Starting phenix.real_space_refine
on Wed Mar  4 01:15:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pde_13335/03_2026/7pde_13335.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pde_13335/03_2026/7pde_13335.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pde_13335/03_2026/7pde_13335.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pde_13335/03_2026/7pde_13335.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pde_13335/03_2026/7pde_13335.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pde_13335/03_2026/7pde_13335.map"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 81 atoms to isotropic.
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       3      5.49       5
     Mg      1      5.21       5
     S      69      5.16       5
     C    6144      2.51       5
     N    1604      2.21       5
     O    1732      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9553
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 846, 6711
          Classifications: {'peptide': 846}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 20, 'TRANS': 825}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2809
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 13, 'TRANS': 327}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GSP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.88, per 1000 atoms: 0.20
  Number of scatterers: 9553
  At special positions: 0
  Unit cell: (166.05, 103.68, 115.02, 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      69     16.00
     P       3     15.00
     Mg      1     11.99
     O    1732      8.00
     N    1604      7.00
     C    6144      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: 0.76
  Conformation dependent library (CDL) restraints added in 309.7 milliseconds
  

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2246

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 5 sheets defined
      62.0% alpha, 9.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 137
      removed outlier: 3.552A  pdb=" N   MET A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
      removed outlier: 3.896A  pdb=" N   HIS A 137 " --> pdb=" O   TYR A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 163
    Processing helix  chain 'A' and resid 171 through 193
      removed outlier: 4.528A  pdb=" N   GLN A 193 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 238
      removed outlier: 4.309A  pdb=" N   SER A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 261
    Processing helix  chain 'A' and resid 279 through 336
      removed outlier: 4.254A  pdb=" N   VAL A 325 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 347
    Processing helix  chain 'A' and resid 354 through 358
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 413 through 434
      removed outlier: 3.850A  pdb=" N   GLU A 432 " --> pdb=" O   ARG A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 480
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 3.549A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 782 through 808
    Processing helix  chain 'A' and resid 817 through 843
      removed outlier: 3.972A  pdb=" N   LEU A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 858
    Processing helix  chain 'A' and resid 862 through 881
      Proline residue:  A 876  - end of helix
    Processing helix  chain 'A' and resid 882 through 884
      No H-bonds generated for 'chain 'A' and resid 882 through 884'
    Processing helix  chain 'A' and resid 891 through 907
    Processing helix  chain 'A' and resid 908 through 912
      removed outlier: 3.847A  pdb=" N   PHE A 912 " --> pdb=" O   TYR A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 936
      Proline residue:  A 931  - end of helix
    Processing helix  chain 'A' and resid 977 through 1037
      removed outlier: 3.564A  pdb=" N   GLN A 981 " --> pdb=" O   SER A 977 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1048
    Processing helix  chain 'A' and resid 1067 through 1072
    Processing helix  chain 'A' and resid 1079 through 1098
      removed outlier: 3.797A  pdb=" N   TYR A1083 " --> pdb=" O   GLY A1079 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LEU A1096 " --> pdb=" O   ASP A1092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1100 through 1105
      removed outlier: 3.561A  pdb=" N   SER A1104 " --> pdb=" O   ASP A1101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1134 through 1156
      removed outlier: 3.967A  pdb=" N   ASP A1151 " --> pdb=" O   MET A1147 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASP A1152 " --> pdb=" O   ARG A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1189 through 1200
      removed outlier: 3.718A  pdb=" N   ASN A1193 " --> pdb=" O   GLY A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1211 through 1220
      removed outlier: 3.503A  pdb=" N   VAL A1216 " --> pdb=" O   GLU A1212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 39
    Processing helix  chain 'B' and resid 52 through 65
    Processing helix  chain 'B' and resid 89 through 111
      removed outlier: 4.111A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LYS B  96 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL B 107 " --> pdb=" O   ILE B 103 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 123
      No H-bonds generated for 'chain 'B' and resid 121 through 123'
    Processing helix  chain 'B' and resid 124 through 134
    Processing helix  chain 'B' and resid 143 through 156
    Processing helix  chain 'B' and resid 156 through 165
      removed outlier: 3.534A  pdb=" N   ARG B 165 " --> pdb=" O   ALA B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 169
    Processing helix  chain 'B' and resid 174 through 182
      removed outlier: 3.509A  pdb=" N   ASP B 180 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 199
    Processing helix  chain 'B' and resid 228 through 238
      removed outlier: 3.898A  pdb=" N   TRP B 234 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   ILE B 235 " --> pdb=" O   ARG B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 278
    Processing helix  chain 'B' and resid 293 through 304
    Processing helix  chain 'B' and resid 307 through 312
    Processing helix  chain 'B' and resid 313 through 316
    Processing helix  chain 'B' and resid 331 through 351
      removed outlier: 4.104A  pdb=" N   ILE B 348 " --> pdb=" O   GLU B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 388
      removed outlier: 4.389A  pdb=" N   LEU B 388 " --> pdb=" O   GLN B 384 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 439
      removed outlier: 7.291A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   SER A 394 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   GLY A 493 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   SER A 394 " --> pdb=" O   HIS A 491 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   HIS A 491 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   LEU A 396 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   GLY A 489 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ALA A 398 " --> pdb=" O   ARG A 487 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ARG A 487 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 531
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1106 through 1111
      removed outlier: 4.821A  pdb=" N   LYS A1107 " --> pdb=" O   ALA A1118 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA A1118 " --> pdb=" O   LYS A1107 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   HIS A1170 " --> pdb=" O   SER A1210 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLY A1228 " --> pdb=" O   THR A1240 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 213
      removed outlier: 6.036A  pdb=" N   HIS B  41 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   PHE B 222 " --> pdb=" O   HIS B  41 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   LEU B  43 " --> pdb=" O   PHE B 222 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   ALA B 243 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ARG B  42 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ILE B 245 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   LEU B  44 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   VAL B 247 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   LEU B  46 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   ALA B 249 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   ILE B 244 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   PHE B 290 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   PHE B 246 " --> pdb=" O   PHE B 290 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   ASN B 292 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL B 248 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)

    583 hydrogen bonds defined for protein.
