Starting phenix.real_space_refine
on Wed Feb 12 12:19:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d3r_7793/02_2025/6d3r_7793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d3r_7793/02_2025/6d3r_7793.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6d3r_7793/02_2025/6d3r_7793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d3r_7793/02_2025/6d3r_7793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d3r_7793/02_2025/6d3r_7793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d3r_7793/02_2025/6d3r_7793.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      27      5.16       5
     C    4854      2.51       5
     N    1348      2.21       5
     O    1375      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7610
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1127, 7548
          Classifications: {'peptide': 1127}
          Incomplete info: {'truncation_to_alanine': 423}
          Link IDs: {'PTRANS': 27, 'TRANS': 1099}
          Chain breaks: 3
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 1524
          Unresolved non-hydrogen angles: 1957
          Unresolved non-hydrogen dihedrals: 1274
          Unresolved non-hydrogen chiralities: 149
          Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 8, 'TYR:plan': 19, 'ASN:plan1': 10, 'TRP:plan': 6, 'ASP:plan': 27, 'PHE:plan': 29, 'GLU:plan': 36, 'ARG:plan': 18}
          Unresolved non-hydrogen planarities: 834
    Chain: "A"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 62
          Unusual residues: {'ATP': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.86, per 1000 atoms: 0.77
  Number of scatterers: 7610
  At special positions: 0
  Unit cell: (74.3748, 97.7891, 136.354, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       6     15.00
     O    1375      8.00
     N    1348      7.00
     C    4854      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: 2.44
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2116

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      71.6% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 63
    Processing helix  chain 'A' and resid 69 through 94
      removed outlier: 3.842A  pdb=" N   CYS A  77 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   TRP A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   LYS A  81 " --> pdb=" O   CYS A  77 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   PHE A  84 " --> pdb=" O   TRP A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 97
      No H-bonds generated for 'chain 'A' and resid 95 through 97'
    Processing helix  chain 'A' and resid 98 through 109
    Processing helix  chain 'A' and resid 117 through 166
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 171 through 175
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.856A  pdb=" N   LEU A 181 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 196
      removed outlier: 4.035A  pdb=" N   LEU A 196 " --> pdb=" O   PHE A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 199
      No H-bonds generated for 'chain 'A' and resid 197 through 199'
    Processing helix  chain 'A' and resid 200 through 215
      Proline residue:  A 206  - end of helix
    Processing helix  chain 'A' and resid 222 through 268
    Processing helix  chain 'A' and resid 269 through 277
    Processing helix  chain 'A' and resid 279 through 322
      removed outlier: 3.504A  pdb=" N   LYS A 299 " --> pdb=" O   LYS A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 328
    Processing helix  chain 'A' and resid 333 through 353
      removed outlier: 3.927A  pdb=" N   THR A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 377
      removed outlier: 3.588A  pdb=" N   SER A 358 " --> pdb=" O   GLN A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 473
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 514 through 525
    Processing helix  chain 'A' and resid 527 through 532
    Processing helix  chain 'A' and resid 536 through 539
    Processing helix  chain 'A' and resid 550 through 565
    Processing helix  chain 'A' and resid 580 through 592
    Processing helix  chain 'A' and resid 607 through 614
    Processing helix  chain 'A' and resid 630 through 638
    Processing helix  chain 'A' and resid 638 through 648
      removed outlier: 4.104A  pdb=" N   PHE A 648 " --> pdb=" O   GLU A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 654
    Processing helix  chain 'A' and resid 655 through 670
    Processing helix  chain 'A' and resid 851 through 860
    Processing helix  chain 'A' and resid 860 through 884
      removed outlier: 3.614A  pdb=" N   ILE A 864 " --> pdb=" O   HIS A 860 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 885 through 888
    Processing helix  chain 'A' and resid 918 through 938
      removed outlier: 3.889A  pdb=" N   GLY A 938 " --> pdb=" O   GLY A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 962
