Starting phenix.real_space_refine
on Thu Jul  2 17:20:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oe9_70391/07_2026/9oe9_70391.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oe9_70391/07_2026/9oe9_70391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oe9_70391/07_2026/9oe9_70391.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oe9_70391/07_2026/9oe9_70391.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oe9_70391/07_2026/9oe9_70391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oe9_70391/07_2026/9oe9_70391.map"
  }
  resolution = 4.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      49      5.16       5
     C    5754      2.51       5
     N    1528      2.21       5
     O    1674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9013
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1155, 8949
          Classifications: {'peptide': 1155}
          Link IDs: {'PTRANS': 27, 'TRANS': 1127}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 64
          Unusual residues: {' MG': 2, 'AGS': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.64, per 1000 atoms: 0.18
  Number of scatterers: 9013
  At special positions: 0
  Unit cell: (71.38, 124.5, 134.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      49     16.00
     P       6     15.00
     Mg      2     11.99
     O    1674      8.00
     N    1528      7.00
     C    5754      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: 0.57
  Conformation dependent library (CDL) restraints added in 227.3 milliseconds
  

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 5 sheets defined
      70.2% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 49 through 83
      removed outlier: 4.075A  pdb=" N   LEU A  70 " --> pdb=" O   ASN A  66 " (cutoff:3.500A)
      Proline residue:  A  71  - end of helix
      removed outlier: 4.380A  pdb=" N   VAL A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 162
    Processing helix  chain 'A' and resid 164 through 171
    Processing helix  chain 'A' and resid 172 through 193
      removed outlier: 4.905A  pdb=" N   VAL A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   TYR A 185 " --> pdb=" O   THR A 181 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ASP A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 216
    Processing helix  chain 'A' and resid 217 through 227
    Processing helix  chain 'A' and resid 228 through 232
    Processing helix  chain 'A' and resid 236 through 242
    Processing helix  chain 'A' and resid 246 through 265
      removed outlier: 4.950A  pdb=" N   VAL A 258 " --> pdb=" O   LYS A 254 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ALA A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 273
      removed outlier: 3.672A  pdb=" N   VAL A 269 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 325
    Processing helix  chain 'A' and resid 332 through 352
      removed outlier: 3.539A  pdb=" N   LEU A 336 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 337 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 376
      removed outlier: 3.627A  pdb=" N   HIS A 376 " --> pdb=" O   GLN A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 462 through 466
    Processing helix  chain 'A' and resid 467 through 474
      removed outlier: 3.694A  pdb=" N   LEU A 474 " --> pdb=" O   GLY A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 495
    Processing helix  chain 'A' and resid 501 through 512
      removed outlier: 3.579A  pdb=" N   ALA A 512 " --> pdb=" O   ALA A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 553
      removed outlier: 3.537A  pdb=" N   LYS A 541 " --> pdb=" O   SER A 537 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLN A 542 " --> pdb=" O   GLY A 538 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ARG A 543 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG A 552 " --> pdb=" O   ARG A 548 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASN A 553 " --> pdb=" O   ALA A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 582
    Processing helix  chain 'A' and resid 593 through 599
      removed outlier: 3.550A  pdb=" N   ILE A 597 " --> pdb=" O   ARG A 593 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ASN A 599 " --> pdb=" O   SER A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 624
    Processing helix  chain 'A' and resid 625 through 638
    Processing helix  chain 'A' and resid 695 through 704
      removed outlier: 3.603A  pdb=" N   VAL A 699 " --> pdb=" O   SER A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 740
      Proline residue:  A 725  - end of helix
    Processing helix  chain 'A' and resid 742 through 795
    Processing helix  chain 'A' and resid 798 through 803
    Processing helix  chain 'A' and resid 804 through 807
    Processing helix  chain 'A' and resid 808 through 852
      removed outlier: 3.672A  pdb=" N   ASP A 819 " --> pdb=" O   ARG A 815 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   THR A 820 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ALA A 821 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   GLY A 828 " --> pdb=" O   GLN A 824 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A 829 " --> pdb=" O   GLY A 825 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ARG A 830 " --> pdb=" O   ALA A 826 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   LEU A 831 " --> pdb=" O   THR A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 901
