processing helix  chain 'A' and resid 802 through 804
      No H-bonds generated for 'chain 'A' and resid 802 through 804'
    Processing helix  chain 'A' and resid 824 through 836
      removed outlier: 3.668A  pdb=" N   LEU A 836 " --> pdb=" O   TYR A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 904
      removed outlier: 3.656A  pdb=" N   ALA A 888 " --> pdb=" O   THR A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 921 through 929
      removed outlier: 3.642A  pdb=" N   GLU A 926 " --> pdb=" O   PRO A 923 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   CYS A 927 " --> pdb=" O   ASP A 924 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLU A 929 " --> pdb=" O   GLU A 926 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1062
    Processing helix  chain 'A' and resid 1098 through 1108
      removed outlier: 3.698A  pdb=" N   LEU A1102 " --> pdb=" O   ASP A1098 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1123
      removed outlier: 3.556A  pdb=" N   ARG A1121 " --> pdb=" O   PRO A1117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1171 through 1181
    Processing helix  chain 'A' and resid 1218 through 1222
      removed outlier: 4.095A  pdb=" N   GLU A1221 " --> pdb=" O   THR A1218 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   GLU A1222 " --> pdb=" O   SER A1219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1218 through 1222'
    Processing helix  chain 'A' and resid 1223 through 1232
    Processing helix  chain 'A' and resid 1248 through 1256
    Processing helix  chain 'A' and resid 1261 through 1281
      removed outlier: 3.722A  pdb=" N   ASN A1266 " --> pdb=" O   LEU A1262 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU A1270 " --> pdb=" O   ASN A1266 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA A1271 " --> pdb=" O   GLY A1267 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   ASP A1272 " --> pdb=" O   LEU A1268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1519 through 1535
      removed outlier: 3.800A  pdb=" N   THR A1535 " --> pdb=" O   ILE A1531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1538 through 1549
      removed outlier: 4.526A  pdb=" N   LEU A1549 " --> pdb=" O   THR A1545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1561 through 1579
      removed outlier: 3.779A  pdb=" N   ILE A1565 " --> pdb=" O   GLU A1561 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ALA A1572 " --> pdb=" O   GLU A1568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1608 through 1616
    Processing helix  chain 'A' and resid 1620 through 1629
      removed outlier: 3.909A  pdb=" N   GLY A1629 " --> pdb=" O   ALA A1625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1635 through 1648
      removed outlier: 3.714A  pdb=" N   LEU A1639 " --> pdb=" O   LEU A1635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1665 through 1669
      removed outlier: 4.152A  pdb=" N   ASN A1668 " --> pdb=" O   ASP A1665 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1722 through 1730
      removed outlier: 3.917A  pdb=" N   ILE A1726 " --> pdb=" O   SER A1722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1741 through 1763
      removed outlier: 4.227A  pdb=" N   THR A1746 " --> pdb=" O   GLU A1742 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   ILE A1747 " --> pdb=" O   ARG A1743 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   SER A1750 " --> pdb=" O   THR A1746 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   TYR A1754 " --> pdb=" O   SER A1750 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   THR A1758 " --> pdb=" O   TYR A1754 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   TYR A1759 " --> pdb=" O   ALA A1755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1768 through 1780
      removed outlier: 4.331A  pdb=" N   LEU A1772 " --> pdb=" O   HIS A1768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1781 through 1793
    Processing helix  chain 'A' and resid 1899 through 1914
      removed outlier: 3.741A  pdb=" N   ALA A1909 " --> pdb=" O   ASP A1905 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE A1911 " --> pdb=" O   VAL A1907 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLY A1912 " --> pdb=" O   GLU A1908 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ALA A1913 " --> pdb=" O   ALA A1909 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   TYR A1914 " --> pdb=" O   LEU A1910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1920 through 1931
      removed outlier: 4.214A  pdb=" N   LEU A1924 " --> pdb=" O   PRO A1920 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU A1925 " --> pdb=" O   ARG A1921 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1981 through 1989
    Processing helix  chain 'A' and resid 1992 through 2001