      removed outlier: 3.564A  pdb=" N   HIS A 943 " --> pdb=" O   LEU A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 971
    Processing helix  chain 'A' and resid 973 through 1016
      Proline residue:  A 992  - end of helix
      removed outlier: 4.970A  pdb=" N   PHE A 996 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1045
      removed outlier: 4.139A  pdb=" N   PHE A1020 " --> pdb=" O   GLN A1016 " (cutoff:3.500A)
      Proline residue:  A1025  - end of helix
    Processing helix  chain 'A' and resid 1045 through 1065
      removed outlier: 4.031A  pdb=" N   SER A1049 " --> pdb=" O   LYS A1045 " (cutoff:3.500A)
      Proline residue:  A1054  - end of helix
    Processing helix  chain 'A' and resid 1065 through 1072
    Processing helix  chain 'A' and resid 1074 through 1125
    Processing helix  chain 'A' and resid 1130 through 1142
    Processing helix  chain 'A' and resid 1143 through 1169
    Processing helix  chain 'A' and resid 1251 through 1260
      removed outlier: 3.552A  pdb=" N   LEU A1255 " --> pdb=" O   GLY A1251 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU A1256 " --> pdb=" O   LYS A1252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1279
      No H-bonds generated for 'chain 'A' and resid 1277 through 1279'
    Processing helix  chain 'A' and resid 1280 through 1287
    Processing helix  chain 'A' and resid 1302 through 1307
    Processing helix  chain 'A' and resid 1313 through 1324
    Processing helix  chain 'A' and resid 1326 through 1333
    Processing helix  chain 'A' and resid 1335 through 1338
    Processing helix  chain 'A' and resid 1349 through 1364
    Processing helix  chain 'A' and resid 1374 through 1377
    Processing helix  chain 'A' and resid 1379 through 1394
      removed outlier: 4.847A  pdb=" N   VAL A1385 " --> pdb=" O   ILE A1381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1405 through 1410
    Processing helix  chain 'A' and resid 1428 through 1439
    Processing sheet with id=AA1, first strand: chain 'A' and resid 442 through 449
      removed outlier: 7.024A  pdb=" N   GLN A 443 " --> pdb=" O   THR A 399 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   THR A 399 " --> pdb=" O   GLN A 443 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   ILE A 445 " --> pdb=" O   LYS A 397 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS A 397 " --> pdb=" O   ILE A 445 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   VAL A 398 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   GLU A 480 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 492
      removed outlier: 6.775A  pdb=" N   SER A 490 " --> pdb=" O   LEU A 571 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU A 455 " --> pdb=" O   LEU A 603 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE A 617 " --> pdb=" O   TYR A 628 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   TYR A 628 " --> pdb=" O   ILE A 617 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE A 619 " --> pdb=" O   TYR A 626 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 501 through 502
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1236
      removed outlier: 3.540A  pdb=" N   LEU A1229 " --> pdb=" O   ALA A1219 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   LEU A1217 " --> pdb=" O   ASN A1231 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   SER A1233 " --> pdb=" O   THR A1215 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   THR A1215 " --> pdb=" O   SER A1233 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   SER A1235 " --> pdb=" O   THR A1213 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   THR A1213 " --> pdb=" O   SER A1235 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   LEU A1217 " --> pdb=" O   GLU A1266 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLU A1266 " --> pdb=" O   LEU A1217 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ALA A1219 " --> pdb=" O   ASN A1264 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ASN A1264 " --> pdb=" O   ALA A1219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1288 through 1291
      removed outlier: 6.163A  pdb=" N   LEU A1369 " --> pdb=" O   VAL A1400 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   SER A1402 " --> pdb=" O   LEU A1369 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU A1371 " --> pdb=" O   SER A1402 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL A1242 " --> pdb=" O   LEU A1401 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   GLY A1243 " --> pdb=" O   LEU A1416 " (cutoff:3.500A)
      removed outlier: 7.700A  pdb=" N   ILE A1418 " --> pdb=" O   GLY A1243 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU A1245 " --> pdb=" O   ILE A1418 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1300 through 1301

    613 hydrogen bonds defined for protein.
    1785 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.94

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1652
        1.32 -     1.45: 2199