      removed outlier: 3.688A  pdb=" N   LEU A 857 " --> pdb=" O   TRP A 853 " (cutoff:3.500A)
      Proline residue:  A 864  - end of helix
      removed outlier: 4.174A  pdb=" N   GLN A 890 " --> pdb=" O   LYS A 886 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ALA A 891 " --> pdb=" O   GLU A 887 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ILE A 894 " --> pdb=" O   GLN A 890 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ALA A 895 " --> pdb=" O   ALA A 891 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN A 901 " --> pdb=" O   GLU A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 909
      removed outlier: 3.517A  pdb=" N   VAL A 905 " --> pdb=" O   ASN A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 964
      removed outlier: 3.560A  pdb=" N   GLU A 915 " --> pdb=" O   GLU A 911 " (cutoff:3.500A)
      Proline residue:  A 925  - end of helix
      removed outlier: 3.778A  pdb=" N   LYS A 931 " --> pdb=" O   LYS A 927 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 992
      removed outlier: 3.521A  pdb=" N   PHE A 992 " --> pdb=" O   GLU A 988 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1012
      removed outlier: 4.269A  pdb=" N   TYR A 996 " --> pdb=" O   PHE A 992 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ALA A 997 " --> pdb=" O   THR A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1082
      removed outlier: 3.860A  pdb=" N   GLU A1082 " --> pdb=" O   ILE A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1103 through 1110
    Processing helix  chain 'A' and resid 1124 through 1129
    Processing helix  chain 'A' and resid 1130 through 1133
    Processing helix  chain 'A' and resid 1139 through 1150
      removed outlier: 3.810A  pdb=" N   ILE A1143 " --> pdb=" O   ASP A1139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1158
    Processing helix  chain 'A' and resid 1175 through 1189
      removed outlier: 4.662A  pdb=" N   ARG A1181 " --> pdb=" O   GLY A1177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1205 through 1221
      removed outlier: 3.528A  pdb=" N   LYS A1221 " --> pdb=" O   ASP A1217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1231 through 1236
      removed outlier: 3.631A  pdb=" N   ILE A1235 " --> pdb=" O   ARG A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1254 through 1261
    Processing helix  chain 'A' and resid 1262 through 1274
      removed outlier: 3.512A  pdb=" N   TYR A1266 " --> pdb=" O   GLN A1262 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 398
    Processing sheet with id=AA2, first strand: chain 'A' and resid 428 through 430
      removed outlier: 6.008A  pdb=" N   ALA A 429 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 476
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1051 through 1058
      removed outlier: 6.879A  pdb=" N   GLN A1052 " --> pdb=" O   TYR A1039 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   TYR A1039 " --> pdb=" O   GLN A1052 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   LEU A1054 " --> pdb=" O   HIS A1037 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   VAL A1038 " --> pdb=" O   GLN A1089 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLN A1089 " --> pdb=" O   VAL A1038 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1112 through 1114
      removed outlier: 6.323A  pdb=" N   GLY A1112 " --> pdb=" O   LEU A1196 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU A1064 " --> pdb=" O   ILE A1227 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   THR A1063 " --> pdb=" O   CYS A1240 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   ALA A1242 " --> pdb=" O   THR A1063 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   ALA A1065 " --> pdb=" O   ALA A1242 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   VAL A1244 " --> pdb=" O   ALA A1065 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   VAL A1067 " --> pdb=" O   VAL A1244 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU A1251 " --> pdb=" O   VAL A1243 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   GLN A1245 " --> pdb=" O   VAL A1249 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   VAL A1249 " --> pdb=" O   GLN A1245 " (cutoff:3.500A)

    595 hydrogen bonds defined for protein.
    1752 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.23

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.36: 2958
        1.36 -     1.51: 2434
        1.51 -     1.66: 3690
        1.66 -     1.80: 56
        1.80 -     1.95: 31
  Bond restraints: 9169
  Sorted by residual:
  bond pdb=" O3B AGS A1303 "
       pdb=" PB  AGS A1303 "
    ideal  model  delta    sigma   weight residual
    1.673  1.580  0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" O3B AGS A1304 "
       pdb=" PB  AGS A1304 "
    ideal  model  delta    sigma   weight residual
    1.673  1.582  0.091 2.00e-02 2.50e+03 2.07e+01
  bond pdb=" O3A AGS A1303 "