      removed outlier: 3.935A  pdb=" N   PHE A1996 " --> pdb=" O   GLY A1992 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A2000 " --> pdb=" O   PHE A1996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2007 through 2014
    Processing helix  chain 'A' and resid 2030 through 2049
      removed outlier: 4.590A  pdb=" N   ALA A2037 " --> pdb=" O   PHE A2033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2055 through 2067
      removed outlier: 3.544A  pdb=" N   VAL A2067 " --> pdb=" O   ARG A2063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2068 through 2079
    Processing helix  chain 'A' and resid 2081 through 2085
      removed outlier: 3.633A  pdb=" N   PHE A2084 " --> pdb=" O   PHE A2081 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE A2085 " --> pdb=" O   HIS A2082 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2081 through 2085'
    Processing helix  chain 'A' and resid 2091 through 2107
      removed outlier: 3.806A  pdb=" N   ASN A2106 " --> pdb=" O   ILE A2102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2110 through 2119
    Processing helix  chain 'A' and resid 2132 through 2148
      removed outlier: 4.660A  pdb=" N   PHE A2138 " --> pdb=" O   LEU A2134 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLU A2139 " --> pdb=" O   GLY A2135 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A2142 " --> pdb=" O   PHE A2138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2152 through 2174
      removed outlier: 3.716A  pdb=" N   VAL A2156 " --> pdb=" O   SER A2152 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ASN A2162 " --> pdb=" O   HIS A2158 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   MET A2163 " --> pdb=" O   VAL A2159 " (cutoff:3.500A)
      Proline residue:  A2166  - end of helix
    Processing helix  chain 'A' and resid 2179 through 2185
    Processing helix  chain 'A' and resid 2223 through 2238
      removed outlier: 3.716A  pdb=" N   ALA A2227 " --> pdb=" O   ASN A2223 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 359 through 371
    Processing helix  chain 'N' and resid 376 through 385
      removed outlier: 3.661A  pdb=" N   LEU N 380 " --> pdb=" O   GLY N 376 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 393 through 405
    Processing helix  chain 'N' and resid 443 through 464
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95
      removed outlier: 6.065A  pdb=" N   VAL A  64 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   LEU A 137 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   CYS A  36 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 529
      removed outlier: 6.727A  pdb=" N   GLN A 528 " --> pdb=" O   ILE A 567 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ALA A 495 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU A 496 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   VAL A 584 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   LEU A 613 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   ARG A 586 " --> pdb=" O   LEU A 613 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   VAL A1585 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   ILE A 223 " --> pdb=" O   VAL A1585 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 847 through 855
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1022 through 1026
      removed outlier: 3.721A  pdb=" N   PHE A1022 " --> pdb=" O   VAL A1033 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   LYS A1032 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   LEU A 983 " --> pdb=" O   LYS A1032 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   SER A1034 " --> pdb=" O   LEU A 981 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   LEU A 981 " --> pdb=" O   SER A1034 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   GLU A1036 " --> pdb=" O   ILE A 979 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   ILE A 979 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   PHE A1008 " --> pdb=" O   ILE A 979 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   LEU A 981 " --> pdb=" O   GLN A1006 " (cutoff:3.500A)
      removed outlier: 9.601A  pdb=" N   GLN A1006 " --> pdb=" O   LEU A 981 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1236 through 1237
      removed outlier: 7.165A  pdb=" N   ASP A1193 " --> pdb=" O   ALA A1152 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   VAL A1135 " --> pdb=" O   HIS A1245 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1937 through 1941
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2192 through 2193
      removed outlier: 3.510A  pdb=" N   GLU A2197 " --> pdb=" O   ARG A2206 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2192 through 2193
    Processing sheet with id=AA9, first strand: chain 'N' and resid 409 through 413

    618 hydrogen bonds defined for protein.