        1.45 -     1.57: 3802
        1.57 -     1.70: 22
        1.70 -     1.83: 51
  Bond restraints: 7726
  Sorted by residual:
  bond pdb=" O5' ATP A1502 "
       pdb=" PA  ATP A1502 "
    ideal  model  delta    sigma   weight residual
    1.579  1.725 -0.146 1.10e-02 8.26e+03 1.77e+02
  bond pdb=" O5' ATP A1501 "
       pdb=" PA  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.579  1.700 -0.121 1.10e-02 8.26e+03 1.22e+02
  bond pdb=" C1' ATP A1502 "
       pdb=" N9  ATP A1502 "
    ideal  model  delta    sigma   weight residual
    1.459  1.592 -0.133 1.40e-02 5.10e+03 8.97e+01
  bond pdb=" C1' ATP A1501 "
       pdb=" N9  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.459  1.558 -0.099 1.40e-02 5.10e+03 5.03e+01
  bond pdb=" C1' ATP A1502 "
       pdb=" C2' ATP A1502 "
    ideal  model  delta    sigma   weight residual
    1.531  1.607 -0.076 1.20e-02 6.94e+03 4.02e+01
  ... (remaining 7721 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.34: 10265
        4.34 -     8.69: 270
        8.69 -    13.03: 15
       13.03 -    17.38: 3
       17.38 -    21.72: 1
  Bond angle restraints: 10554
  Sorted by residual:
  angle pdb=" PB  ATP A1501 "
        pdb=" O3B ATP A1501 "
        pdb=" PG  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     139.87  118.15   21.72 1.00e+00 1.00e+00 4.72e+02
  angle pdb=" PB  ATP A1502 "
        pdb=" O3B ATP A1502 "
        pdb=" PG  ATP A1502 "
      ideal   model   delta    sigma   weight residual
     139.87  124.24   15.63 1.00e+00 1.00e+00 2.44e+02
  angle pdb=" PA  ATP A1501 "
        pdb=" O3A ATP A1501 "
        pdb=" PB  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     136.83  121.81   15.02 1.00e+00 1.00e+00 2.26e+02
  angle pdb=" PA  ATP A1502 "
        pdb=" O3A ATP A1502 "
        pdb=" PB  ATP A1502 "
      ideal   model   delta    sigma   weight residual
     136.83  123.71   13.12 1.00e+00 1.00e+00 1.72e+02
  angle pdb=" C2' ATP A1502 "
        pdb=" C1' ATP A1502 "
        pdb=" N9  ATP A1502 "
      ideal   model   delta    sigma   weight residual
     114.08  127.10  -13.02 1.53e+00 4.27e-01 7.23e+01
  ... (remaining 10549 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 4411
       16.80 -    33.60: 101
       33.60 -    50.39: 30
       50.39 -    67.19: 28
       67.19 -    83.99: 13
  Dihedral angle restraints: 4583
    sinusoidal: 1326
      harmonic: 3257
  Sorted by residual:
  dihedral pdb=" CA  GLY A1129 "
           pdb=" C   GLY A1129 "
           pdb=" N   PRO A1130 "
           pdb=" CA  PRO A1130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.63  -20.37     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  ASN A1264 "
           pdb=" C   ASN A1264 "
           pdb=" N   THR A1265 "
           pdb=" CA  THR A1265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.08  -18.92     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" C   PHE A1120 "
           pdb=" N   PHE A1120 "
           pdb=" CA  PHE A1120 "
           pdb=" CB  PHE A1120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.97    9.37     0      2.50e+00 1.60e-01 1.41e+01
  ... (remaining 4580 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 894
       0.093 -    0.185: 333
       0.185 -    0.278: 61
       0.278 -    0.370: 11
       0.370 -    0.463: 3
  Chirality restraints: 1302
  Sorted by residual:
  chirality pdb=" CA  PHE A1120 "
            pdb=" N   PHE A1120 "
            pdb=" C   PHE A1120 "
            pdb=" CB  PHE A1120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.36e+00
  chirality pdb=" CA  PHE A 317 "
            pdb=" N   PHE A 317 "
            pdb=" C   PHE A 317 "
            pdb=" CB  PHE A 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.00e+00
  chirality pdb=" CB  THR A 466 "
            pdb=" CA  THR A 466 "
            pdb=" OG1 THR A 466 "
            pdb=" CG2 THR A 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.17    0.39 2.00e-01 2.50e+01 3.71e+00
  ... (remaining 1299 not shown)

  Planarity restraints: 1344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 968 "    0.089 2.00e-02 2.50e+03   5.50e-02 5.29e+01
        pdb=" CG  PHE A 968 "   -0.086 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 968 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 968 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 968 "    0.021 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 968 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 968 "    0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 230 "    0.085 2.00e-02 2.50e+03   5.23e-02 4.79e+01
        pdb=" CG  PHE A 230 "   -0.083 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 230 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 230 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 230 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 230 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 230 "    0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 381 "    0.072 2.00e-02 2.50e+03   3.68e-02 2.71e+01