    1686 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: 1.47

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3055
        1.34 -     1.46: 2250
        1.46 -     1.58: 4343
        1.58 -     1.69: 5
        1.69 -     1.81: 106
  Bond restraints: 9759
  Sorted by residual:
  bond pdb=" C   HIS A 239 "
       pdb=" N   LEU A 240 "
    ideal  model  delta    sigma   weight residual
    1.331  1.238  0.093 2.07e-02 2.33e+03 2.03e+01
  bond pdb=" CA  TYR A 909 "
       pdb=" C   TYR A 909 "
    ideal  model  delta    sigma   weight residual
    1.522  1.476  0.046 1.45e-02 4.76e+03 9.97e+00
  bond pdb=" CA  LEU B  43 "
       pdb=" CB  LEU B  43 "
    ideal  model  delta    sigma   weight residual
    1.526  1.503  0.024 1.53e-02 4.27e+03 2.39e+00
  bond pdb=" CA  GLY A1167 "
       pdb=" C   GLY A1167 "
    ideal  model  delta    sigma   weight residual
    1.520  1.509  0.011 7.30e-03 1.88e+04 2.29e+00
  bond pdb=" CB  PHE A1001 "
       pdb=" CG  PHE A1001 "
    ideal  model  delta    sigma   weight residual
    1.502  1.467  0.035 2.30e-02 1.89e+03 2.27e+00
  ... (remaining 9754 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 13016
        2.47 -     4.95: 166
        4.95 -     7.42: 17
        7.42 -     9.90: 2
        9.90 -    12.37: 3
  Bond angle restraints: 13204
  Sorted by residual:
  angle pdb=" N   VAL A 337 "
        pdb=" CA  VAL A 337 "
        pdb=" C   VAL A 337 "
      ideal   model   delta    sigma   weight residual
     113.71  109.46    4.25 9.50e-01 1.11e+00 2.00e+01
  angle pdb=" N   VAL B 134 "
        pdb=" CA  VAL B 134 "
        pdb=" C   VAL B 134 "
      ideal   model   delta    sigma   weight residual
     111.91  107.99    3.92 8.90e-01 1.26e+00 1.94e+01
  angle pdb=" C   SER A1130 "
        pdb=" N   HIS A1131 "
        pdb=" CA  HIS A1131 "
      ideal   model   delta    sigma   weight residual
     120.65  114.79    5.86 1.36e+00 5.41e-01 1.86e+01
  angle pdb=" C   THR A 196 "
        pdb=" N   PRO A 197 "
        pdb=" CD  PRO A 197 "
      ideal   model   delta    sigma   weight residual
     125.00  137.37  -12.37 4.10e+00 5.95e-02 9.11e+00
  angle pdb=" N   VAL B 367 "
        pdb=" CA  VAL B 367 "
        pdb=" C   VAL B 367 "
      ideal   model   delta    sigma   weight residual
     112.98  109.41    3.57 1.25e+00 6.40e-01 8.17e+00
  ... (remaining 13199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 5132
       17.52 -    35.03: 547
       35.03 -    52.55: 99
       52.55 -    70.07: 10
       70.07 -    87.58: 12
  Dihedral angle restraints: 5800
    sinusoidal: 2329
      harmonic: 3471
  Sorted by residual:
  dihedral pdb=" CA  VAL B 114 "
           pdb=" C   VAL B 114 "
           pdb=" N   PRO B 115 "
           pdb=" CA  PRO B 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.28   26.72     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  CYS A 910 "
           pdb=" C   CYS A 910 "
           pdb=" N   ASN A 911 "
           pdb=" CA  ASN A 911 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.27  -19.73     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  THR A 236 "
           pdb=" C   THR A 236 "
           pdb=" N   VAL A 237 "
           pdb=" CA  VAL A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.66  -19.34     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 5797 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 880
       0.033 -    0.067: 424
       0.067 -    0.100: 146
       0.100 -    0.133: 33
       0.133 -    0.166: 5
  Chirality restraints: 1488
  Sorted by residual:
  chirality pdb=" CA  ASP B 215 "
            pdb=" N   ASP B 215 "
            pdb=" C   ASP B 215 "
            pdb=" CB  ASP B 215 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" C3' GSP B 501 "
            pdb=" C2' GSP B 501 "
            pdb=" C4' GSP B 501 "
            pdb=" O3' GSP B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.63    0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CA  HIS B  64 "
            pdb=" N   HIS B  64 "
            pdb=" C   HIS B  64 "
            pdb=" CB  HIS B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.68e-01
  ... (remaining 1485 not shown)

  Planarity restraints: 1660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1037 "   -0.031 5.00e-02 4.00e+02   4.72e-02 3.57e+00
        pdb=" N   PRO A1038 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A1038 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A1038 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 993 "    0.009 2.00e-02 2.50e+03   1.80e-02 3.23e+00
        pdb=" C   LEU A 993 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   LEU A 993 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A 994 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 815 "    0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO A 816 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 816 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 816 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1657 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 152