       pdb=" PA  AGS A1303 "
    ideal  model  delta    sigma   weight residual
    1.664  1.581  0.083 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" O3A AGS A1304 "
       pdb=" PA  AGS A1304 "
    ideal  model  delta    sigma   weight residual
    1.664  1.587  0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" O5' AGS A1303 "
       pdb=" PA  AGS A1303 "
    ideal  model  delta    sigma   weight residual
    1.634  1.571  0.063 2.00e-02 2.50e+03 9.91e+00
  ... (remaining 9164 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 11902
        2.22 -     4.43: 388
        4.43 -     6.65: 69
        6.65 -     8.87: 36
        8.87 -    11.09: 10
  Bond angle restraints: 12405
  Sorted by residual:
  angle pdb=" C   THR A1206 "
        pdb=" CA  THR A1206 "
        pdb=" CB  THR A1206 "
      ideal   model   delta    sigma   weight residual
     116.63  109.76    6.87 1.16e+00 7.43e-01 3.51e+01
  angle pdb=" N   GLU A 260 "
        pdb=" CA  GLU A 260 "
        pdb=" CB  GLU A 260 "
      ideal   model   delta    sigma   weight residual
     110.40  118.48   -8.08 1.63e+00 3.76e-01 2.46e+01
  angle pdb=" C   ALA A 568 "
        pdb=" CA  ALA A 568 "
        pdb=" CB  ALA A 568 "
      ideal   model   delta    sigma   weight residual
     115.89  109.92    5.97 1.32e+00 5.74e-01 2.05e+01
  angle pdb=" C   THR A1201 "
        pdb=" N   SER A1202 "
        pdb=" CA  SER A1202 "
      ideal   model   delta    sigma   weight residual
     120.54  126.14   -5.60 1.35e+00 5.49e-01 1.72e+01
  angle pdb=" C   ALA A 259 "
        pdb=" N   GLU A 260 "
        pdb=" CA  GLU A 260 "
      ideal   model   delta    sigma   weight residual
     121.14  113.93    7.21 1.75e+00 3.27e-01 1.70e+01
  ... (remaining 12400 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.90: 5262
       28.90 -    57.80: 210
       57.80 -    86.71: 49
       86.71 -   115.61: 3
      115.61 -   144.51: 4
  Dihedral angle restraints: 5528
    sinusoidal: 2213
      harmonic: 3315
  Sorted by residual:
  dihedral pdb=" CA  THR A 527 "
           pdb=" C   THR A 527 "
           pdb=" N   LEU A 528 "
           pdb=" CA  LEU A 528 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.95   23.05     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  GLU A  37 "
           pdb=" C   GLU A  37 "
           pdb=" N   MET A  38 "
           pdb=" CA  MET A  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.44  -22.56     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" O1A AGS A1303 "
           pdb=" O3A AGS A1303 "
           pdb=" PA  AGS A1303 "
           pdb=" PB  AGS A1303 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.37 -133.12 -144.51     1      3.00e+01 1.11e-03 1.94e+01
  ... (remaining 5525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1057
       0.052 -    0.103: 292
       0.103 -    0.155: 72
       0.155 -    0.206: 11
       0.206 -    0.258: 2
  Chirality restraints: 1434
  Sorted by residual:
  chirality pdb=" C3' AGS A1303 "
            pdb=" C2' AGS A1303 "
            pdb=" C4' AGS A1303 "
            pdb=" O3' AGS A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.37   -2.63    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" C3' AGS A1304 "
            pdb=" C2' AGS A1304 "
            pdb=" C4' AGS A1304 "
            pdb=" O3' AGS A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.37   -2.60    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  VAL A 602 "
            pdb=" CA  VAL A 602 "
            pdb=" CG1 VAL A 602 "
            pdb=" CG2 VAL A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1431 not shown)

  Planarity restraints: 1567
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  70 "   -0.059 5.00e-02 4.00e+02   8.82e-02 1.24e+01
        pdb=" N   PRO A  71 "    0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO A  71 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A  71 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 309 "   -0.028 2.00e-02 2.50e+03   2.53e-02 1.12e+01
        pdb=" CG  PHE A 309 "    0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 309 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 309 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 309 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 309 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 309 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1004 "    0.014 2.00e-02 2.50e+03   2.83e-02 7.99e+00
        pdb=" C   SER A1004 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   SER A1004 "    0.019 2.00e-02 2.50e+03
        pdb=" N   HIS A1005 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1564 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 123
        2.63 -     3.20: 8212
        3.20 -     3.77: 15349
        3.77 -     4.33: 19373
        4.33 -     4.90: 30649
  Nonbonded interactions: 73706
  Sorted by model distance:
  nonbonded pdb="MG    MG A1301 "
            pdb=" O2B AGS A1303 "
     model   vdw
     2.066 2.170
  nonbonded pdb=" OD2 ASP A 560 "
            pdb="MG    MG A1302 "
     model   vdw
     2.113 2.170
  nonbonded pdb=" O   VAL A 823 "