        pdb=" CG  TYR A 381 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 381 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 381 "   -0.033 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 381 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 381 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 381 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 381 "    0.044 2.00e-02 2.50e+03
  ... (remaining 1341 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.89: 3205
        2.89 -     3.39: 8122
        3.39 -     3.89: 11849
        3.89 -     4.40: 13723
        4.40 -     4.90: 20506
  Nonbonded interactions: 57405
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  50 "
            pdb=" OG  SER A 159 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" O   TRP A 278 "
            pdb=" OH  TYR A1309 "
     model   vdw
     2.441 3.040
  nonbonded pdb=" N   ASP A  44 "
            pdb=" OD1 ASP A  44 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" N   ASN A 188 "
            pdb=" OD1 ASN A 188 "
     model   vdw
     2.469 3.120
  nonbonded pdb=" N   SER A 223 "
            pdb=" N   ALA A 224 "
     model   vdw
     2.497 2.560
  ... (remaining 57400 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.250
  Find NCS groups from input model:        0.090
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
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      :  0.017   0.146   7726  Z= 1.108
  Angle     :  1.749  21.719  10554  Z= 1.235
  Chirality :  0.098   0.463   1302
  Planarity :  0.010   0.100   1344
  Dihedral  : 11.893  83.991   2467
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 0.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.23), residues: 1119
  helix:  0.49 (0.17), residues: 724
  sheet:  1.24 (0.58), residues: 60
  loop :  0.52 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.008   TRP A 362 
 HIS   0.037   0.004   HIS A 200 
 PHE   0.089   0.008   PHE A 968 
 TYR   0.072   0.006   TYR A 381 
 ARG   0.010   0.001   ARG A1070 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8867 (mt) cc_final: 0.8376 (mt)
REVERT: A  172 VAL cc_start: 0.7894 (m) cc_final: 0.7461 (m)
REVERT: A  184 LEU cc_start: 0.9316 (tp) cc_final: 0.9026 (tp)
REVERT: A  193 ASP cc_start: 0.8724 (p0) cc_final: 0.8349 (t0)
REVERT: A  213 MET cc_start: 0.8496 (ttp) cc_final: 0.8154 (tmm)
REVERT: A  245 MET cc_start: 0.9239 (ttm) cc_final: 0.8889 (tpp)
REVERT: A  246 MET cc_start: 0.8902 (mmm) cc_final: 0.8594 (tmm)
REVERT: A  250 ASP cc_start: 0.8871 (m-30) cc_final: 0.8669 (m-30)
REVERT: A  351 VAL cc_start: 0.8989 (t) cc_final: 0.8767 (p)
REVERT: A  379 GLU cc_start: 0.8193 (mp0) cc_final: 0.7797 (tp30)
REVERT: A  402 TRP cc_start: 0.8814 (m100) cc_final: 0.8455 (m100)
REVERT: A 1141 MET cc_start: 0.8502 (ttp) cc_final: 0.8246 (tmm)
REVERT: A 1370 LEU cc_start: 0.8681 (mp) cc_final: 0.8403 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1942
  time to fit residues: 65.7186
Evaluate side-chains
  121 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0040
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 65 optimal weight:    0.5980
   chunk 101 optimal weight:    6.9990
   overall best weight:    1.3198

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.097234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.082091 restraints weight = 30367.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.084483 restraints weight = 15912.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.086101 restraints weight = 9851.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7726  Z= 0.254
  Angle     :  0.677   8.432  10554  Z= 0.391
  Chirality :  0.044   0.205   1302
  Planarity :  0.005   0.059   1344
  Dihedral  : 11.196  74.516   1242
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.01 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.24), residues: 1119
  helix:  1.92 (0.18), residues: 727
  sheet:  1.62 (0.58), residues: 70
  loop :  0.42 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 278 
 HIS   0.006   0.002   HIS A 953 
 PHE   0.023   0.002   PHE A 491 
 TYR   0.011   0.001   TYR A 564 
 ARG   0.008   0.001   ARG A 348 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.9182 (tp) cc_final: 0.8882 (tp)
REVERT: A   90 TYR cc_start: 0.8687 (t80) cc_final: 0.8331 (t80)
REVERT: A  193 ASP cc_start: 0.8700 (p0) cc_final: 0.8172 (t0)
REVERT: A  194 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8408 (tp30)
REVERT: A  200 HIS cc_start: 0.6562 (p90) cc_final: 0.6338 (p90)
REVERT: A  213 MET cc_start: 0.8328 (ttp) cc_final: 0.7988 (ppp)
REVERT: A  245 MET cc_start: 0.9299 (ttm) cc_final: 0.9037 (tpp)
REVERT: A  246 MET cc_start: 0.8856 (mmm) cc_final: 0.8220 (tmm)
REVERT: A  250 ASP cc_start: 0.8882 (m-30) cc_final: 0.8448 (m-30)
REVERT: A  290 ARG cc_start: 0.9040 (tpt170) cc_final: 0.8288 (tpt90)