    1788 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: 5.08

  Time building geometry restraints manager: 3.78 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 4039
        1.34 -     1.46: 3235
        1.46 -     1.59: 6500
        1.59 -     1.71: 0
        1.71 -     1.84: 99
  Bond restraints: 13873
  Sorted by residual:
  bond pdb=" CA  SER A1750 "
       pdb=" C   SER A1750 "
    ideal  model  delta    sigma   weight residual
    1.523  1.451  0.072 1.41e-02 5.03e+03 2.61e+01
  bond pdb=" CA  HIS A 610 "
       pdb=" CB  HIS A 610 "
    ideal  model  delta    sigma   weight residual
    1.525  1.487  0.039 1.29e-02 6.01e+03 8.95e+00
  bond pdb=" C   LEU A1258 "
       pdb=" N   PRO A1259 "
    ideal  model  delta    sigma   weight residual
    1.334  1.387 -0.053 2.34e-02 1.83e+03 5.09e+00
  bond pdb=" CB  PHE A2033 "
       pdb=" CG  PHE A2033 "
    ideal  model  delta    sigma   weight residual
    1.502  1.453  0.049 2.30e-02 1.89e+03 4.52e+00
  bond pdb=" N   LEU A1675 "
       pdb=" CA  LEU A1675 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.15e-02 7.56e+03 4.11e+00
  ... (remaining 13868 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.13: 18515
        4.13 -     8.27: 257
        8.27 -    12.40: 30
       12.40 -    16.53: 5
       16.53 -    20.66: 1
  Bond angle restraints: 18808
  Sorted by residual:
  angle pdb=" C   GLN A2029 "
        pdb=" N   ARG A2030 "
        pdb=" CA  ARG A2030 "
      ideal   model   delta    sigma   weight residual
     121.52  133.02  -11.50 1.74e+00 3.30e-01 4.37e+01
  angle pdb=" CA  LEU A  85 "
        pdb=" CB  LEU A  85 "
        pdb=" CG  LEU A  85 "
      ideal   model   delta    sigma   weight residual
     116.30  136.96  -20.66 3.50e+00 8.16e-02 3.49e+01
  angle pdb=" N   ILE A2110 "
        pdb=" CA  ILE A2110 "
        pdb=" C   ILE A2110 "
      ideal   model   delta    sigma   weight residual
     113.42  106.73    6.69 1.17e+00 7.31e-01 3.27e+01
  angle pdb=" N   GLU N 457 "
        pdb=" CA  GLU N 457 "
        pdb=" CB  GLU N 457 "
      ideal   model   delta    sigma   weight residual
     110.40  118.56   -8.16 1.63e+00 3.76e-01 2.50e+01
  angle pdb=" CA  GLU N 457 "
        pdb=" CB  GLU N 457 "
        pdb=" CG  GLU N 457 "
      ideal   model   delta    sigma   weight residual
     114.10  124.02   -9.92 2.00e+00 2.50e-01 2.46e+01
  ... (remaining 18803 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 7460
       16.90 -    33.80: 838
       33.80 -    50.69: 132
       50.69 -    67.59: 21
       67.59 -    84.49: 14
  Dihedral angle restraints: 8465
    sinusoidal: 3503
      harmonic: 4962
  Sorted by residual:
  dihedral pdb=" CA  TYR A 215 "
           pdb=" C   TYR A 215 "
           pdb=" N   CYS A 216 "
           pdb=" CA  CYS A 216 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.20   34.80     0      5.00e+00 4.00e-02 4.84e+01
  dihedral pdb=" CA  LEU A1258 "
           pdb=" C   LEU A1258 "
           pdb=" N   PRO A1259 "
           pdb=" CA  PRO A1259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.00  -32.00     0      5.00e+00 4.00e-02 4.10e+01
  dihedral pdb=" CA  ASP A1665 "
           pdb=" C   ASP A1665 "
           pdb=" N   ASN A1666 "
           pdb=" CA  ASN A1666 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.14   31.86     0      5.00e+00 4.00e-02 4.06e+01
  ... (remaining 8462 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1551
       0.059 -    0.118: 424
       0.118 -    0.178: 92
       0.178 -    0.237: 22
       0.237 -    0.296: 8
  Chirality restraints: 2097
  Sorted by residual:
  chirality pdb=" CB  VAL A2100 "
            pdb=" CA  VAL A2100 "
            pdb=" CG1 VAL A2100 "
            pdb=" CG2 VAL A2100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" CG  LEU A2034 "
            pdb=" CB  LEU A2034 "
            pdb=" CD1 LEU A2034 "
            pdb=" CD2 LEU A2034 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.88    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CB  ILE A1097 "
            pdb=" CA  ILE A1097 "
            pdb=" CG1 ILE A1097 "
            pdb=" CG2 ILE A1097 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.16e+00
  ... (remaining 2094 not shown)

  Planarity restraints: 2447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A1718 "   -0.073 5.00e-02 4.00e+02   1.11e-01 1.98e+01
        pdb=" N   PRO A1719 "    0.192 5.00e-02 4.00e+02
        pdb=" CA  PRO A1719 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO A1719 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A2045 "    0.315 9.50e-02 1.11e+02   1.42e-01 1.30e+01
        pdb=" NE  ARG A2045 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A2045 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG A2045 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A2045 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A2020 "   -0.050 5.00e-02 4.00e+02   7.51e-02 9.02e+00
        pdb=" N   PRO A2021 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A2021 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A2021 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 2444 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1625