        2.47 -     3.08: 8059
        3.08 -     3.69: 16539
        3.69 -     4.29: 23342
        4.29 -     4.90: 34643
  Nonbonded interactions: 82735
  Sorted by model distance:
  nonbonded pdb=" O2B GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     1.869 2.170
  nonbonded pdb=" O3G GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     2.027 2.170
  nonbonded pdb=" O   ALA A 412 "
            pdb=" OG  SER A1052 "
     model   vdw
     2.097 3.040
  nonbonded pdb=" OG  SER B  54 "
            pdb=" OG1 THR B 204 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" O   ARG A 503 "
            pdb=" NZ  LYS A1107 "
     model   vdw
     2.131 3.120
  ... (remaining 82730 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:             2.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.480
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
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      :  0.006   0.093   9759  Z= 0.300
  Angle     :  0.788  12.375  13204  Z= 0.459
  Chirality :  0.043   0.166   1488
  Planarity :  0.004   0.047   1660
  Dihedral  : 14.841  87.582   3554
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 29.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  8.45 %
    Favored  : 91.35 %
  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: -3.63 (0.21), residues: 1169
  helix: -2.14 (0.16), residues: 669
  sheet: -2.59 (0.38), residues: 126
  loop : -2.43 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 305 
 TYR   0.018   0.002   TYR A 445 
 PHE   0.023   0.002   PHE A 232 
 TRP   0.011   0.002   TRP A 130 
 HIS   0.008   0.002   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 9759)
  covalent geometry    : angle       0.78846 (13204)
  hydrogen bonds       : bond        0.15687 (  583)
  hydrogen bonds       : angle       6.86279 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 154
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 TRP cc_start: 0.8591 (m100) cc_final: 0.8330 (m100)
REVERT: A  229 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8525 (mt-10)
REVERT: A  288 HIS cc_start: 0.9197 (m90) cc_final: 0.8955 (m90)
REVERT: A  338 MET cc_start: 0.9000 (mtp) cc_final: 0.8622 (ttm)
REVERT: A  502 MET cc_start: 0.8407 (mmm) cc_final: 0.8130 (mmm)
REVERT: A  840 ARG cc_start: 0.5571 (mtt-85) cc_final: 0.4866 (ttp80)
REVERT: A  849 MET cc_start: 0.8664 (ttt) cc_final: 0.8104 (tpp)
REVERT: A  991 LEU cc_start: 0.9797 (mm) cc_final: 0.9513 (tt)
REVERT: A 1002 GLU cc_start: 0.9194 (tp30) cc_final: 0.8814 (mt-10)
REVERT: A 1022 ILE cc_start: 0.8276 (tp) cc_final: 0.7769 (tp)
REVERT: A 1146 MET cc_start: 0.9504 (ptm) cc_final: 0.9187 (ppp)
REVERT: A 1147 MET cc_start: 0.9401 (tpp) cc_final: 0.9170 (tpp)
REVERT: B   65 VAL cc_start: 0.8254 (t) cc_final: 0.7620 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0933
  time to fit residues: 20.0854
Evaluate side-chains
  118 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   30.0000
   chunk 117 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 HIS
A 315 GLN
A1040 HIS
A1075 ASN
A1156 ASN
A1237 GLN
** B  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 ASN
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 267 GLN
B 271 ASN
B 362 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.053267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.042955 restraints weight = 76590.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.044256 restraints weight = 47207.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.045132 restraints weight = 33781.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.045666 restraints weight = 26705.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.046220 restraints weight = 22766.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9759  Z= 0.164
  Angle     :  0.684  12.024  13204  Z= 0.351
  Chirality :  0.042   0.175   1488
  Planarity :  0.004   0.058   1660
  Dihedral  :  5.197  48.837   1302
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 16.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  5.28 %
    Favored  : 94.62 %
  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: -1.57 (0.23), residues: 1169
  helix: -0.39 (0.18), residues: 693
  sheet: -1.95 (0.40), residues: 123
  loop : -1.74 (0.36), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 999 
 TYR   0.020   0.002   TYR A 252 
 PHE   0.024   0.002   PHE A 121 
 TRP   0.009   0.001   TRP A 130 
 HIS   0.009   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9759)
  covalent geometry    : angle       0.68406 (13204)
  hydrogen bonds       : bond        0.05031 (  583)