REVERT: A  344 CYS cc_start: 0.9170 (m) cc_final: 0.8947 (m)
REVERT: A  360 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8759 (tm-30)
REVERT: A  370 ASN cc_start: 0.9453 (m-40) cc_final: 0.9187 (m110)
REVERT: A  379 GLU cc_start: 0.8279 (mp0) cc_final: 0.8053 (tp30)
REVERT: A  489 ILE cc_start: 0.8923 (mp) cc_final: 0.8488 (tp)
REVERT: A  572 MET cc_start: 0.8381 (mpp) cc_final: 0.8023 (mpp)
REVERT: A  573 ASP cc_start: 0.7926 (t70) cc_final: 0.7401 (t0)
REVERT: A 1037 PHE cc_start: 0.8439 (t80) cc_final: 0.8211 (t80)
REVERT: A 1105 MET cc_start: 0.8730 (ttm) cc_final: 0.8285 (ttp)
REVERT: A 1108 GLU cc_start: 0.8744 (tt0) cc_final: 0.8279 (tt0)
REVERT: A 1356 MET cc_start: 0.9251 (mtm) cc_final: 0.8983 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1855
  time to fit residues: 41.7365
Evaluate side-chains
  110 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 74 optimal weight:    0.2980
   chunk 47 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 59 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 92 optimal weight:   30.0000
   chunk 50 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A1089 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.095904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.082488 restraints weight = 31005.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.084631 restraints weight = 16056.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.086067 restraints weight = 9911.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.4384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7726  Z= 0.192
  Angle     :  0.570   6.507  10554  Z= 0.330
  Chirality :  0.041   0.186   1302
  Planarity :  0.004   0.037   1344
  Dihedral  : 10.711  71.962   1242
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.30 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.25), residues: 1119
  helix:  2.21 (0.19), residues: 728
  sheet:  1.48 (0.58), residues: 70
  loop :  0.33 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 278 
 HIS   0.005   0.001   HIS A 953 
 PHE   0.030   0.002   PHE A 313 
 TYR   0.009   0.001   TYR A 564 
 ARG   0.007   0.001   ARG A 348 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.9197 (tp) cc_final: 0.8910 (tp)
REVERT: A  190 ASN cc_start: 0.8593 (p0) cc_final: 0.8338 (p0)
REVERT: A  193 ASP cc_start: 0.8683 (p0) cc_final: 0.8200 (t0)
REVERT: A  194 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8405 (tp30)
REVERT: A  200 HIS cc_start: 0.6816 (p90) cc_final: 0.6511 (p90)
REVERT: A  211 LEU cc_start: 0.8320 (tp) cc_final: 0.8114 (tp)
REVERT: A  213 MET cc_start: 0.8248 (ttp) cc_final: 0.7907 (ppp)
REVERT: A  245 MET cc_start: 0.9307 (ttm) cc_final: 0.8551 (tmm)
REVERT: A  246 MET cc_start: 0.8860 (mmm) cc_final: 0.8504 (tmm)
REVERT: A  290 ARG cc_start: 0.8847 (tpt170) cc_final: 0.8169 (tpt90)
REVERT: A  344 CYS cc_start: 0.9115 (m) cc_final: 0.8868 (m)
REVERT: A  370 ASN cc_start: 0.9423 (m-40) cc_final: 0.9113 (m110)
REVERT: A  489 ILE cc_start: 0.8993 (mp) cc_final: 0.8669 (tp)
REVERT: A  572 MET cc_start: 0.8415 (mpp) cc_final: 0.8119 (mpp)
REVERT: A  573 ASP cc_start: 0.8014 (t70) cc_final: 0.7598 (t0)
REVERT: A  989 ASP cc_start: 0.8749 (t70) cc_final: 0.8485 (t70)
REVERT: A 1037 PHE cc_start: 0.8439 (t80) cc_final: 0.8114 (t80)
REVERT: A 1105 MET cc_start: 0.8561 (ttm) cc_final: 0.8345 (ttp)
REVERT: A 1141 MET cc_start: 0.9047 (tmm) cc_final: 0.8501 (tmm)
REVERT: A 1356 MET cc_start: 0.9228 (mtm) cc_final: 0.8933 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1740
  time to fit residues: 39.0665
Evaluate side-chains
  107 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 52 optimal weight:   10.0000
   chunk 99 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A1092 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 = 0.3664 r_free = 0.3664 target = 0.090902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.077553 restraints weight = 31617.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.079547 restraints weight = 16818.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.080910 restraints weight = 10662.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7726  Z= 0.309
  Angle     :  0.652   8.682  10554  Z= 0.361
  Chirality :  0.042   0.200   1302
  Planarity :  0.004   0.035   1344
  Dihedral  : 10.370  81.781   1242
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.25), residues: 1119
  helix:  2.11 (0.19), residues: 721
  sheet:  0.92 (0.58), residues: 60
  loop : -0.01 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 362 
 HIS   0.006   0.002   HIS A1089 
 PHE   0.015   0.002   PHE A 317 
 TYR   0.012   0.002   TYR A  90 
 ARG   0.006   0.001   ARG A1106 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8738 (p0) cc_final: 0.8461 (p0)
REVERT: A  213 MET cc_start: 0.8196 (ttp) cc_final: 0.7677 (tmm)
REVERT: A  245 MET cc_start: 0.9221 (ttm) cc_final: 0.8963 (tpp)
REVERT: A  344 CYS cc_start: 0.9119 (m) cc_final: 0.8905 (m)