            pdb=" OG1 THR A 827 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER A 455 "
            pdb=" OG  SER A 457 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG  SER A1020 "
            pdb=" OD1 ASP A1022 "
     model   vdw
     2.249 3.040
  ... (remaining 73701 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:             3.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.090
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.093   9169  Z= 0.241
  Angle     :  1.018  11.086  12405  Z= 0.517
  Chirality :  0.052   0.258   1434
  Planarity :  0.006   0.088   1567
  Dihedral  : 17.170 144.512   3400
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.22 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.23), residues: 1149
  helix: -0.04 (0.18), residues: 735
  sheet: -0.09 (0.66), residues: 52
  loop : -2.26 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 364 
 TYR   0.019   0.001   TYR A 252 
 PHE   0.059   0.002   PHE A 309 
 TRP   0.009   0.001   TRP A 141 
 HIS   0.007   0.001   HIS A 880 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00469 /  0.24 ( 9169)
  covalent geometry    : angle       1.01781 /  0.52 (12405)
  hydrogen bonds       : bond        0.13287 /  8.74 (  595)
  hydrogen bonds       : angle       6.17448 /  4.42 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.7660 (tpp) cc_final: 0.6974 (tpp)
REVERT: A   73 MET cc_start: 0.9709 (ppp) cc_final: 0.9478 (ppp)
REVERT: A  197 MET cc_start: 0.9332 (mmm) cc_final: 0.8919 (mmm)
REVERT: A  310 MET cc_start: 0.9585 (mmp) cc_final: 0.9289 (mmm)
REVERT: A  340 PHE cc_start: 0.9670 (t80) cc_final: 0.9375 (t80)
REVERT: A  415 LEU cc_start: 0.9829 (tp) cc_final: 0.9506 (tp)
REVERT: A  536 MET cc_start: 0.7574 (ttt) cc_final: 0.7243 (ttt)
REVERT: A  946 MET cc_start: 0.9473 (mmp) cc_final: 0.9159 (mmm)
REVERT: A 1008 MET cc_start: 0.9780 (ppp) cc_final: 0.9567 (ppp)
REVERT: A 1009 LEU cc_start: 0.9654 (tt) cc_final: 0.9400 (mt)
REVERT: A 1093 MET cc_start: 0.8961 (mmm) cc_final: 0.8183 (tpp)
REVERT: A 1107 LEU cc_start: 0.9727 (tp) cc_final: 0.9459 (pp)
REVERT: A 1180 GLN cc_start: 0.9724 (mm110) cc_final: 0.9417 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0612
  time to fit residues: 7.5730
Evaluate side-chains
  65 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 301 ASN
A 426 GLN
** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 743 GLN
** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1255 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.031457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.023377 restraints weight = 91210.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2568 r_free = 0.2568 target = 0.024390 restraints weight = 53629.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.025087 restraints weight = 37432.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.025582 restraints weight = 29070.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.025929 restraints weight = 24220.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9169  Z= 0.216
  Angle     :  0.642   8.107  12405  Z= 0.348
  Chirality :  0.040   0.145   1434
  Planarity :  0.005   0.073   1567
  Dihedral  : 12.435 138.404   1311
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.01 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.24), residues: 1149
  helix:  1.03 (0.18), residues: 758
  sheet: -0.46 (0.67), residues: 52
  loop : -2.25 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1181 
 TYR   0.015   0.001   TYR A 252 
 PHE   0.041   0.002   PHE A 309 
 TRP   0.011   0.001   TRP A 320 
 HIS   0.004   0.001   HIS A 368 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.22 ( 9169)
  covalent geometry    : angle       0.64194 /  0.35 (12405)
  hydrogen bonds       : bond        0.04778 /  3.17 (  595)
  hydrogen bonds       : angle       4.92241 /  3.60 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8111 (tpp) cc_final: 0.7629 (tpp)
REVERT: A  161 MET cc_start: 0.9492 (tmm) cc_final: 0.9243 (tmm)
REVERT: A  197 MET cc_start: 0.9386 (mmm) cc_final: 0.8958 (mmm)
REVERT: A  310 MET cc_start: 0.9616 (mmp) cc_final: 0.9221 (mmm)
REVERT: A  340 PHE cc_start: 0.9684 (t80) cc_final: 0.9328 (t80)
REVERT: A  415 LEU cc_start: 0.9815 (tp) cc_final: 0.9515 (tp)
REVERT: A  794 MET cc_start: 0.9422 (tpp) cc_final: 0.8807 (tmm)
REVERT: A  946 MET cc_start: 0.9447 (mmp) cc_final: 0.9153 (mmm)
REVERT: A 1008 MET cc_start: 0.9707 (ppp) cc_final: 0.9438 (ppp)
REVERT: A 1009 LEU cc_start: 0.9748 (tt) cc_final: 0.9393 (mt)
REVERT: A 1093 MET cc_start: 0.9300 (mmm) cc_final: 0.9088 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0575
  time to fit residues: 6.4022
Evaluate side-chains
  56 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0970
   chunk 53 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   chunk 69 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 824 GLN