        2.75 -     3.29: 13294
        3.29 -     3.83: 23480
        3.83 -     4.36: 27075
        4.36 -     4.90: 43566
  Nonbonded interactions: 109040
  Sorted by model distance:
  nonbonded pdb=" O   GLU A2182 "
            pdb=" O   GLU A2185 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OG1 THR A1218 "
            pdb=" OE2 GLU A1221 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR A 863 "
            pdb=" OE1 GLN A 885 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   PRO A 923 "
            pdb=" NH2 ARG A1933 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" O   TYR A  82 "
            pdb=" OG1 THR A  86 "
     model   vdw
     2.268 3.040
  ... (remaining 109035 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.050
  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:          0.580
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     34.050
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5587
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      :  0.007   0.072  13873  Z= 0.316
  Angle     :  1.242  20.664  18808  Z= 0.663
  Chirality :  0.061   0.296   2097
  Planarity :  0.010   0.142   2447
  Dihedral  : 14.250  84.488   5245
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.38 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.80 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.32 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.18), residues: 1667
  helix: -1.97 (0.15), residues: 764
  sheet: -0.77 (0.38), residues: 165
  loop : -1.70 (0.22), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 848 
 HIS   0.010   0.002   HIS A2046 
 PHE   0.043   0.004   PHE A2084 
 TYR   0.033   0.003   TYR A  29 
 ARG   0.015   0.001   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15170 (  616)
  hydrogen bonds       : angle       7.81350 ( 1788)
  covalent geometry    : bond        0.00685 (13873)
  covalent geometry    : angle       1.24228 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 154
  time to evaluate  : 1.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  882 MET cc_start: 0.5388 (tpp) cc_final: 0.4314 (tpp)
REVERT: A 1137 MET cc_start: -0.0292 (mmm) cc_final: -0.0734 (mmm)
REVERT: A 1782 ASN cc_start: 0.6639 (OUTLIER) cc_final: 0.5851 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2819
  time to fit residues: 63.6955
Evaluate side-chains
  109 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    0.6980
   chunk 127 optimal weight:    0.9990
   chunk 70 optimal weight:    7.9990
   chunk 43 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 131 optimal weight:    0.3980
   chunk 50 optimal weight:    0.6980
   chunk 80 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 152 optimal weight:    0.3980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 598 GLN
A 813 HIS
A 870 ASN
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 980 GLN
A1096 HIS
A1526 GLN
A1668 ASN
A1768 HIS
** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 454 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4937 r_free = 0.4937 target = 0.175919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.157377 restraints weight = 41958.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.156481 restraints weight = 52386.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.157620 restraints weight = 44693.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.4687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5301
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13873  Z= 0.130
  Angle     :  0.654  11.270  18808  Z= 0.335
  Chirality :  0.042   0.145   2097
  Planarity :  0.006   0.071   2447
  Dihedral  :  6.061  30.745   1855
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.58 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.53 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.19), residues: 1667
  helix: -0.84 (0.17), residues: 792
  sheet: -0.79 (0.39), residues: 166
  loop : -1.50 (0.23), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 848 
 HIS   0.004   0.001   HIS A 341 
 PHE   0.020   0.001   PHE A1552 
 TYR   0.016   0.001   TYR A 863 
 ARG   0.006   0.001   ARG A2045 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04497 (  616)
  hydrogen bonds       : angle       5.55288 ( 1788)
  covalent geometry    : bond        0.00279 (13873)
  covalent geometry    : angle       0.65418 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 169
  time to evaluate  : 1.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 THR cc_start: 0.8739 (t) cc_final: 0.8387 (m)
REVERT: A  546 LEU cc_start: 0.7672 (mt) cc_final: 0.7164 (mt)
REVERT: A 1137 MET cc_start: 0.0793 (mmm) cc_final: 0.0039 (mmm)
REVERT: A 1261 ILE cc_start: 0.5099 (mm) cc_final: 0.4713 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2931
  time to fit residues: 72.5495
Evaluate side-chains
  109 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 164 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 91 optimal weight:    8.9990
   chunk 113 optimal weight:    0.0970
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
A 304 HIS
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1096 HIS