REVERT: A  370 ASN cc_start: 0.9415 (m-40) cc_final: 0.9075 (m110)
REVERT: A  559 LEU cc_start: 0.9704 (mm) cc_final: 0.9499 (mm)
REVERT: A  573 ASP cc_start: 0.8234 (t70) cc_final: 0.7597 (t0)
REVERT: A  954 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8307 (tm-30)
REVERT: A  955 LYS cc_start: 0.9384 (mmtt) cc_final: 0.9081 (tppt)
REVERT: A  989 ASP cc_start: 0.8838 (t70) cc_final: 0.8632 (t70)
REVERT: A 1037 PHE cc_start: 0.8443 (t80) cc_final: 0.8149 (t80)
REVERT: A 1041 SER cc_start: 0.8642 (p) cc_final: 0.8364 (p)
REVERT: A 1141 MET cc_start: 0.9010 (tmm) cc_final: 0.8397 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1843
  time to fit residues: 34.0093
Evaluate side-chains
  94 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 90 optimal weight:   20.0000
   chunk 103 optimal weight:    0.9980
   chunk 95 optimal weight:    8.9990
   chunk 79 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 107 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 96 optimal weight:    5.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    1.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.093315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.079795 restraints weight = 32299.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.081774 restraints weight = 17553.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.083162 restraints weight = 11271.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7726  Z= 0.231
  Angle     :  0.580   6.612  10554  Z= 0.322
  Chirality :  0.040   0.183   1302
  Planarity :  0.003   0.033   1344
  Dihedral  :  9.853  87.736   1242
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.25), residues: 1119
  helix:  2.37 (0.19), residues: 718
  sheet:  0.72 (0.59), residues: 60
  loop : -0.04 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 362 
 HIS   0.004   0.001   HIS A1039 
 PHE   0.013   0.002   PHE A1078 
 TYR   0.009   0.001   TYR A1309 
 ARG   0.007   0.001   ARG A 348 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8706 (p0) cc_final: 0.8308 (p0)
REVERT: A  213 MET cc_start: 0.8171 (ttp) cc_final: 0.7628 (tmm)
REVERT: A  245 MET cc_start: 0.9268 (ttm) cc_final: 0.8957 (tpp)
REVERT: A  290 ARG cc_start: 0.8878 (tpt170) cc_final: 0.8261 (tpt90)
REVERT: A  370 ASN cc_start: 0.9399 (m-40) cc_final: 0.9071 (m110)
REVERT: A  559 LEU cc_start: 0.9661 (mm) cc_final: 0.9452 (mm)
REVERT: A  573 ASP cc_start: 0.8263 (t70) cc_final: 0.7616 (t0)
REVERT: A  954 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8740 (tm-30)
REVERT: A 1037 PHE cc_start: 0.8379 (t80) cc_final: 0.7993 (t80)
REVERT: A 1041 SER cc_start: 0.8575 (p) cc_final: 0.8309 (p)
REVERT: A 1072 PHE cc_start: 0.8229 (m-80) cc_final: 0.8006 (m-80)
REVERT: A 1105 MET cc_start: 0.8615 (ttm) cc_final: 0.8115 (ttp)
REVERT: A 1141 MET cc_start: 0.8942 (tmm) cc_final: 0.8299 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1897
  time to fit residues: 34.1159
Evaluate side-chains
  98 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0370
   chunk 35 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A1092 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 = 0.3720 r_free = 0.3720 target = 0.094021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.080699 restraints weight = 31197.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.082781 restraints weight = 16785.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.084166 restraints weight = 10539.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.5707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7726  Z= 0.159
  Angle     :  0.537   6.875  10554  Z= 0.294
  Chirality :  0.039   0.181   1302
  Planarity :  0.004   0.058   1344
  Dihedral  :  9.334  85.300   1242
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.25), residues: 1119
  helix:  2.61 (0.19), residues: 719
  sheet:  0.64 (0.58), residues: 60
  loop :  0.08 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1093 
 HIS   0.004   0.001   HIS A 953 
 PHE   0.014   0.001   PHE A 201 
 TYR   0.008   0.001   TYR A1077 
 ARG   0.011   0.001   ARG A 252 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8735 (p0) cc_final: 0.8342 (p0)
REVERT: A  213 MET cc_start: 0.8105 (ttp) cc_final: 0.7693 (ppp)
REVERT: A  245 MET cc_start: 0.9265 (ttm) cc_final: 0.8897 (tpp)
REVERT: A  282 MET cc_start: 0.8128 (mmm) cc_final: 0.7709 (mmt)
REVERT: A  290 ARG cc_start: 0.8768 (tpt170) cc_final: 0.8064 (tpt90)
REVERT: A  395 VAL cc_start: 0.8489 (t) cc_final: 0.8137 (p)
REVERT: A  559 LEU cc_start: 0.9676 (mm) cc_final: 0.9447 (mm)
REVERT: A  572 MET cc_start: 0.8199 (mpp) cc_final: 0.7858 (mpp)
REVERT: A  573 ASP cc_start: 0.8271 (t70) cc_final: 0.7555 (t0)
REVERT: A 1037 PHE cc_start: 0.8301 (t80) cc_final: 0.7988 (t80)
REVERT: A 1050 GLU cc_start: 0.8787 (pt0) cc_final: 0.8438 (pt0)
REVERT: A 1064 LYS cc_start: 0.5928 (mmtt) cc_final: 0.5714 (mptt)
REVERT: A 1105 MET cc_start: 0.8594 (ttm) cc_final: 0.8096 (ttp)