  hydrogen bonds       : angle       5.23302 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 TRP cc_start: 0.8368 (m100) cc_final: 0.8076 (m100)
REVERT: A  224 PHE cc_start: 0.9664 (t80) cc_final: 0.9296 (t80)
REVERT: A  228 ILE cc_start: 0.9708 (mm) cc_final: 0.9485 (mm)
REVERT: A  238 MET cc_start: 0.8624 (mmp) cc_final: 0.8411 (mmm)
REVERT: A  256 PHE cc_start: 0.8720 (t80) cc_final: 0.8389 (t80)
REVERT: A  318 MET cc_start: 0.8976 (tmm) cc_final: 0.8627 (tmm)
REVERT: A  338 MET cc_start: 0.9114 (mtp) cc_final: 0.8655 (ttm)
REVERT: A  469 MET cc_start: 0.9557 (ptp) cc_final: 0.8994 (ptp)
REVERT: A  502 MET cc_start: 0.8066 (mmm) cc_final: 0.7852 (mmm)
REVERT: A  849 MET cc_start: 0.8486 (ttt) cc_final: 0.7920 (tpp)
REVERT: A 1092 ASP cc_start: 0.9062 (m-30) cc_final: 0.8768 (m-30)
REVERT: A 1108 ILE cc_start: 0.9461 (mm) cc_final: 0.9145 (mt)
REVERT: A 1220 MET cc_start: 0.9500 (mtm) cc_final: 0.9216 (mtm)
REVERT: B  110 MET cc_start: 0.9345 (mtt) cc_final: 0.8888 (mmm)
REVERT: B  255 MET cc_start: 0.9430 (mtp) cc_final: 0.9223 (mtp)
REVERT: B  289 LEU cc_start: 0.9456 (tt) cc_final: 0.9224 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 158
  average time/residue: 0.0795
  time to fit residues: 18.6771
Evaluate side-chains
  124 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 56 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 45 optimal weight:    8.9990
   chunk 113 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 83 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 137 HIS
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 883 HIS
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.051961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.042047 restraints weight = 79873.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.043263 restraints weight = 49464.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.043958 restraints weight = 35474.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.044667 restraints weight = 28698.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.044996 restraints weight = 23868.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9759  Z= 0.247
  Angle     :  0.728  13.450  13204  Z= 0.378
  Chirality :  0.043   0.237   1488
  Planarity :  0.005   0.059   1660
  Dihedral  :  5.277  49.519   1302
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 20.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.24), residues: 1169
  helix: -0.02 (0.18), residues: 684
  sheet: -1.73 (0.42), residues: 123
  loop : -1.46 (0.36), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 305 
 TYR   0.024   0.002   TYR A 445 
 PHE   0.045   0.002   PHE A 184 
 TRP   0.013   0.001   TRP A 130 
 HIS   0.007   0.002   HIS A1170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 9759)
  covalent geometry    : angle       0.72772 (13204)
  hydrogen bonds       : bond        0.04769 (  583)
  hydrogen bonds       : angle       5.25554 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 TRP cc_start: 0.8416 (m100) cc_final: 0.8108 (m100)
REVERT: A  224 PHE cc_start: 0.9661 (t80) cc_final: 0.9287 (t80)
REVERT: A  228 ILE cc_start: 0.9709 (mm) cc_final: 0.9482 (mm)
REVERT: A  229 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8639 (mt-10)
REVERT: A  238 MET cc_start: 0.8642 (mmp) cc_final: 0.8376 (mmm)
REVERT: A  300 ILE cc_start: 0.9737 (pt) cc_final: 0.9530 (pt)
REVERT: A  318 MET cc_start: 0.9106 (tmm) cc_final: 0.8828 (tmm)
REVERT: A  469 MET cc_start: 0.9317 (ptp) cc_final: 0.9070 (ptm)
REVERT: A  502 MET cc_start: 0.8195 (mmm) cc_final: 0.7968 (mmm)
REVERT: A 1092 ASP cc_start: 0.9131 (m-30) cc_final: 0.8822 (m-30)
REVERT: A 1108 ILE cc_start: 0.9446 (mm) cc_final: 0.9022 (mt)
REVERT: A 1184 LEU cc_start: 0.9623 (tt) cc_final: 0.8789 (mt)
REVERT: A 1220 MET cc_start: 0.9575 (mtm) cc_final: 0.9218 (mtm)
REVERT: B  289 LEU cc_start: 0.9452 (tt) cc_final: 0.9168 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0777
  time to fit residues: 15.7234
Evaluate side-chains
  115 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 94 optimal weight:   50.0000
   chunk 71 optimal weight:   20.0000
   chunk 18 optimal weight:    2.9990
   chunk 87 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 96 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1193 ASN
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 GLN
** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.051863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.041814 restraints weight = 79829.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.043048 restraints weight = 49024.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.043737 restraints weight = 35170.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.044213 restraints weight = 28463.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.044825 restraints weight = 24399.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9759  Z= 0.233
  Angle     :  0.712  13.438  13204  Z= 0.367