A1185 GLN
A1233 GLN
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1668 ASN
** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 454 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4923 r_free = 0.4923 target = 0.174814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.156125 restraints weight = 42129.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.155595 restraints weight = 46863.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.157004 restraints weight = 42352.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5319
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13873  Z= 0.142
  Angle     :  0.657   8.961  18808  Z= 0.333
  Chirality :  0.043   0.142   2097
  Planarity :  0.005   0.064   2447
  Dihedral  :  5.699  30.214   1855
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.36 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.20), residues: 1667
  helix: -0.36 (0.17), residues: 791
  sheet: -0.57 (0.39), residues: 162
  loop : -1.37 (0.23), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 848 
 HIS   0.004   0.001   HIS A 144 
 PHE   0.020   0.001   PHE A1552 
 TYR   0.030   0.002   TYR A 498 
 ARG   0.008   0.001   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04271 (  616)
  hydrogen bonds       : angle       5.23000 ( 1788)
  covalent geometry    : bond        0.00313 (13873)
  covalent geometry    : angle       0.65668 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ASP cc_start: 0.6174 (t0) cc_final: 0.5892 (t0)
REVERT: A  529 TYR cc_start: 0.7467 (p90) cc_final: 0.7149 (p90)
REVERT: A  530 THR cc_start: 0.8788 (t) cc_final: 0.8381 (m)
REVERT: A  546 LEU cc_start: 0.7609 (mt) cc_final: 0.7105 (mt)
REVERT: A  882 MET cc_start: 0.5094 (tpp) cc_final: 0.3990 (tpp)
REVERT: A 1137 MET cc_start: 0.0815 (mmm) cc_final: 0.0055 (mmm)
REVERT: A 1261 ILE cc_start: 0.5121 (mm) cc_final: 0.4643 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2763
  time to fit residues: 64.1859
Evaluate side-chains
  108 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 120 optimal weight:    4.9990
   chunk 149 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 151 optimal weight:    5.9990
   chunk 162 optimal weight:    0.6980
   chunk 125 optimal weight:    2.9990
   chunk 141 optimal weight:    0.7980
   chunk 119 optimal weight:    0.0870
   chunk 160 optimal weight:    4.9990
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 HIS
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1096 HIS
A1526 GLN
A1668 ASN
** A2087 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 454 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4941 r_free = 0.4941 target = 0.176309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.158494 restraints weight = 42267.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.157596 restraints weight = 47644.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.158749 restraints weight = 39528.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.4699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5255
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13873  Z= 0.125
  Angle     :  0.622  10.457  18808  Z= 0.314
  Chirality :  0.042   0.138   2097
  Planarity :  0.005   0.063   2447
  Dihedral  :  5.407  27.459   1855
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.82 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.47 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.20), residues: 1667
  helix: -0.08 (0.18), residues: 794
  sheet: -0.65 (0.38), residues: 167
  loop : -1.19 (0.24), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 848 
 HIS   0.005   0.001   HIS A2158 
 PHE   0.019   0.001   PHE A1552 
 TYR   0.021   0.001   TYR A1914 
 ARG   0.010   0.000   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  616)
  hydrogen bonds       : angle       5.00909 ( 1788)
  covalent geometry    : bond        0.00275 (13873)
  covalent geometry    : angle       0.62199 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 1.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 TYR cc_start: 0.7469 (p90) cc_final: 0.7133 (p90)
REVERT: A  530 THR cc_start: 0.8796 (t) cc_final: 0.8321 (m)
REVERT: A  546 LEU cc_start: 0.7449 (mt) cc_final: 0.7140 (mt)
REVERT: A  882 MET cc_start: 0.5199 (tpp) cc_final: 0.4167 (tpp)
REVERT: A  925 TRP cc_start: 0.5795 (m100) cc_final: 0.5509 (m100)
REVERT: A 1137 MET cc_start: 0.0536 (mmm) cc_final: -0.0145 (mmm)
REVERT: A 1261 ILE cc_start: 0.5190 (mm) cc_final: 0.4678 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2906
  time to fit residues: 70.5406
Evaluate side-chains
  110 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 151 optimal weight:    0.0770
   chunk 105 optimal weight:    0.0470
   chunk 109 optimal weight:    0.8980
   chunk 135 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 158 optimal weight:    9.9990
   chunk 27 optimal weight:    0.6980
   chunk 95 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 159 optimal weight:   10.0000
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
A 304 HIS
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1096 HIS
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1668 ASN