** A1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1255 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.032877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.024696 restraints weight = 86731.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.025727 restraints weight = 51378.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.026464 restraints weight = 35859.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.026993 restraints weight = 27698.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.027377 restraints weight = 22912.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9169  Z= 0.116
  Angle     :  0.581   6.899  12405  Z= 0.302
  Chirality :  0.040   0.152   1434
  Planarity :  0.004   0.066   1567
  Dihedral  : 11.830 142.852   1311
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.96 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.25), residues: 1149
  helix:  1.42 (0.19), residues: 752
  sheet: -0.54 (0.67), residues: 52
  loop : -2.15 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1057 
 TYR   0.014   0.001   TYR A 252 
 PHE   0.029   0.001   PHE A 309 
 TRP   0.009   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 880 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.12 ( 9169)
  covalent geometry    : angle       0.58087 /  0.30 (12405)
  hydrogen bonds       : bond        0.04263 /  2.82 (  595)
  hydrogen bonds       : angle       4.55100 /  3.32 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.9709 (ppp) cc_final: 0.9382 (ppp)
REVERT: A  161 MET cc_start: 0.9564 (tmm) cc_final: 0.9281 (tmm)
REVERT: A  197 MET cc_start: 0.9284 (mmm) cc_final: 0.8800 (mmm)
REVERT: A  310 MET cc_start: 0.9571 (mmp) cc_final: 0.9240 (mmm)
REVERT: A  340 PHE cc_start: 0.9677 (t80) cc_final: 0.9308 (t80)
REVERT: A  415 LEU cc_start: 0.9805 (tp) cc_final: 0.9438 (tp)
REVERT: A  794 MET cc_start: 0.9350 (tpp) cc_final: 0.8866 (tmm)
REVERT: A  946 MET cc_start: 0.9403 (mmp) cc_final: 0.9130 (mmm)
REVERT: A 1107 LEU cc_start: 0.9732 (tp) cc_final: 0.9500 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0564
  time to fit residues: 6.4512
Evaluate side-chains
  58 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0970
   chunk 17 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 69 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 111 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.5982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1005 HIS
** A1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1255 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.032608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.024456 restraints weight = 89504.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.025476 restraints weight = 53276.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.026187 restraints weight = 37482.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.026687 restraints weight = 29211.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.027056 restraints weight = 24453.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9169  Z= 0.135
  Angle     :  0.581   6.458  12405  Z= 0.306
  Chirality :  0.039   0.140   1434
  Planarity :  0.004   0.063   1567
  Dihedral  : 11.556 140.700   1311
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.48 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.45 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.25), residues: 1149
  helix:  1.55 (0.19), residues: 750
  sheet: -0.59 (0.68), residues: 52
  loop : -2.09 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1181 
 TYR   0.013   0.001   TYR A 252 
 PHE   0.028   0.001   PHE A 309 
 TRP   0.005   0.001   TRP A 320 
 HIS   0.004   0.001   HIS A 403 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.14 ( 9169)
  covalent geometry    : angle       0.58064 /  0.31 (12405)
  hydrogen bonds       : bond        0.04104 /  2.71 (  595)
  hydrogen bonds       : angle       4.54935 /  3.35 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.7891 (tpp) cc_final: 0.7313 (tpp)
REVERT: A  161 MET cc_start: 0.9545 (tmm) cc_final: 0.9254 (tmm)
REVERT: A  197 MET cc_start: 0.9278 (mmm) cc_final: 0.8832 (mmm)
REVERT: A  310 MET cc_start: 0.9559 (mmp) cc_final: 0.9245 (mmm)
REVERT: A  340 PHE cc_start: 0.9666 (t80) cc_final: 0.9278 (t80)
REVERT: A  415 LEU cc_start: 0.9792 (tp) cc_final: 0.9480 (tp)
REVERT: A  536 MET cc_start: 0.7511 (ttt) cc_final: 0.7168 (ttt)
REVERT: A  794 MET cc_start: 0.9280 (tpp) cc_final: 0.8766 (tmm)
REVERT: A  802 TYR cc_start: 0.8908 (m-80) cc_final: 0.6973 (m-80)
REVERT: A  946 MET cc_start: 0.9421 (mmp) cc_final: 0.9139 (mmm)
REVERT: A 1180 GLN cc_start: 0.9733 (mm110) cc_final: 0.9327 (mm110)
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0535
  time to fit residues: 5.9806
Evaluate side-chains
  57 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 83 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0980
   chunk 93 optimal weight:    6.9990
   chunk 110 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    3.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 291 ASN
** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1103 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 = 0.2856 r_free = 0.2856 target = 0.031640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.023551 restraints weight = 89556.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.024546 restraints weight = 53630.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.025257 restraints weight = 37816.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.025764 restraints weight = 29324.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.026128 restraints weight = 24412.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9169  Z= 0.201
  Angle     :  0.620   6.749  12405  Z= 0.331
