Starting phenix.real_space_refine
on Wed Mar 12 12:43:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d3r_7793/03_2025/6d3r_7793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d3r_7793/03_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_7793/03_2025/6d3r_7793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d3r_7793/03_2025/6d3r_7793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d3r_7793/03_2025/6d3r_7793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d3r_7793/03_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-5624/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: 5.96, per 1000 atoms: 0.78
  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: 2.09
  Conformation dependent library (CDL) restraints added in 992.5 milliseconds
  

  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: 1.05
  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: 3.02

  Time building geometry restraints manager: 2.46 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:             8.230
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     22.990
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.700
-------------------------------------------------------------------------------
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  : 0.845 
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: 0.1851
  time to fit residues: 62.9958
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  : 0.877 
-------------------------------------------------------------------------------
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 = 0.082092 restraints weight = 30367.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.084484 restraints weight = 15913.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086120 restraints weight = 9851.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
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  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.9186 (tp) cc_final: 0.8885 (tp)
REVERT: A   90 TYR cc_start: 0.8687 (t80) cc_final: 0.8332 (t80)
REVERT: A  193 ASP cc_start: 0.8701 (p0) cc_final: 0.8172 (t0)
REVERT: A  194 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8409 (tp30)
REVERT: A  200 HIS cc_start: 0.6567 (p90) cc_final: 0.6343 (p90)
REVERT: A  213 MET cc_start: 0.8330 (ttp) cc_final: 0.7988 (ppp)
REVERT: A  245 MET cc_start: 0.9301 (ttm) cc_final: 0.9037 (tpp)
REVERT: A  246 MET cc_start: 0.8857 (mmm) cc_final: 0.8217 (tmm)
REVERT: A  250 ASP cc_start: 0.8887 (m-30) cc_final: 0.8452 (m-30)
REVERT: A  290 ARG cc_start: 0.9040 (tpt170) cc_final: 0.8290 (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: 0.8760 (tm-30)
REVERT: A  370 ASN cc_start: 0.9455 (m-40) cc_final: 0.9188 (m110)
REVERT: A  379 GLU cc_start: 0.8273 (mp0) cc_final: 0.8057 (tp30)
REVERT: A  489 ILE cc_start: 0.8925 (mp) cc_final: 0.8491 (tp)
REVERT: A  572 MET cc_start: 0.8377 (mpp) cc_final: 0.8020 (mpp)
REVERT: A  573 ASP cc_start: 0.7922 (t70) cc_final: 0.7401 (t0)
REVERT: A 1037 PHE cc_start: 0.8430 (t80) cc_final: 0.8203 (t80)
REVERT: A 1105 MET cc_start: 0.8727 (ttm) cc_final: 0.8284 (ttp)
REVERT: A 1108 GLU cc_start: 0.8744 (tt0) cc_final: 0.8281 (tt0)
REVERT: A 1356 MET cc_start: 0.9249 (mtm) cc_final: 0.8981 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2252
  time to fit residues: 50.8575
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  : 1.063 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 74 optimal weight:    0.0470
   chunk 47 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 92 optimal weight:   30.0000
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6678

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.096330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.082885 restraints weight = 30949.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.085043 restraints weight = 16002.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.086491 restraints weight = 9925.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7726  Z= 0.185
  Angle     :  0.568   6.379  10554  Z= 0.324
  Chirality :  0.041   0.186   1302
  Planarity :  0.004   0.038   1344
  Dihedral  : 10.656  71.788   1242
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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:  2.41 (0.25), residues: 1119
  helix:  2.19 (0.19), residues: 734
  sheet:  1.40 (0.62), residues: 59
  loop :  0.33 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 278 
 HIS   0.005   0.001   HIS A 953 
 PHE   0.027   0.002   PHE A 313 
 TYR   0.008   0.001   TYR A 248 
 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
  159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.9164 (tp) cc_final: 0.8872 (tp)
REVERT: A  190 ASN cc_start: 0.8598 (p0) cc_final: 0.8331 (p0)
REVERT: A  193 ASP cc_start: 0.8681 (p0) cc_final: 0.8197 (t0)
REVERT: A  194 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8394 (tp30)
REVERT: A  200 HIS cc_start: 0.6802 (p90) cc_final: 0.6447 (p90)
REVERT: A  213 MET cc_start: 0.8235 (ttp) cc_final: 0.7906 (ppp)
REVERT: A  245 MET cc_start: 0.9299 (ttm) cc_final: 0.8544 (tmm)
REVERT: A  246 MET cc_start: 0.8858 (mmm) cc_final: 0.8532 (tmm)
REVERT: A  290 ARG cc_start: 0.8854 (tpt170) cc_final: 0.8162 (tpt90)
REVERT: A  344 CYS cc_start: 0.9084 (m) cc_final: 0.8839 (m)
REVERT: A  370 ASN cc_start: 0.9410 (m-40) cc_final: 0.9098 (m110)
REVERT: A  489 ILE cc_start: 0.8993 (mp) cc_final: 0.8611 (tp)
REVERT: A  559 LEU cc_start: 0.9680 (mm) cc_final: 0.9476 (mm)
REVERT: A  572 MET cc_start: 0.8439 (mpp) cc_final: 0.8143 (mpp)
REVERT: A  573 ASP cc_start: 0.8021 (t70) cc_final: 0.7614 (t0)
REVERT: A  989 ASP cc_start: 0.8724 (t70) cc_final: 0.8458 (t70)
REVERT: A 1037 PHE cc_start: 0.8452 (t80) cc_final: 0.8136 (t80)
REVERT: A 1141 MET cc_start: 0.9048 (tmm) cc_final: 0.8501 (tmm)
REVERT: A 1356 MET cc_start: 0.9206 (mtm) cc_final: 0.8931 (ttt)
REVERT: A 1360 ARG cc_start: 0.8331 (mtt180) cc_final: 0.8114 (mtt180)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2040
  time to fit residues: 47.5241
Evaluate side-chains
  109 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 99 optimal weight:    0.0010
   chunk 109 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0070
   chunk 48 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.5606