** A2104 GLN ** 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 = 0.4954 r_free = 0.4954 target = 0.177356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.159559 restraints weight = 42203.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.158895 restraints weight = 49321.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.159986 restraints weight = 39966.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.4720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5192
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13873  Z= 0.118
  Angle     :  0.612   9.294  18808  Z= 0.308
  Chirality :  0.042   0.153   2097
  Planarity :  0.005   0.063   2447
  Dihedral  :  5.171  27.404   1855
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.88 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.80 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.20), residues: 1667
  helix:  0.11 (0.18), residues: 796
  sheet: -0.50 (0.39), residues: 163
  loop : -1.04 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A1252 
 HIS   0.007   0.001   HIS A1670 
 PHE   0.019   0.001   PHE A1552 
 TYR   0.016   0.001   TYR A2028 
 ARG   0.010   0.000   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  616)
  hydrogen bonds       : angle       4.82405 ( 1788)
  covalent geometry    : bond        0.00262 (13873)
  covalent geometry    : angle       0.61237 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 1.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 TYR cc_start: 0.7378 (p90) cc_final: 0.7092 (p90)
REVERT: A  530 THR cc_start: 0.8708 (t) cc_final: 0.8322 (m)
REVERT: A  546 LEU cc_start: 0.7555 (mt) cc_final: 0.7277 (mt)
REVERT: A  882 MET cc_start: 0.5113 (tpp) cc_final: 0.4363 (tpp)
REVERT: A  925 TRP cc_start: 0.5865 (m100) cc_final: 0.5450 (m100)
REVERT: A 1137 MET cc_start: 0.0417 (mmm) cc_final: 0.0174 (mmm)
REVERT: A 1526 GLN cc_start: 0.6548 (pp30) cc_final: 0.6304 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2712
  time to fit residues: 66.2397
Evaluate side-chains
  112 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 144 optimal weight:    0.9990
   chunk 162 optimal weight:    1.9990
   chunk 163 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 53 optimal weight:    0.3980
   chunk 154 optimal weight:   10.0000
   chunk 110 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 149 optimal weight:    4.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
A 304 HIS
A 309 ASN
A 503 HIS
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1096 HIS
A1174 HIS
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1668 ASN
A1960 ASN
** A2093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2106 ASN
N 454 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4908 r_free = 0.4908 target = 0.173759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.155006 restraints weight = 42658.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.154400 restraints weight = 55133.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.155617 restraints weight = 44165.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.4658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5381
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  13873  Z= 0.170
  Angle     :  0.691   9.188  18808  Z= 0.349
  Chirality :  0.044   0.149   2097
  Planarity :  0.005   0.066   2447
  Dihedral  :  5.353  29.363   1855
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.78 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.33 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.20), residues: 1667
  helix:  0.03 (0.18), residues: 798
  sheet: -0.42 (0.40), residues: 149
  loop : -1.08 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A1252 
 HIS   0.011   0.001   HIS A2016 
 PHE   0.020   0.002   PHE A1552 
 TYR   0.020   0.002   TYR A2028 
 ARG   0.011   0.001   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04341 (  616)
  hydrogen bonds       : angle       4.95540 ( 1788)
  covalent geometry    : bond        0.00385 (13873)
  covalent geometry    : angle       0.69098 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  546 LEU cc_start: 0.7671 (mt) cc_final: 0.7386 (mt)
REVERT: A  882 MET cc_start: 0.5000 (tpp) cc_final: 0.4182 (tpp)
REVERT: A 1137 MET cc_start: 0.0584 (mmm) cc_final: -0.0152 (mmm)
REVERT: A 1526 GLN cc_start: 0.6722 (pp30) cc_final: 0.6452 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2908
  time to fit residues: 67.5479
Evaluate side-chains
  105 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0970
   chunk 144 optimal weight:    0.7980
   chunk 142 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   chunk 82 optimal weight:    0.2980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 304 HIS
** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1096 HIS
A1196 HIS
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1668 ASN
** A1768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 454 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4937 r_free = 0.4937 target = 0.176418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.158441 restraints weight = 42292.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.157600 restraints weight = 49640.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.158741 restraints weight = 43450.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5269
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13873  Z= 0.127