  Chirality :  0.040   0.145   1434
  Planarity :  0.004   0.063   1567
  Dihedral  : 11.537 145.444   1311
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.35 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.25), residues: 1149
  helix:  1.46 (0.19), residues: 759
  sheet: -0.88 (0.67), residues: 54
  loop : -2.04 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 405 
 TYR   0.011   0.001   TYR A 252 
 PHE   0.025   0.002   PHE A 309 
 TRP   0.007   0.001   TRP A 853 
 HIS   0.005   0.001   HIS A1255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.20 ( 9169)
  covalent geometry    : angle       0.62017 /  0.33 (12405)
  hydrogen bonds       : bond        0.04265 /  2.81 (  595)
  hydrogen bonds       : angle       4.66315 /  3.43 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.9741 (ppp) cc_final: 0.9427 (ppp)
REVERT: A  161 MET cc_start: 0.9558 (tmm) cc_final: 0.9253 (tmm)
REVERT: A  197 MET cc_start: 0.9349 (mmm) cc_final: 0.8836 (mmm)
REVERT: A  310 MET cc_start: 0.9560 (mmp) cc_final: 0.9263 (mmp)
REVERT: A  340 PHE cc_start: 0.9691 (t80) cc_final: 0.9249 (t80)
REVERT: A  536 MET cc_start: 0.7764 (ttt) cc_final: 0.7048 (ttt)
REVERT: A  794 MET cc_start: 0.9129 (tpp) cc_final: 0.8653 (tmm)
REVERT: A  802 TYR cc_start: 0.8687 (m-80) cc_final: 0.7174 (m-80)
REVERT: A  946 MET cc_start: 0.9429 (mmp) cc_final: 0.9136 (mmm)
REVERT: A 1180 GLN cc_start: 0.9721 (mm110) cc_final: 0.9345 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0529
  time to fit residues: 5.8643
Evaluate side-chains
  55 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 57 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 70 optimal weight:    9.9990
   chunk 100 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 ASN
** A1103 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 = 0.2886 r_free = 0.2886 target = 0.032622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.024418 restraints weight = 87981.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.025440 restraints weight = 52444.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.026148 restraints weight = 37114.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.026653 restraints weight = 28857.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.027027 restraints weight = 24151.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9169  Z= 0.125
  Angle     :  0.601   8.383  12405  Z= 0.310
  Chirality :  0.040   0.158   1434
  Planarity :  0.004   0.061   1567
  Dihedral  : 11.416 141.999   1311
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.31 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.25), residues: 1149
  helix:  1.55 (0.19), residues: 758
  sheet: -0.71 (0.69), residues: 54
  loop : -2.01 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 364 
 TYR   0.014   0.001   TYR A 704 
 PHE   0.022   0.001   PHE A 448 
 TRP   0.007   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 880 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.12 ( 9169)
  covalent geometry    : angle       0.60105 /  0.31 (12405)
  hydrogen bonds       : bond        0.04089 /  2.69 (  595)
  hydrogen bonds       : angle       4.51523 /  3.31 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.9608 (tmm) cc_final: 0.9197 (tmm)
REVERT: A  197 MET cc_start: 0.9281 (mmm) cc_final: 0.9031 (mmm)
REVERT: A  310 MET cc_start: 0.9564 (mmp) cc_final: 0.9269 (mmp)
REVERT: A  340 PHE cc_start: 0.9665 (t80) cc_final: 0.9302 (t80)
REVERT: A  415 LEU cc_start: 0.9765 (tp) cc_final: 0.9436 (tp)
REVERT: A  794 MET cc_start: 0.9078 (tpp) cc_final: 0.8659 (tmm)
REVERT: A  795 MET cc_start: 0.9307 (tpp) cc_final: 0.8896 (tmm)
REVERT: A  802 TYR cc_start: 0.8524 (m-80) cc_final: 0.6958 (m-80)
REVERT: A  946 MET cc_start: 0.9410 (mmp) cc_final: 0.9126 (mmm)
REVERT: A 1180 GLN cc_start: 0.9732 (mm110) cc_final: 0.9346 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0532
  time to fit residues: 6.0973
Evaluate side-chains
  57 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 108 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 40 optimal weight:    9.9990
   chunk 96 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   chunk 35 optimal weight:    9.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 291 ASN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.033439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.025113 restraints weight = 86936.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.026125 restraints weight = 53403.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.026856 restraints weight = 38047.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.027367 restraints weight = 29723.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.027748 restraints weight = 24822.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9169  Z= 0.115
  Angle     :  0.598   8.026  12405  Z= 0.307