  Chirality :  0.043   0.198   1488
  Planarity :  0.005   0.061   1660
  Dihedral  :  5.246  49.542   1302
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 19.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  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: -0.84 (0.24), residues: 1169
  helix:  0.18 (0.19), residues: 687
  sheet: -1.70 (0.42), residues: 127
  loop : -1.35 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1084 
 TYR   0.023   0.002   TYR A 445 
 PHE   0.041   0.002   PHE A 184 
 TRP   0.012   0.001   TRP A 130 
 HIS   0.006   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 9759)
  covalent geometry    : angle       0.71209 (13204)
  hydrogen bonds       : bond        0.04587 (  583)
  hydrogen bonds       : angle       5.12141 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9446 (t80) cc_final: 0.9240 (t80)
REVERT: A  130 TRP cc_start: 0.8393 (m100) cc_final: 0.8053 (m100)
REVERT: A  184 PHE cc_start: 0.9547 (m-80) cc_final: 0.9328 (m-80)
REVERT: A  224 PHE cc_start: 0.9660 (t80) cc_final: 0.9237 (t80)
REVERT: A  238 MET cc_start: 0.8636 (mmp) cc_final: 0.8371 (mmm)
REVERT: A  300 ILE cc_start: 0.9738 (pt) cc_final: 0.9529 (pt)
REVERT: A  318 MET cc_start: 0.8954 (tmm) cc_final: 0.8723 (tmm)
REVERT: A  338 MET cc_start: 0.9091 (mtp) cc_final: 0.7989 (ttm)
REVERT: A  849 MET cc_start: 0.7921 (ttm) cc_final: 0.7308 (tpp)
REVERT: A 1184 LEU cc_start: 0.9597 (tt) cc_final: 0.8769 (mt)
REVERT: A 1220 MET cc_start: 0.9556 (mtm) cc_final: 0.8874 (mtp)
REVERT: B  289 LEU cc_start: 0.9436 (tt) cc_final: 0.9134 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0820
  time to fit residues: 17.3022
Evaluate side-chains
  116 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 91 optimal weight:   30.0000
   chunk 35 optimal weight:    0.2980
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 GLN
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.053686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.043191 restraints weight = 75401.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.044472 restraints weight = 46062.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.045294 restraints weight = 33037.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.046029 restraints weight = 26445.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.046387 restraints weight = 21982.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9759  Z= 0.136
  Angle     :  0.642  11.852  13204  Z= 0.326
  Chirality :  0.042   0.199   1488
  Planarity :  0.004   0.058   1660
  Dihedral  :  4.945  44.589   1302
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  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: -0.43 (0.25), residues: 1169
  helix:  0.54 (0.19), residues: 699
  sheet: -1.32 (0.47), residues: 111
  loop : -1.44 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  61 
 TYR   0.028   0.002   TYR A 252 
 PHE   0.043   0.002   PHE A 184 
 TRP   0.007   0.001   TRP A 130 
 HIS   0.008   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9759)
  covalent geometry    : angle       0.64159 (13204)
  hydrogen bonds       : bond        0.04289 (  583)
  hydrogen bonds       : angle       4.65201 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 TRP cc_start: 0.8330 (m100) cc_final: 0.8026 (m100)
REVERT: A  184 PHE cc_start: 0.9479 (m-80) cc_final: 0.9216 (m-80)
REVERT: A  224 PHE cc_start: 0.9661 (t80) cc_final: 0.9206 (t80)
REVERT: A  256 PHE cc_start: 0.8331 (t80) cc_final: 0.8127 (t80)
REVERT: A  338 MET cc_start: 0.9122 (mtp) cc_final: 0.8023 (ttm)
REVERT: A  849 MET cc_start: 0.7777 (ttm) cc_final: 0.7179 (tpp)
REVERT: A  987 PHE cc_start: 0.9249 (t80) cc_final: 0.8889 (t80)
REVERT: A 1092 ASP cc_start: 0.8985 (m-30) cc_final: 0.8730 (m-30)
REVERT: A 1182 LYS cc_start: 0.8999 (tptt) cc_final: 0.8706 (mmmt)
REVERT: A 1220 MET cc_start: 0.9472 (mtm) cc_final: 0.8755 (mtp)
REVERT: B  255 MET cc_start: 0.9396 (mtp) cc_final: 0.9037 (tpp)
REVERT: B  289 LEU cc_start: 0.9417 (tt) cc_final: 0.9090 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0819
  time to fit residues: 19.1961
Evaluate side-chains
  124 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 96 optimal weight:   10.0000
   chunk 101 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 115 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.053689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.043162 restraints weight = 75902.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.044493 restraints weight = 46750.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.045447 restraints weight = 33263.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.045917 restraints weight = 25928.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.046521 restraints weight = 22194.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9759  Z= 0.153