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

Flipped N/Q/H residues before XYZ refinement:
A1089 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 = 0.3777 r_free = 0.3777 target = 0.097515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.083881 restraints weight = 30888.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.086053 restraints weight = 16174.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.087508 restraints weight = 10094.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.4985

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= 0.177
  Angle     :  0.536   6.840  10554  Z= 0.298
  Chirality :  0.039   0.176   1302
  Planarity :  0.003   0.031   1344
  Dihedral  : 10.206  72.969   1242
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  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:  2.57 (0.25), residues: 1119
  helix:  2.37 (0.19), residues: 734
  sheet:  1.28 (0.62), residues: 59
  loop :  0.28 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 362 
 HIS   0.003   0.001   HIS A 953 
 PHE   0.014   0.001   PHE A 491 
 TYR   0.012   0.001   TYR A  90 
 ARG   0.007   0.001   ARG A 348 

*********************** 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
  146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8662 (p0) cc_final: 0.8319 (p0)
REVERT: A  193 ASP cc_start: 0.8692 (p0) cc_final: 0.8116 (t0)
REVERT: A  194 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8391 (tp30)
REVERT: A  213 MET cc_start: 0.8116 (ttp) cc_final: 0.7791 (ppp)
REVERT: A  245 MET cc_start: 0.9124 (ttm) cc_final: 0.8872 (tpp)
REVERT: A  290 ARG cc_start: 0.8747 (tpt170) cc_final: 0.8039 (tpt90)
REVERT: A  344 CYS cc_start: 0.9073 (m) cc_final: 0.8846 (m)
REVERT: A  559 LEU cc_start: 0.9661 (mm) cc_final: 0.9429 (mm)
REVERT: A  573 ASP cc_start: 0.8054 (t70) cc_final: 0.7644 (t0)
REVERT: A  954 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8728 (tm-30)
REVERT: A  961 LEU cc_start: 0.7339 (tp) cc_final: 0.7104 (tt)
REVERT: A  989 ASP cc_start: 0.8633 (t70) cc_final: 0.8421 (t70)
REVERT: A 1037 PHE cc_start: 0.8361 (t80) cc_final: 0.8067 (t80)
REVERT: A 1050 GLU cc_start: 0.8700 (pt0) cc_final: 0.8393 (pt0)
REVERT: A 1105 MET cc_start: 0.8336 (ttp) cc_final: 0.8100 (ttp)
REVERT: A 1141 MET cc_start: 0.9017 (tmm) cc_final: 0.8488 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1728
  time to fit residues: 35.3992
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  : 0.847 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 107 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 109 optimal weight:    0.3980
   overall best weight:    2.6964

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.090296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.076934 restraints weight = 31788.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.078936 restraints weight = 16921.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.080291 restraints weight = 10767.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.5347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   7726  Z= 0.318
  Angle     :  0.656   8.195  10554  Z= 0.364
  Chirality :  0.042   0.181   1302
  Planarity :  0.004   0.040   1344
  Dihedral  :  9.995  89.668   1242
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    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:  2.25 (0.25), residues: 1119
  helix:  2.26 (0.19), residues: 719
  sheet:  1.07 (0.63), residues: 53
  loop : -0.05 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 203 
 HIS   0.016   0.003   HIS A 200 
 PHE   0.017   0.002   PHE A1078 
 TYR   0.017   0.002   TYR A  90 
 ARG   0.007   0.001   ARG A1101 