  Angle     :  0.644   9.369  18808  Z= 0.323
  Chirality :  0.043   0.164   2097
  Planarity :  0.005   0.065   2447
  Dihedral  :  5.105  27.260   1855
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.82 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.20), residues: 1667
  helix:  0.20 (0.18), residues: 798
  sheet: -0.80 (0.38), residues: 160
  loop : -0.91 (0.24), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A1252 
 HIS   0.007   0.001   HIS A2054 
 PHE   0.020   0.001   PHE A1552 
 TYR   0.018   0.001   TYR A2028 
 ARG   0.009   0.001   ARG A 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  616)
  hydrogen bonds       : angle       4.80291 ( 1788)
  covalent geometry    : bond        0.00281 (13873)
  covalent geometry    : angle       0.64416 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 TYR cc_start: 0.7410 (p90) cc_final: 0.7154 (p90)
REVERT: A  546 LEU cc_start: 0.7570 (mt) cc_final: 0.7258 (mt)
REVERT: A  882 MET cc_start: 0.4885 (tpp) cc_final: 0.3990 (tpp)
REVERT: A 1071 MET cc_start: -0.2508 (tpt) cc_final: -0.4266 (mmt)
REVERT: A 1137 MET cc_start: 0.0390 (mmm) cc_final: -0.0208 (mmm)
REVERT: A 1526 GLN cc_start: 0.6645 (pp30) cc_final: 0.6432 (pp30)
REVERT: A 1924 LEU cc_start: 0.8251 (mp) cc_final: 0.8050 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2723
  time to fit residues: 62.3535
Evaluate side-chains
  105 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 80 optimal weight:   20.0000
   chunk 146 optimal weight:    0.0670
   chunk 7 optimal weight:    0.8980
   chunk 45 optimal weight:    0.4980
   chunk 109 optimal weight:    0.7980
   chunk 33 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   chunk 123 optimal weight:    7.9990
   chunk 61 optimal weight:    0.5980
   chunk 143 optimal weight:    0.5980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A1174 HIS
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1668 ASN
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4951 r_free = 0.4951 target = 0.177382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.159286 restraints weight = 42170.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.158693 restraints weight = 47485.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.160061 restraints weight = 40010.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.4719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5210
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13873  Z= 0.119
  Angle     :  0.633   9.700  18808  Z= 0.318
  Chirality :  0.042   0.150   2097
  Planarity :  0.005   0.065   2447
  Dihedral  :  4.955  27.850   1855
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.94 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.20), residues: 1667
  helix:  0.34 (0.18), residues: 802
  sheet: -0.70 (0.39), residues: 160
  loop : -0.82 (0.24), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A1252 
 HIS   0.005   0.001   HIS A2016 
 PHE   0.019   0.001   PHE A1552 
 TYR   0.019   0.001   TYR A2028 
 ARG   0.012   0.001   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  616)
  hydrogen bonds       : angle       4.68149 ( 1788)
  covalent geometry    : bond        0.00262 (13873)
  covalent geometry    : angle       0.63323 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 THR cc_start: 0.8463 (t) cc_final: 0.8174 (m)
REVERT: A  546 LEU cc_start: 0.7593 (mt) cc_final: 0.7335 (mt)
REVERT: A  882 MET cc_start: 0.4945 (tpp) cc_final: 0.4204 (tpp)
REVERT: A 1071 MET cc_start: -0.2535 (tpt) cc_final: -0.4299 (mmt)
REVERT: A 1137 MET cc_start: 0.0442 (mmm) cc_final: -0.0193 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2804
  time to fit residues: 65.7943
Evaluate side-chains
  115 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 140 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 137 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1174 HIS
A1196 HIS
A1526 GLN
A1668 ASN
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.174900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.156651 restraints weight = 42146.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.155800 restraints weight = 52764.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.157002 restraints weight = 43097.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.4675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5335
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  13873  Z= 0.154
  Angle     :  0.673   9.314  18808  Z= 0.338
  Chirality :  0.043   0.155   2097
  Planarity :  0.005   0.065   2447
  Dihedral  :  5.084  27.487   1855
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.90 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.73 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.20), residues: 1667
  helix:  0.28 (0.18), residues: 800
  sheet: -0.51 (0.41), residues: 145
  loop : -0.86 (0.24), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A1252 
 HIS   0.013   0.001   HIS A1670 