  Angle     :  0.648  11.889  13204  Z= 0.330
  Chirality :  0.042   0.183   1488
  Planarity :  0.004   0.070   1660
  Dihedral  :  4.852  41.859   1302
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.25), residues: 1169
  helix:  0.61 (0.19), residues: 694
  sheet: -1.30 (0.46), residues: 121
  loop : -1.18 (0.36), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 231 
 TYR   0.021   0.002   TYR A 122 
 PHE   0.026   0.002   PHE A 184 
 TRP   0.049   0.002   TRP A 995 
 HIS   0.013   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9759)
  covalent geometry    : angle       0.64808 (13204)
  hydrogen bonds       : bond        0.04152 (  583)
  hydrogen bonds       : angle       4.65209 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8339 (mtp85)
REVERT: A  130 TRP cc_start: 0.8287 (m100) cc_final: 0.7978 (m100)
REVERT: A  224 PHE cc_start: 0.9644 (t80) cc_final: 0.9278 (t80)
REVERT: A  229 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8517 (mt-10)
REVERT: A  230 VAL cc_start: 0.9833 (m) cc_final: 0.9624 (p)
REVERT: A  238 MET cc_start: 0.8667 (mmp) cc_final: 0.8378 (mmm)
REVERT: A  849 MET cc_start: 0.7825 (ttm) cc_final: 0.7208 (tpp)
REVERT: A  987 PHE cc_start: 0.9281 (t80) cc_final: 0.8841 (t80)
REVERT: A 1001 PHE cc_start: 0.9271 (m-80) cc_final: 0.8889 (m-80)
REVERT: A 1092 ASP cc_start: 0.9031 (m-30) cc_final: 0.8753 (m-30)
REVERT: A 1108 ILE cc_start: 0.9282 (mt) cc_final: 0.8696 (mm)
REVERT: A 1182 LYS cc_start: 0.8962 (tptt) cc_final: 0.8682 (mmmt)
REVERT: A 1220 MET cc_start: 0.9464 (mtm) cc_final: 0.9147 (mtp)
REVERT: B   60 MET cc_start: 0.8885 (tpt) cc_final: 0.8518 (tpt)
REVERT: B  255 MET cc_start: 0.9358 (mtp) cc_final: 0.9085 (mmm)
REVERT: B  289 LEU cc_start: 0.9430 (tt) cc_final: 0.9087 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0933
  time to fit residues: 20.3457
Evaluate side-chains
  125 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 116 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   chunk 96 optimal weight:    8.9990
   chunk 110 optimal weight:    7.9990
   chunk 41 optimal weight:    0.5980
   chunk 66 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 104 optimal weight:    4.9990
   overall best weight:    4.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 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 = 0.3341 r_free = 0.3341 target = 0.053198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.042717 restraints weight = 78390.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.043978 restraints weight = 48333.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.044767 restraints weight = 34886.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.045525 restraints weight = 28146.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.045937 restraints weight = 23343.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9759  Z= 0.191
  Angle     :  0.668  11.972  13204  Z= 0.345
  Chirality :  0.042   0.163   1488
  Planarity :  0.004   0.053   1660
  Dihedral  :  4.930  41.941   1302
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 18.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  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: -0.16 (0.25), residues: 1169
  helix:  0.69 (0.19), residues: 690
  sheet: -1.33 (0.51), residues: 104
  loop : -1.11 (0.35), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 305 
 TYR   0.021   0.002   TYR A 445 
 PHE   0.049   0.002   PHE A 184 
 TRP   0.022   0.001   TRP A 995 
 HIS   0.007   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 9759)
  covalent geometry    : angle       0.66753 (13204)
  hydrogen bonds       : bond        0.04320 (  583)
  hydrogen bonds       : angle       4.77829 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 ARG cc_start: 0.9034 (mtt180) cc_final: 0.8359 (mtp85)
REVERT: A  238 MET cc_start: 0.8727 (mmp) cc_final: 0.8420 (mmm)
REVERT: A  300 ILE cc_start: 0.9729 (pt) cc_final: 0.9524 (pt)
REVERT: A  469 MET cc_start: 0.9497 (ptm) cc_final: 0.9268 (ptm)
REVERT: A  849 MET cc_start: 0.7754 (ttm) cc_final: 0.7165 (tpp)
REVERT: A  987 PHE cc_start: 0.9199 (t80) cc_final: 0.8994 (t80)
REVERT: A 1001 PHE cc_start: 0.9291 (m-80) cc_final: 0.8922 (m-80)
REVERT: A 1092 ASP cc_start: 0.9020 (m-30) cc_final: 0.8735 (m-30)
REVERT: A 1220 MET cc_start: 0.9483 (mtm) cc_final: 0.9156 (mtp)
REVERT: B   60 MET cc_start: 0.9018 (tpt) cc_final: 0.8805 (tpp)
REVERT: B  255 MET cc_start: 0.9377 (mtp) cc_final: 0.9155 (mmm)
REVERT: B  289 LEU cc_start: 0.9431 (tt) cc_final: 0.9109 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1019
  time to fit residues: 21.3824
Evaluate side-chains