*********************** 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
  126 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8726 (p0) cc_final: 0.8385 (p0)
REVERT: A  193 ASP cc_start: 0.9036 (p0) cc_final: 0.8099 (t0)
REVERT: A  194 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8407 (tp30)
REVERT: A  213 MET cc_start: 0.8165 (ttp) cc_final: 0.7777 (ppp)
REVERT: A  219 MET cc_start: 0.6372 (tmm) cc_final: 0.6066 (tmm)
REVERT: A  245 MET cc_start: 0.9279 (ttm) cc_final: 0.8948 (tpp)
REVERT: A  282 MET cc_start: 0.8527 (mmt) cc_final: 0.8070 (mmt)
REVERT: A  370 ASN cc_start: 0.9423 (m-40) cc_final: 0.9056 (m110)
REVERT: A  559 LEU cc_start: 0.9692 (mm) cc_final: 0.9482 (mm)
REVERT: A  573 ASP cc_start: 0.8289 (t70) cc_final: 0.7661 (t0)
REVERT: A  954 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8764 (tm-30)
REVERT: A  989 ASP cc_start: 0.8801 (t70) cc_final: 0.8594 (t70)
REVERT: A 1037 PHE cc_start: 0.8400 (t80) cc_final: 0.7986 (t80)
REVERT: A 1041 SER cc_start: 0.8639 (p) cc_final: 0.8272 (p)
REVERT: A 1141 MET cc_start: 0.8945 (tmm) cc_final: 0.8342 (tmm)
REVERT: A 1142 ASN cc_start: 0.8618 (t0) cc_final: 0.8398 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1875
  time to fit residues: 33.1546
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  : 0.834 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 28 optimal weight:    0.0370
   chunk 35 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0770
   chunk 38 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.3416

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.094803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.081359 restraints weight = 31019.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.083506 restraints weight = 16504.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.084949 restraints weight = 10415.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.5673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7726  Z= 0.164
  Angle     :  0.547   6.197  10554  Z= 0.295
  Chirality :  0.039   0.180   1302
  Planarity :  0.003   0.033   1344
  Dihedral  :  9.382  88.116   1242
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  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:  2.65 (0.26), residues: 1119
  helix:  2.56 (0.19), residues: 725
  sheet:  0.90 (0.59), residues: 59
  loop :  0.12 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1149 
 HIS   0.003   0.001   HIS A 148 
 PHE   0.014   0.001   PHE A 980 
 TYR   0.018   0.001   TYR A  90 
 ARG   0.010   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
  145 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8693 (p0) cc_final: 0.8309 (p0)
REVERT: A  213 MET cc_start: 0.8098 (ttp) cc_final: 0.7719 (ppp)
REVERT: A  245 MET cc_start: 0.9226 (ttm) cc_final: 0.8872 (tpp)
REVERT: A  290 ARG cc_start: 0.8741 (tpt170) cc_final: 0.8081 (tpt90)
REVERT: A  370 ASN cc_start: 0.9408 (m-40) cc_final: 0.9050 (m110)
REVERT: A  489 ILE cc_start: 0.9607 (pt) cc_final: 0.9093 (tp)
REVERT: A  559 LEU cc_start: 0.9668 (mm) cc_final: 0.9439 (mm)
REVERT: A  572 MET cc_start: 0.8282 (mpp) cc_final: 0.7841 (mpp)
REVERT: A  573 ASP cc_start: 0.8227 (t70) cc_final: 0.7587 (t0)
REVERT: A 1037 PHE cc_start: 0.8269 (t80) cc_final: 0.7914 (t80)
REVERT: A 1050 GLU cc_start: 0.8805 (pt0) cc_final: 0.8460 (pt0)
REVERT: A 1141 MET cc_start: 0.8963 (tmm) cc_final: 0.8331 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1750
  time to fit residues: 36.4304
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  : 0.830 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 39 optimal weight:    0.0980
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 60 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.093936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.080762 restraints weight = 30866.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.082880 restraints weight = 16546.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.084285 restraints weight = 10437.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.5959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7726  Z= 0.158
  Angle     :  0.531   6.855  10554  Z= 0.288
  Chirality :  0.039   0.171   1302
  Planarity :  0.003   0.042   1344
  Dihedral  :  8.927  82.115   1242
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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:  2.66 (0.26), residues: 1119
  helix:  2.62 (0.19), residues: 727
  sheet:  0.95 (0.63), residues: 53
  loop : -0.02 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1093 
 HIS   0.006   0.001   HIS A 200 
 PHE   0.011   0.001   PHE A 980 
 TYR   0.007   0.001   TYR A1077 
 ARG   0.004   0.001   ARG A 488 