 PHE   0.020   0.002   PHE A1552 
 TYR   0.019   0.002   TYR A2028 
 ARG   0.010   0.001   ARG A 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03997 (  616)
  hydrogen bonds       : angle       4.82227 ( 1788)
  covalent geometry    : bond        0.00351 (13873)
  covalent geometry    : angle       0.67339 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 1.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.3146 (mmm) cc_final: 0.2378 (mmm)
REVERT: A  530 THR cc_start: 0.8491 (t) cc_final: 0.8131 (m)
REVERT: A  546 LEU cc_start: 0.7662 (mt) cc_final: 0.7448 (mt)
REVERT: A  882 MET cc_start: 0.4835 (tpp) cc_final: 0.4233 (tpp)
REVERT: A 1071 MET cc_start: -0.2372 (tpt) cc_final: -0.4202 (mmt)
REVERT: A 1137 MET cc_start: 0.0610 (mmm) cc_final: 0.0227 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2778
  time to fit residues: 63.9237
Evaluate side-chains
  106 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 120 optimal weight:    0.8980
   chunk 106 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 113 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 127 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0870
   chunk 67 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A1062 ASN
A1096 HIS
A1174 HIS
A1668 ASN
** A1670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2054 HIS
** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4939 r_free = 0.4939 target = 0.176419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.158380 restraints weight = 41983.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.157763 restraints weight = 50355.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.159195 restraints weight = 44390.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.4707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5238
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13873  Z= 0.129
  Angle     :  0.652   9.491  18808  Z= 0.325
  Chirality :  0.043   0.185   2097
  Planarity :  0.005   0.065   2447
  Dihedral  :  4.989  27.697   1855
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.18 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.20), residues: 1667
  helix:  0.33 (0.18), residues: 800
  sheet: -0.69 (0.41), residues: 151
  loop : -0.79 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A1252 
 HIS   0.008   0.001   HIS A1670 
 PHE   0.025   0.001   PHE A1552 
 TYR   0.019   0.001   TYR A2028 
 ARG   0.011   0.001   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03815 (  616)
  hydrogen bonds       : angle       4.72373 ( 1788)
  covalent geometry    : bond        0.00293 (13873)
  covalent geometry    : angle       0.65186 (18808)

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

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

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3334 Ramachandran restraints generated.
    1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.2577 (mmm) cc_final: 0.2274 (mmm)
REVERT: A  546 LEU cc_start: 0.7396 (mt) cc_final: 0.7190 (mt)
REVERT: A  882 MET cc_start: 0.4678 (tpp) cc_final: 0.4069 (tpp)
REVERT: A 1071 MET cc_start: -0.2472 (tpt) cc_final: -0.4281 (mmt)
REVERT: A 1137 MET cc_start: 0.0625 (mmm) cc_final: -0.0003 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2971
  time to fit residues: 70.7502
Evaluate side-chains
  113 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 154 optimal weight:    7.9990
   chunk 123 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   chunk 140 optimal weight:    0.9990
   chunk 125 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0050
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
A1062 ASN
A1096 HIS
A1668 ASN
** A1670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2054 HIS
** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.175748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.157915 restraints weight = 42107.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.157607 restraints weight = 51673.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.159049 restraints weight = 44197.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.4708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5235
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13873  Z= 0.138
  Angle     :  0.658   9.430  18808  Z= 0.331
  Chirality :  0.043   0.169   2097
  Planarity :  0.005   0.065   2447
  Dihedral  :  4.984  27.422   1855
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.66 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.20), residues: 1667
  helix:  0.31 (0.18), residues: 801
  sheet: -0.70 (0.41), residues: 156
  loop : -0.78 (0.24), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A1252 
 HIS   0.007   0.001   HIS A1670 
 PHE   0.024   0.001   PHE A1552 
 TYR   0.019   0.001   TYR A2028 
 ARG   0.009   0.001   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03869 (  616)
  hydrogen bonds       : angle       4.75108 ( 1788)
  covalent geometry    : bond        0.00312 (13873)
  covalent geometry    : angle       0.65826 (18808)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4174.07 seconds
wall clock time: 73 minutes 28.32 seconds (4408.32 seconds total)