Starting phenix.real_space_refine
on Wed Sep 17 09:53:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d3r_7793/09_2025/6d3r_7793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d3r_7793/09_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_7793/09_2025/6d3r_7793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d3r_7793/09_2025/6d3r_7793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d3r_7793/09_2025/6d3r_7793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d3r_7793/09_2025/6d3r_7793.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'PHE:plan': 29, 'TRP:plan': 6, 'TYR:plan': 19, 'ASP:plan': 27, 'ASN:plan1': 10, 'GLU:plan': 36, 'ARG:plan': 18, 'GLN:plan1': 22, 'HIS:plan': 8}
          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: 2.12, per 1000 atoms: 0.28
  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: 0.77
  Conformation dependent library (CDL) restraints added in 458.2 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.35
  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: 1.85

  Time building geometry restraints manager: 1.02 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:             6.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.210
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.650
-------------------------------------------------------------------------------
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= 1.014
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.010   0.001   ARG A1070 
 TYR   0.072   0.006   TYR A 381 
 PHE   0.089   0.008   PHE A 968 
 TRP   0.030   0.008   TRP A 362 
 HIS   0.037   0.004   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.01659 ( 7726)
  covalent geometry    : angle       1.74859 (10554)
  hydrogen bonds       : bond        0.21034 (  613)
  hydrogen bonds       : angle       6.83771 ( 1785)

*********************** 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  : 0.304 
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: 0.0876
  time to fit residues: 29.8240
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  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.1188

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.097530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.082458 restraints weight = 30576.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.084803 restraints weight = 15829.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.086439 restraints weight = 9965.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.087415 restraints weight = 6897.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.088237 restraints weight = 5371.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7726  Z= 0.203
  Angle     :  0.672   7.615  10554  Z= 0.387
  Chirality :  0.043   0.207   1302
  Planarity :  0.005   0.059   1344
  Dihedral  : 11.152  74.862   1242
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.66
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.24), residues: 1119
  helix:  1.90 (0.18), residues: 727
  sheet:  1.64 (0.59), residues: 70
  loop :  0.39 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 348 
 TYR   0.011   0.001   TYR A 564 
 PHE   0.026   0.002   PHE A 491 
 TRP   0.036   0.002   TRP A 278 
 HIS   0.006   0.002   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 7726)
  covalent geometry    : angle       0.67243 (10554)
  hydrogen bonds       : bond        0.09328 (  613)
  hydrogen bonds       : angle       4.76091 ( 1785)

*********************** 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
  170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.9209 (tp) cc_final: 0.8892 (tp)
REVERT: A   90 TYR cc_start: 0.8688 (t80) cc_final: 0.8296 (t80)
REVERT: A  193 ASP cc_start: 0.8703 (p0) cc_final: 0.8184 (t0)
REVERT: A  194 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8387 (tp30)
REVERT: A  200 HIS cc_start: 0.6501 (p90) cc_final: 0.6247 (p90)
REVERT: A  213 MET cc_start: 0.8327 (ttp) cc_final: 0.7961 (ppp)
REVERT: A  245 MET cc_start: 0.9294 (ttm) cc_final: 0.8802 (tmm)
REVERT: A  246 MET cc_start: 0.8847 (mmm) cc_final: 0.8527 (tmm)
REVERT: A  290 ARG cc_start: 0.9003 (tpt170) cc_final: 0.8234 (tpt90)
REVERT: A  344 CYS cc_start: 0.9158 (m) cc_final: 0.8916 (m)
REVERT: A  360 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8774 (tm-30)
REVERT: A  370 ASN cc_start: 0.9463 (m-40) cc_final: 0.9191 (m110)
REVERT: A  489 ILE cc_start: 0.8886 (mp) cc_final: 0.8419 (tp)
REVERT: A  542 LEU cc_start: 0.8761 (mt) cc_final: 0.8448 (mp)
REVERT: A  572 MET cc_start: 0.8334 (mpp) cc_final: 0.7985 (mpp)
REVERT: A  573 ASP cc_start: 0.7848 (t70) cc_final: 0.7367 (t0)
REVERT: A 1037 PHE cc_start: 0.8418 (t80) cc_final: 0.8208 (t80)
REVERT: A 1105 MET cc_start: 0.8774 (ttm) cc_final: 0.8323 (ttp)
REVERT: A 1108 GLU cc_start: 0.8733 (tt0) cc_final: 0.8231 (tt0)
REVERT: A 1356 MET cc_start: 0.9233 (mtm) cc_final: 0.8973 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0854
  time to fit residues: 19.8047
Evaluate side-chains
  114 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 96 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   chunk 44 optimal weight:    8.9990
   chunk 29 optimal weight:    0.4980
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1089 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.091791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.078499 restraints weight = 31575.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.080517 restraints weight = 16584.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.081837 restraints weight = 10350.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.082765 restraints weight = 7431.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.083254 restraints weight = 5786.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.4476

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= 0.226
  Angle     :  0.642   8.562  10554  Z= 0.366
  Chirality :  0.042   0.189   1302
  Planarity :  0.004   0.040   1344
  Dihedral  : 10.718  72.050   1242
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.25), residues: 1119
  helix:  2.04 (0.19), residues: 734
  sheet:  1.24 (0.54), residues: 70
  loop :  0.28 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 348 
 TYR   0.010   0.001   TYR A 305 
 PHE   0.035   0.002   PHE A 313 
 TRP   0.022   0.002   TRP A 362 
 HIS   0.005   0.002   HIS A1089 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 7726)
  covalent geometry    : angle       0.64174 (10554)
  hydrogen bonds       : bond        0.08161 (  613)
  hydrogen bonds       : angle       4.54379 ( 1785)