  121 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 114 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 101 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 79 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 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 = 0.3354 r_free = 0.3354 target = 0.053809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.043389 restraints weight = 77257.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.044633 restraints weight = 48072.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.045485 restraints weight = 34616.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.046167 restraints weight = 27983.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.046754 restraints weight = 23227.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9759  Z= 0.166
  Angle     :  0.667  12.093  13204  Z= 0.340
  Chirality :  0.042   0.144   1488
  Planarity :  0.004   0.052   1660
  Dihedral  :  4.858  40.494   1302
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  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: -0.14 (0.25), residues: 1169
  helix:  0.73 (0.19), residues: 692
  sheet: -1.49 (0.44), residues: 123
  loop : -1.02 (0.37), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 356 
 TYR   0.056   0.002   TYR A 252 
 PHE   0.048   0.002   PHE A 184 
 TRP   0.022   0.001   TRP A 995 
 HIS   0.007   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9759)
  covalent geometry    : angle       0.66739 (13204)
  hydrogen bonds       : bond        0.04316 (  583)
  hydrogen bonds       : angle       4.70227 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.8714 (mmp) cc_final: 0.8373 (mmm)
REVERT: A  469 MET cc_start: 0.9452 (ptm) cc_final: 0.9238 (ptm)
REVERT: A  849 MET cc_start: 0.7692 (ttm) cc_final: 0.7120 (tpp)
REVERT: A  896 MET cc_start: 0.8979 (tpp) cc_final: 0.8744 (tpp)
REVERT: A 1001 PHE cc_start: 0.9272 (m-80) cc_final: 0.9057 (m-80)
REVERT: A 1073 GLU cc_start: 0.7634 (mp0) cc_final: 0.7394 (mp0)
REVERT: A 1092 ASP cc_start: 0.9032 (m-30) cc_final: 0.8754 (m-30)
REVERT: A 1182 LYS cc_start: 0.8960 (tptt) cc_final: 0.8653 (mmmt)
REVERT: A 1220 MET cc_start: 0.9458 (mtm) cc_final: 0.8548 (mtp)
REVERT: B   60 MET cc_start: 0.9012 (tpt) cc_final: 0.8808 (tpp)
REVERT: B  110 MET cc_start: 0.9127 (mtt) cc_final: 0.8655 (mmm)
REVERT: B  255 MET cc_start: 0.9359 (mtp) cc_final: 0.8914 (tpp)
REVERT: B  289 LEU cc_start: 0.9399 (tt) cc_final: 0.9144 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0869
  time to fit residues: 18.9390
Evaluate side-chains
  126 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 96 optimal weight:    0.0980
   chunk 45 optimal weight:   20.0000
   chunk 84 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0270
   chunk 102 optimal weight:    0.4980
   chunk 93 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.056456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.045771 restraints weight = 73469.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.047048 restraints weight = 46902.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.048099 restraints weight = 34110.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.048609 restraints weight = 26909.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.049246 restraints weight = 23051.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.4398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9759  Z= 0.131
  Angle     :  0.672  11.760  13204  Z= 0.336
  Chirality :  0.042   0.151   1488
  Planarity :  0.004   0.053   1660
  Dihedral  :  4.557  32.400   1302
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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:  0.00 (0.25), residues: 1169
  helix:  0.89 (0.19), residues: 694
  sheet: -1.29 (0.46), residues: 120
  loop : -1.17 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 356 
 TYR   0.023   0.001   TYR A1102 
 PHE   0.051   0.002   PHE A 184 
 TRP   0.025   0.002   TRP A 995 
 HIS   0.005   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9759)
  covalent geometry    : angle       0.67189 (13204)
  hydrogen bonds       : bond        0.04252 (  583)
  hydrogen bonds       : angle       4.47609 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 LEU cc_start: 0.9101 (tt) cc_final: 0.8830 (mt)
REVERT: A  184 PHE cc_start: 0.9581 (m-80) cc_final: 0.9329 (m-80)
REVERT: A  238 MET cc_start: 0.8587 (mmp) cc_final: 0.8353 (mmm)
REVERT: A  469 MET cc_start: 0.9400 (ptm) cc_final: 0.9199 (ptm)
REVERT: A  849 MET cc_start: 0.7553 (ttm) cc_final: 0.7006 (tpp)
REVERT: A  992 LEU cc_start: 0.9535 (mm) cc_final: 0.9028 (mm)
REVERT: A  995 TRP cc_start: 0.8258 (m100) cc_final: 0.7395 (m100)
REVERT: A 1001 PHE cc_start: 0.9198 (m-80) cc_final: 0.8974 (m-80)
REVERT: A 1025 MET cc_start: 0.8385 (tpp) cc_final: 0.7693 (tpp)
REVERT: A 1073 GLU cc_start: 0.7516 (mp0) cc_final: 0.7305 (mp0)
REVERT: A 1092 ASP cc_start: 0.8966 (m-30) cc_final: 0.8697 (m-30)
REVERT: A 1182 LYS cc_start: 0.8912 (tptt) cc_final: 0.8629 (mmmt)
REVERT: A 1220 MET cc_start: 0.9361 (mtm) cc_final: 0.8516 (mtp)