REVERT: A 1141 MET cc_start: 0.8982 (tmm) cc_final: 0.8330 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1812
  time to fit residues: 34.4802
Evaluate side-chains
  102 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 60 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 52 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.095198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.081657 restraints weight = 32012.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.083703 restraints weight = 17522.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.085083 restraints weight = 11258.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.5891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7726  Z= 0.175
  Angle     :  0.546   7.350  10554  Z= 0.292
  Chirality :  0.039   0.176   1302
  Planarity :  0.003   0.029   1344
  Dihedral  :  8.906  78.506   1242
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.25), residues: 1119
  helix:  2.64 (0.19), residues: 720
  sheet:  0.65 (0.58), residues: 60
  loop :  0.02 (0.36), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1093 
 HIS   0.004   0.001   HIS A 953 
 PHE   0.014   0.001   PHE A 980 
 TYR   0.019   0.001   TYR A  90 
 ARG   0.004   0.001   ARG A 252 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8715 (p0) cc_final: 0.8295 (p0)
REVERT: A  213 MET cc_start: 0.8040 (ttp) cc_final: 0.7653 (ppp)
REVERT: A  245 MET cc_start: 0.9303 (ttm) cc_final: 0.8539 (tpp)
REVERT: A  282 MET cc_start: 0.8144 (mmm) cc_final: 0.7804 (mmt)
REVERT: A  290 ARG cc_start: 0.8711 (tpt170) cc_final: 0.7954 (tpt90)
REVERT: A  572 MET cc_start: 0.8160 (mpp) cc_final: 0.7936 (mpp)
REVERT: A  573 ASP cc_start: 0.8283 (t70) cc_final: 0.7618 (t0)
REVERT: A  989 ASP cc_start: 0.8755 (t70) cc_final: 0.8520 (t70)
REVERT: A 1037 PHE cc_start: 0.8282 (t80) cc_final: 0.7905 (t80)
REVERT: A 1041 SER cc_start: 0.8413 (p) cc_final: 0.8112 (p)
REVERT: A 1050 GLU cc_start: 0.8780 (pt0) cc_final: 0.8432 (pt0)
REVERT: A 1105 MET cc_start: 0.8529 (ttm) cc_final: 0.8045 (ttp)
REVERT: A 1141 MET cc_start: 0.8966 (tmm) cc_final: 0.8316 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1647
  time to fit residues: 30.7065
Evaluate side-chains
  98 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 55 optimal weight:   20.0000
   chunk 71 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A1092 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 = 0.3714 r_free = 0.3714 target = 0.093846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.080716 restraints weight = 31738.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.082809 restraints weight = 16871.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.084204 restraints weight = 10606.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.6046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7726  Z= 0.160
  Angle     :  0.550   7.372  10554  Z= 0.290
  Chirality :  0.039   0.176   1302
  Planarity :  0.003   0.028   1344
  Dihedral  :  8.522  72.381   1242
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.26), residues: 1119
  helix:  2.59 (0.19), residues: 721
  sheet:  0.78 (0.59), residues: 60
  loop :  0.02 (0.37), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1149 
 HIS   0.004   0.001   HIS A 953 
 PHE   0.011   0.001   PHE A 980 
 TYR   0.019   0.001   TYR A  90 
 ARG   0.003   0.000   ARG A 252 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8676 (p0) cc_final: 0.8270 (p0)
REVERT: A  213 MET cc_start: 0.8074 (ttp) cc_final: 0.7687 (ppp)
REVERT: A  245 MET cc_start: 0.9217 (ttm) cc_final: 0.8892 (tpp)
REVERT: A  290 ARG cc_start: 0.8666 (tpt170) cc_final: 0.7919 (tpt90)
REVERT: A  316 PHE cc_start: 0.8539 (t80) cc_final: 0.8214 (t80)
REVERT: A  572 MET cc_start: 0.8256 (mpp) cc_final: 0.7936 (mpp)
REVERT: A  573 ASP cc_start: 0.8312 (t70) cc_final: 0.7631 (t70)
REVERT: A 1037 PHE cc_start: 0.8263 (t80) cc_final: 0.7875 (t80)
REVERT: A 1050 GLU cc_start: 0.8767 (pt0) cc_final: 0.8415 (pt0)
REVERT: A 1105 MET cc_start: 0.8554 (ttm) cc_final: 0.8047 (ttp)
REVERT: A 1141 MET cc_start: 0.8959 (tmm) cc_final: 0.8326 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1606
  time to fit residues: 31.3562
Evaluate side-chains
  99 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 84 optimal weight:    0.2980
   chunk 1 optimal weight:    7.9990
   chunk 52 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 88 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 92 optimal weight:   20.0000
   chunk 26 optimal weight:    0.7980
   chunk 63 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A1092 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 = 0.3723 r_free = 0.3723 target = 0.096712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.083180 restraints weight = 32564.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.085256 restraints weight = 17672.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.086689 restraints weight = 11305.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.6273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7726  Z= 0.151