  Chirality :  0.040   0.138   1434
  Planarity :  0.004   0.062   1567
  Dihedral  : 11.298 141.229   1311
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.57 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.25), residues: 1149
  helix:  1.61 (0.19), residues: 752
  sheet: -0.37 (0.70), residues: 52
  loop : -1.98 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 543 
 TYR   0.012   0.001   TYR A 252 
 PHE   0.049   0.001   PHE A 309 
 TRP   0.008   0.001   TRP A 167 
 HIS   0.003   0.001   HIS A 880 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.12 ( 9169)
  covalent geometry    : angle       0.59807 /  0.31 (12405)
  hydrogen bonds       : bond        0.04030 /  2.67 (  595)
  hydrogen bonds       : angle       4.41682 /  3.24 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.9729 (ppp) cc_final: 0.9366 (ppp)
REVERT: A  197 MET cc_start: 0.9225 (mmm) cc_final: 0.8980 (mmm)
REVERT: A  310 MET cc_start: 0.9538 (mmp) cc_final: 0.9336 (mmm)
REVERT: A  340 PHE cc_start: 0.9646 (t80) cc_final: 0.9282 (t80)
REVERT: A  415 LEU cc_start: 0.9776 (tp) cc_final: 0.9455 (tp)
REVERT: A  780 GLU cc_start: 0.9539 (tp30) cc_final: 0.9048 (tp30)
REVERT: A  794 MET cc_start: 0.8974 (tpp) cc_final: 0.8589 (tmm)
REVERT: A  795 MET cc_start: 0.9281 (tpp) cc_final: 0.8943 (tmm)
REVERT: A  802 TYR cc_start: 0.8344 (m-80) cc_final: 0.6748 (m-80)
REVERT: A  946 MET cc_start: 0.9367 (mmp) cc_final: 0.9112 (mmm)
REVERT: A 1180 GLN cc_start: 0.9740 (mm110) cc_final: 0.9330 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0550
  time to fit residues: 6.5441
Evaluate side-chains
  57 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 50 optimal weight:    0.5980
   chunk 64 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 113 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 76 optimal weight:    7.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.033300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.024949 restraints weight = 87333.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.025969 restraints weight = 53290.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.026694 restraints weight = 37978.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.027209 restraints weight = 29604.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.027595 restraints weight = 24667.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9169  Z= 0.120
  Angle     :  0.601   6.793  12405  Z= 0.308
  Chirality :  0.040   0.175   1434
  Planarity :  0.004   0.061   1567
  Dihedral  : 11.237 142.588   1311
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.13 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.25), residues: 1149
  helix:  1.62 (0.19), residues: 759
  sheet: -0.34 (0.70), residues: 52
  loop : -1.96 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 364 
 TYR   0.011   0.001   TYR A 252 
 PHE   0.056   0.001   PHE A 309 
 TRP   0.005   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 368 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.12 ( 9169)
  covalent geometry    : angle       0.60117 /  0.31 (12405)
  hydrogen bonds       : bond        0.03912 /  2.58 (  595)
  hydrogen bonds       : angle       4.37181 /  3.19 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.9727 (ppp) cc_final: 0.9378 (ppp)
REVERT: A  197 MET cc_start: 0.9221 (mmm) cc_final: 0.8988 (mmm)
REVERT: A  310 MET cc_start: 0.9588 (mmp) cc_final: 0.9303 (mmm)
REVERT: A  340 PHE cc_start: 0.9663 (t80) cc_final: 0.9304 (t80)
REVERT: A  418 MET cc_start: 0.9274 (tpt) cc_final: 0.9063 (tpp)
REVERT: A  536 MET cc_start: 0.7972 (ttt) cc_final: 0.7761 (ttt)
REVERT: A  794 MET cc_start: 0.9025 (tpp) cc_final: 0.8601 (tmm)
REVERT: A  795 MET cc_start: 0.9281 (tpp) cc_final: 0.8992 (tmm)
REVERT: A  802 TYR cc_start: 0.8363 (m-80) cc_final: 0.6813 (m-80)
REVERT: A  946 MET cc_start: 0.9376 (mmp) cc_final: 0.9114 (mmm)
REVERT: A 1180 GLN cc_start: 0.9756 (mm110) cc_final: 0.9347 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0543
  time to fit residues: 6.0930
Evaluate side-chains
  57 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 111 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0870
   overall best weight:    1.1964

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 426 GLN
A 492 ASN
** A1103 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 = 0.2916 r_free = 0.2916 target = 0.033363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.024981 restraints weight = 87496.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.026009 restraints weight = 53498.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.026752 restraints weight = 37911.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.027269 restraints weight = 29521.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.027654 restraints weight = 24574.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9169  Z= 0.122
  Angle     :  0.612   8.325  12405  Z= 0.314
  Chirality :  0.040   0.159   1434
  Planarity :  0.004   0.061   1567
  Dihedral  : 11.175 142.574   1311
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.05 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.42 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.25), residues: 1149