REVERT: B  110 MET cc_start: 0.9059 (mtt) cc_final: 0.8650 (mmm)
REVERT: B  255 MET cc_start: 0.9286 (mtp) cc_final: 0.8837 (mmm)
REVERT: B  289 LEU cc_start: 0.9347 (tt) cc_final: 0.9099 (tt)
REVERT: B  290 PHE cc_start: 0.9316 (m-80) cc_final: 0.8995 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0850
  time to fit residues: 19.4088
Evaluate side-chains
  129 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 78 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 101 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 288 HIS
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 HIS ** 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 = 0.3367 r_free = 0.3367 target = 0.054404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.043936 restraints weight = 77288.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.045120 restraints weight = 49527.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.046108 restraints weight = 36303.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.046575 restraints weight = 28698.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.047145 restraints weight = 24978.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.4273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9759  Z= 0.175
  Angle     :  0.685  12.029  13204  Z= 0.348
  Chirality :  0.042   0.143   1488
  Planarity :  0.004   0.051   1660
  Dihedral  :  4.636  33.572   1302
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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:  0.09 (0.25), residues: 1169
  helix:  0.88 (0.19), residues: 691
  sheet: -1.11 (0.48), residues: 110
  loop : -1.00 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 356 
 TYR   0.040   0.002   TYR A 252 
 PHE   0.045   0.002   PHE A 184 
 TRP   0.016   0.001   TRP A 995 
 HIS   0.012   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9759)
  covalent geometry    : angle       0.68537 (13204)
  hydrogen bonds       : bond        0.04185 (  583)
  hydrogen bonds       : angle       4.62356 ( 1686)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 ARG cc_start: 0.9028 (mtt180) cc_final: 0.8792 (mtp85)
REVERT: A  184 PHE cc_start: 0.9536 (m-80) cc_final: 0.8995 (m-10)
REVERT: A  238 MET cc_start: 0.8645 (mmp) cc_final: 0.8355 (mmm)
REVERT: A  849 MET cc_start: 0.7724 (ttm) cc_final: 0.7165 (tpp)
REVERT: A  992 LEU cc_start: 0.9382 (mm) cc_final: 0.9151 (mm)
REVERT: A  995 TRP cc_start: 0.8209 (m100) cc_final: 0.7362 (m100)
REVERT: A 1001 PHE cc_start: 0.9245 (m-80) cc_final: 0.8929 (m-80)
REVERT: A 1182 LYS cc_start: 0.8940 (tptt) cc_final: 0.8662 (mmmt)
REVERT: A 1220 MET cc_start: 0.9402 (mtm) cc_final: 0.8461 (mtp)
REVERT: B  110 MET cc_start: 0.9095 (mtt) cc_final: 0.8655 (mmm)
REVERT: B  255 MET cc_start: 0.9323 (mtp) cc_final: 0.9064 (mmm)
REVERT: B  289 LEU cc_start: 0.9392 (tt) cc_final: 0.9123 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0862
  time to fit residues: 19.0108
Evaluate side-chains
  121 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 107 optimal weight:   10.0000
   chunk 70 optimal weight:    0.0970
   chunk 9 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0970
   chunk 89 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0970
   chunk 68 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.2578

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 HIS ** 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 = 0.3398 r_free = 0.3398 target = 0.055813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.045166 restraints weight = 74528.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.046393 restraints weight = 47849.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.047402 restraints weight = 34972.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.047938 restraints weight = 27789.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.048457 restraints weight = 23706.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9759  Z= 0.135
  Angle     :  0.687  11.868  13204  Z= 0.344
  Chirality :  0.042   0.236   1488
  Planarity :  0.004   0.051   1660
  Dihedral  :  4.584  31.105   1302
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  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:  0.11 (0.25), residues: 1169
  helix:  0.90 (0.19), residues: 689
  sheet: -1.35 (0.47), residues: 116
  loop : -0.87 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 356 
 TYR   0.030   0.002   TYR A 252 
 PHE   0.070   0.002   PHE A 256 
 TRP   0.018   0.001   TRP A 995 
 HIS   0.004   0.001   HIS A 883 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9759)
  covalent geometry    : angle       0.68697 (13204)
  hydrogen bonds       : bond        0.04226 (  583)
  hydrogen bonds       : angle       4.50352 ( 1686)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1493.99 seconds
wall clock time: 26 minutes 52.62 seconds (1612.62 seconds total)