*********************** 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
  134 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8654 (p0) cc_final: 0.8230 (p0)
REVERT: A  213 MET cc_start: 0.8089 (ttp) cc_final: 0.7707 (ppp)
REVERT: A  245 MET cc_start: 0.9281 (ttm) cc_final: 0.8509 (tpp)
REVERT: A  282 MET cc_start: 0.8530 (mmm) cc_final: 0.7995 (mmt)
REVERT: A  290 ARG cc_start: 0.8682 (tpt170) cc_final: 0.7956 (tpt90)
REVERT: A  316 PHE cc_start: 0.8532 (t80) cc_final: 0.8126 (t80)
REVERT: A  572 MET cc_start: 0.8278 (mpp) cc_final: 0.7855 (mpp)
REVERT: A  573 ASP cc_start: 0.8185 (t70) cc_final: 0.7607 (t0)
REVERT: A  989 ASP cc_start: 0.8728 (t70) cc_final: 0.8454 (t70)
REVERT: A 1037 PHE cc_start: 0.8263 (t80) cc_final: 0.7904 (t80)
REVERT: A 1050 GLU cc_start: 0.8787 (pt0) cc_final: 0.8439 (pt0)
REVERT: A 1141 MET cc_start: 0.9009 (tmm) cc_final: 0.8389 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1525
  time to fit residues: 30.0265
Evaluate side-chains
  100 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 87 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 55 optimal weight:    9.9990
   chunk 71 optimal weight:    0.0980
   chunk 34 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.097266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.083727 restraints weight = 32474.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.085830 restraints weight = 17636.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.087239 restraints weight = 11275.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.6111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7726  Z= 0.152
  Angle     :  0.528   7.124  10554  Z= 0.285
  Chirality :  0.039   0.171   1302
  Planarity :  0.003   0.044   1344
  Dihedral  :  8.514  76.522   1242
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.32 %
    Favored  : 97.59 %
  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:  2.66 (0.26), residues: 1119
  helix:  2.62 (0.19), residues: 726
  sheet:  1.02 (0.64), residues: 53
  loop : -0.03 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1093 
 HIS   0.005   0.001   HIS A 200 
 PHE   0.017   0.001   PHE A 158 
 TYR   0.007   0.001   TYR A1077 
 ARG   0.004   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
  138 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8483 (p0) cc_final: 0.8046 (p0)
REVERT: A  193 ASP cc_start: 0.8820 (p0) cc_final: 0.8528 (p0)
REVERT: A  213 MET cc_start: 0.8034 (ttp) cc_final: 0.7690 (ppp)
REVERT: A  245 MET cc_start: 0.9158 (ttm) cc_final: 0.8733 (tpp)
REVERT: A  290 ARG cc_start: 0.8619 (tpt170) cc_final: 0.7891 (tpt90)
REVERT: A  304 ARG cc_start: 0.9088 (mtt-85) cc_final: 0.8623 (ttm170)
REVERT: A  316 PHE cc_start: 0.8535 (t80) cc_final: 0.8113 (t80)
REVERT: A  573 ASP cc_start: 0.8196 (t70) cc_final: 0.7643 (t0)
REVERT: A 1037 PHE cc_start: 0.8216 (t80) cc_final: 0.7857 (t80)
REVERT: A 1050 GLU cc_start: 0.8733 (pt0) cc_final: 0.8409 (pt0)
REVERT: A 1141 MET cc_start: 0.8961 (tmm) cc_final: 0.8353 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1511
  time to fit residues: 30.3362
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  : 0.790 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 1 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 88 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 92 optimal weight:   20.0000
   chunk 26 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.096217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.081342 restraints weight = 31277.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.083599 restraints weight = 16975.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.085093 restraints weight = 10818.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.6217

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= 0.163
  Angle     :  0.545   8.031  10554  Z= 0.288
  Chirality :  0.039   0.168   1302
  Planarity :  0.003   0.044   1344
  Dihedral  :  8.170  71.448   1242
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.68 %
    Favored  : 97.23 %
  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:  2.69 (0.26), residues: 1119
  helix:  2.71 (0.19), residues: 717
  sheet:  0.95 (0.64), residues: 53
  loop : -0.07 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1093 
 HIS   0.005   0.001   HIS A 200 
 PHE   0.017   0.001   PHE A 201 
 TYR   0.012   0.001   TYR A 962 
 ARG   0.004   0.001   ARG A 252 