  Angle     :  0.535   7.662  10554  Z= 0.283
  Chirality :  0.039   0.173   1302
  Planarity :  0.003   0.027   1344
  Dihedral  :  8.093  68.616   1242
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.59 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.67 (0.26), residues: 1119
  helix:  2.64 (0.19), residues: 720
  sheet:  0.83 (0.60), residues: 60
  loop :  0.02 (0.37), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1149 
 HIS   0.004   0.001   HIS A 953 
 PHE   0.022   0.001   PHE A 158 
 TYR   0.008   0.001   TYR A1077 
 ARG   0.003   0.000   ARG A 154 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8642 (p0) cc_final: 0.8211 (p0)
REVERT: A  213 MET cc_start: 0.8055 (ttp) cc_final: 0.7666 (ppp)
REVERT: A  245 MET cc_start: 0.9218 (ttm) cc_final: 0.8861 (tpp)
REVERT: A  282 MET cc_start: 0.8215 (mmt) cc_final: 0.7921 (mmt)
REVERT: A  290 ARG cc_start: 0.8619 (tpt170) cc_final: 0.7903 (tpt90)
REVERT: A  316 PHE cc_start: 0.8492 (t80) cc_final: 0.8157 (t80)
REVERT: A  320 PHE cc_start: 0.8435 (t80) cc_final: 0.8227 (t80)
REVERT: A  572 MET cc_start: 0.8166 (mpp) cc_final: 0.7914 (mpp)
REVERT: A  573 ASP cc_start: 0.8291 (t70) cc_final: 0.7656 (t70)
REVERT: A  988 ASP cc_start: 0.8701 (t70) cc_final: 0.8432 (t0)
REVERT: A 1037 PHE cc_start: 0.8260 (t80) cc_final: 0.7848 (t80)
REVERT: A 1050 GLU cc_start: 0.8763 (pt0) cc_final: 0.8410 (pt0)
REVERT: A 1105 MET cc_start: 0.8477 (ttm) cc_final: 0.7984 (ttp)
REVERT: A 1141 MET cc_start: 0.8949 (tmm) cc_final: 0.8317 (tmm)
REVERT: A 1142 ASN cc_start: 0.8648 (t0) cc_final: 0.8435 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1674
  time to fit residues: 33.7599
Evaluate side-chains
  105 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 107 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 360 GLN
** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.092161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.077552 restraints weight = 31947.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.079580 restraints weight = 17606.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.080969 restraints weight = 11332.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.6328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7726  Z= 0.297
  Angle     :  0.645   9.262  10554  Z= 0.349
  Chirality :  0.042   0.188   1302
  Planarity :  0.003   0.026   1344
  Dihedral  :  8.029  65.778   1242
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.25), residues: 1119
  helix:  2.33 (0.19), residues: 728
  sheet:  1.26 (0.64), residues: 51
  loop : -0.31 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1093 
 HIS   0.005   0.001   HIS A 200 
 PHE   0.017   0.002   PHE A 192 
 TYR   0.012   0.001   TYR A 305 
 ARG   0.008   0.001   ARG A  75 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8763 (p0) cc_final: 0.8352 (p0)
REVERT: A  213 MET cc_start: 0.8167 (ttp) cc_final: 0.7539 (tmm)
REVERT: A  245 MET cc_start: 0.9251 (ttm) cc_final: 0.8916 (tpp)
REVERT: A  573 ASP cc_start: 0.8379 (t70) cc_final: 0.7701 (t0)
REVERT: A  954 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8815 (tm-30)
REVERT: A 1037 PHE cc_start: 0.8367 (t80) cc_final: 0.7946 (t80)
REVERT: A 1041 SER cc_start: 0.8383 (p) cc_final: 0.8035 (p)
REVERT: A 1050 GLU cc_start: 0.8755 (pt0) cc_final: 0.8359 (pt0)
REVERT: A 1105 MET cc_start: 0.8606 (ttm) cc_final: 0.8112 (ttp)
REVERT: A 1141 MET cc_start: 0.8934 (tmm) cc_final: 0.8280 (tmm)
REVERT: A 1142 ASN cc_start: 0.8757 (t0) cc_final: 0.8511 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1303
  time to fit residues: 26.1139
Evaluate side-chains
  101 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.093184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.080069 restraints weight = 32951.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.081856 restraints weight = 18924.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.083067 restraints weight = 12651.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.6473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7726  Z= 0.227
  Angle     :  0.596   8.615  10554  Z= 0.321
  Chirality :  0.041   0.182   1302
  Planarity :  0.003   0.029   1344
  Dihedral  :  7.872  66.699   1242
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.22 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.26), residues: 1119
  helix:  2.35 (0.19), residues: 721
  sheet:  0.66 (0.59), residues: 61
  loop : -0.25 (0.36), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1093 
 HIS   0.008   0.001   HIS A 200 
 PHE   0.020   0.002   PHE A1170 
 TYR   0.009   0.001   TYR A 305 
 ARG   0.004   0.001   ARG A 979 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2276.49 seconds
wall clock time: 41 minutes 32.61 seconds (2492.61 seconds total)