  helix:  1.64 (0.19), residues: 759
  sheet: -0.26 (0.71), residues: 52
  loop : -1.93 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 543 
 TYR   0.013   0.001   TYR A 704 
 PHE   0.051   0.001   PHE A 309 
 TRP   0.005   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 368 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 ( 9169)
  covalent geometry    : angle       0.61194 /  0.31 (12405)
  hydrogen bonds       : bond        0.03897 /  2.56 (  595)
  hydrogen bonds       : angle       4.44645 /  3.24 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.9721 (ppp) cc_final: 0.9407 (ppp)
REVERT: A  310 MET cc_start: 0.9604 (mmp) cc_final: 0.9304 (mmm)
REVERT: A  340 PHE cc_start: 0.9658 (t80) cc_final: 0.9286 (t80)
REVERT: A  418 MET cc_start: 0.9306 (tpt) cc_final: 0.9088 (tpp)
REVERT: A  795 MET cc_start: 0.9254 (tpp) cc_final: 0.8697 (tmm)
REVERT: A  946 MET cc_start: 0.9363 (mmp) cc_final: 0.9101 (mmm)
REVERT: A 1180 GLN cc_start: 0.9758 (mm110) cc_final: 0.9335 (mm110)
  outliers start: 1
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0595
  time to fit residues: 6.9254
Evaluate side-chains
  56 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 103 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.032473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.024292 restraints weight = 89554.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.025265 restraints weight = 55258.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.025950 restraints weight = 39647.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.026453 restraints weight = 31227.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026794 restraints weight = 26180.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9169  Z= 0.163
  Angle     :  0.639   8.139  12405  Z= 0.332
  Chirality :  0.040   0.164   1434
  Planarity :  0.004   0.060   1567
  Dihedral  : 11.184 148.351   1311
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.57 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.25), residues: 1149
  helix:  1.60 (0.19), residues: 762
  sheet: -0.43 (0.70), residues: 54
  loop : -1.85 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 364 
 TYR   0.014   0.001   TYR A 704 
 PHE   0.049   0.002   PHE A 309 
 TRP   0.009   0.001   TRP A 853 
 HIS   0.004   0.001   HIS A 368 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.16 ( 9169)
  covalent geometry    : angle       0.63864 /  0.33 (12405)
  hydrogen bonds       : bond        0.03994 /  2.62 (  595)
  hydrogen bonds       : angle       4.55142 /  3.32 ( 1752)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.9258 (mmm) cc_final: 0.8769 (mmm)
REVERT: A  310 MET cc_start: 0.9623 (mmp) cc_final: 0.9302 (mmm)
REVERT: A  340 PHE cc_start: 0.9661 (t80) cc_final: 0.9337 (t80)
REVERT: A  418 MET cc_start: 0.9287 (tpt) cc_final: 0.9051 (tpp)
REVERT: A  536 MET cc_start: 0.7823 (ttt) cc_final: 0.7379 (tmm)
REVERT: A  780 GLU cc_start: 0.9545 (tp30) cc_final: 0.9065 (tp30)
REVERT: A  794 MET cc_start: 0.9315 (tpp) cc_final: 0.8592 (tpp)
REVERT: A  795 MET cc_start: 0.9172 (tpp) cc_final: 0.8720 (tmm)
REVERT: A  802 TYR cc_start: 0.8637 (m-80) cc_final: 0.7626 (m-80)
REVERT: A  946 MET cc_start: 0.9386 (mmp) cc_final: 0.9114 (mmm)
REVERT: A 1180 GLN cc_start: 0.9731 (mm110) cc_final: 0.9326 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0600
  time to fit residues: 6.7020
Evaluate side-chains
  59 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 99 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 575 GLN
** A1103 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 = 0.2884 r_free = 0.2884 target = 0.032402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.024341 restraints weight = 88550.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.025290 restraints weight = 54363.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.025987 restraints weight = 39206.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.026478 restraints weight = 30777.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.026849 restraints weight = 25781.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9169  Z= 0.156
  Angle     :  0.633   7.798  12405  Z= 0.329
  Chirality :  0.041   0.155   1434
  Planarity :  0.004   0.061   1567
  Dihedral  : 11.128 151.760   1311
  Min Nonbonded Distance : 1.814

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.22 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.25), residues: 1149
  helix:  1.54 (0.18), residues: 763
  sheet: -0.35 (0.71), residues: 54
  loop : -1.79 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 543 
 TYR   0.013   0.001   TYR A 704 
 PHE   0.048   0.002   PHE A 309 
 TRP   0.011   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 368 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.16 ( 9169)
  covalent geometry    : angle       0.63343 /  0.33 (12405)
  hydrogen bonds       : bond        0.04048 /  2.65 (  595)
  hydrogen bonds       : angle       4.56591 /  3.34 ( 1752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1171.71 seconds
wall clock time: 21 minutes 6.89 seconds (1266.89 seconds total)