*********************** 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
  135 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8549 (p0) cc_final: 0.8118 (p0)
REVERT: A  193 ASP cc_start: 0.8814 (p0) cc_final: 0.8601 (p0)
REVERT: A  213 MET cc_start: 0.8095 (ttp) cc_final: 0.7718 (ppp)
REVERT: A  245 MET cc_start: 0.9151 (ttm) cc_final: 0.8759 (tpp)
REVERT: A  282 MET cc_start: 0.8407 (mmm) cc_final: 0.8056 (mmt)
REVERT: A  290 ARG cc_start: 0.8614 (tpt170) cc_final: 0.7867 (tpt90)
REVERT: A  316 PHE cc_start: 0.8542 (t80) cc_final: 0.8108 (t80)
REVERT: A  573 ASP cc_start: 0.8256 (t70) cc_final: 0.7673 (t0)
REVERT: A 1037 PHE cc_start: 0.8242 (t80) cc_final: 0.7860 (t80)
REVERT: A 1050 GLU cc_start: 0.8746 (pt0) cc_final: 0.8414 (pt0)
REVERT: A 1072 PHE cc_start: 0.8055 (m-80) cc_final: 0.7819 (m-80)
REVERT: A 1141 MET cc_start: 0.8972 (tmm) cc_final: 0.8352 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1559
  time to fit residues: 30.9003
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  : 0.870 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 12 optimal weight:    0.6980
   chunk 73 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0980
   chunk 107 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3751 r_free = 0.3751 target = 0.097844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.081223 restraints weight = 31458.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.083498 restraints weight = 17398.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.085042 restraints weight = 11275.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.6357

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= 0.162
  Angle     :  0.541   7.690  10554  Z= 0.288
  Chirality :  0.039   0.168   1302
  Planarity :  0.003   0.037   1344
  Dihedral  :  7.716  68.285   1242
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.50 %
    Favored  : 97.41 %
  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:  2.74 (0.26), residues: 1119
  helix:  2.73 (0.19), residues: 717
  sheet:  0.94 (0.60), residues: 59
  loop : -0.02 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1093 
 HIS   0.005   0.001   HIS A 200 
 PHE   0.023   0.001   PHE A 320 
 TYR   0.011   0.001   TYR A 564 
 ARG   0.006   0.001   ARG A 154 

********************** 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
  133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8483 (p0) cc_final: 0.8031 (p0)
REVERT: A  213 MET cc_start: 0.8014 (ttp) cc_final: 0.7713 (ppp)
REVERT: A  245 MET cc_start: 0.9256 (ttm) cc_final: 0.8899 (tpp)
REVERT: A  290 ARG cc_start: 0.8603 (tpt170) cc_final: 0.7844 (tpt90)
REVERT: A  316 PHE cc_start: 0.8543 (t80) cc_final: 0.8109 (t80)
REVERT: A  573 ASP cc_start: 0.8251 (t70) cc_final: 0.7740 (t70)
REVERT: A  989 ASP cc_start: 0.8642 (t70) cc_final: 0.8418 (t70)
REVERT: A 1050 GLU cc_start: 0.8721 (pt0) cc_final: 0.8387 (pt0)
REVERT: A 1141 MET cc_start: 0.8914 (tmm) cc_final: 0.8308 (tmm)
REVERT: A 1358 LEU cc_start: 0.9628 (mp) cc_final: 0.9325 (tt)
REVERT: A 1360 ARG cc_start: 0.8511 (mtt180) cc_final: 0.8254 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1546
  time to fit residues: 30.2232
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  : 0.898 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 97 optimal weight:    0.2980
   chunk 38 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0980
   chunk 104 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 94 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3720 r_free = 0.3720 target = 0.096367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.083235 restraints weight = 32294.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.085169 restraints weight = 18313.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.086433 restraints weight = 12069.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.6498

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= 0.167
  Angle     :  0.544   8.222  10554  Z= 0.289
  Chirality :  0.039   0.166   1302
  Planarity :  0.003   0.041   1344
  Dihedral  :  7.285  66.696   1242
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  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:  2.75 (0.26), residues: 1119
  helix:  2.77 (0.19), residues: 726
  sheet:  0.70 (0.59), residues: 63
  loop : -0.13 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1093 
 HIS   0.005   0.001   HIS A 200 
 PHE   0.014   0.001   PHE A 509 
 TYR   0.007   0.001   TYR A 305 
 ARG   0.005   0.001   ARG A 154 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2466.64 seconds
wall clock time: 44 minutes 9.00 seconds (2649.00 seconds total)