*********************** 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
  130 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.9239 (tp) cc_final: 0.8977 (tp)
REVERT: A  190 ASN cc_start: 0.8590 (p0) cc_final: 0.8350 (p0)
REVERT: A  193 ASP cc_start: 0.8854 (p0) cc_final: 0.8211 (t0)
REVERT: A  194 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8364 (tp30)
REVERT: A  213 MET cc_start: 0.8248 (ttp) cc_final: 0.7719 (tmm)
REVERT: A  245 MET cc_start: 0.9326 (ttm) cc_final: 0.8797 (tmm)
REVERT: A  246 MET cc_start: 0.8806 (mmm) cc_final: 0.8592 (tmm)
REVERT: A  344 CYS cc_start: 0.9119 (m) cc_final: 0.8875 (m)
REVERT: A  370 ASN cc_start: 0.9425 (m-40) cc_final: 0.9127 (m110)
REVERT: A  573 ASP cc_start: 0.8130 (t70) cc_final: 0.7649 (t0)
REVERT: A 1037 PHE cc_start: 0.8453 (t80) cc_final: 0.8190 (t80)
REVERT: A 1041 SER cc_start: 0.8710 (p) cc_final: 0.8466 (p)
REVERT: A 1069 LEU cc_start: 0.9205 (mt) cc_final: 0.9002 (mt)
REVERT: A 1105 MET cc_start: 0.8678 (ttm) cc_final: 0.8473 (ttp)
REVERT: A 1141 MET cc_start: 0.8989 (tmm) cc_final: 0.8368 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0664
  time to fit residues: 12.7969
Evaluate side-chains
  93 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0170
   chunk 4 optimal weight:    0.8980
   chunk 60 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   chunk 77 optimal weight:    0.3980
   chunk 98 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.094944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.081518 restraints weight = 31196.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.083664 restraints weight = 16331.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.085086 restraints weight = 10176.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.086055 restraints weight = 7219.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.086548 restraints weight = 5605.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.4941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7726  Z= 0.151
  Angle     :  0.544   7.481  10554  Z= 0.307
  Chirality :  0.040   0.187   1302
  Planarity :  0.003   0.036   1344
  Dihedral  : 10.173  78.335   1242
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.25), residues: 1119
  helix:  2.31 (0.19), residues: 735
  sheet:  1.17 (0.54), residues: 70
  loop :  0.26 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 348 
 TYR   0.007   0.001   TYR A 564 
 PHE   0.013   0.001   PHE A 317 
 TRP   0.018   0.001   TRP A 362 
 HIS   0.004   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7726)
  covalent geometry    : angle       0.54351 (10554)
  hydrogen bonds       : bond        0.07205 (  613)
  hydrogen bonds       : angle       4.00407 ( 1785)

*********************** 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
  142 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8648 (p0) cc_final: 0.8339 (p0)
REVERT: A  213 MET cc_start: 0.8210 (ttp) cc_final: 0.7742 (ppp)
REVERT: A  245 MET cc_start: 0.9136 (ttm) cc_final: 0.8935 (tpp)
REVERT: A  290 ARG cc_start: 0.8858 (tpt170) cc_final: 0.8134 (tpt90)
REVERT: A  370 ASN cc_start: 0.9405 (m-40) cc_final: 0.9069 (m110)
REVERT: A  559 LEU cc_start: 0.9668 (mm) cc_final: 0.9452 (mm)
REVERT: A  572 MET cc_start: 0.8198 (mpp) cc_final: 0.7781 (mpp)
REVERT: A  573 ASP cc_start: 0.8078 (t70) cc_final: 0.7515 (t0)
REVERT: A  954 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8781 (tm-30)
REVERT: A  989 ASP cc_start: 0.8730 (t70) cc_final: 0.8494 (t70)
REVERT: A 1037 PHE cc_start: 0.8319 (t80) cc_final: 0.8017 (t80)
REVERT: A 1105 MET cc_start: 0.8586 (ttm) cc_final: 0.8059 (ttp)
REVERT: A 1141 MET cc_start: 0.9021 (tmm) cc_final: 0.8522 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0771
  time to fit residues: 15.4628
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  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:   20.0000
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0070
   chunk 60 optimal weight:    8.9990
   chunk 108 optimal weight:   30.0000
   chunk 77 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   overall best weight:    0.8202

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.095353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.081970 restraints weight = 31369.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.084075 restraints weight = 16586.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.085500 restraints weight = 10375.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.086417 restraints weight = 7336.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.087108 restraints weight = 5751.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.5358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7726  Z= 0.141
  Angle     :  0.550   8.519  10554  Z= 0.300
  Chirality :  0.040   0.176   1302
  Planarity :  0.003   0.032   1344
  Dihedral  :  9.848  87.870   1242
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.25), residues: 1119
  helix:  2.48 (0.19), residues: 726
  sheet:  1.06 (0.59), residues: 59
  loop :  0.20 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 348 
 TYR   0.007   0.001   TYR A1077 
 PHE   0.011   0.001   PHE A 317 
 TRP   0.015   0.001   TRP A 362 
 HIS   0.003   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7726)
  covalent geometry    : angle       0.55025 (10554)
  hydrogen bonds       : bond        0.06604 (  613)
  hydrogen bonds       : angle       3.86892 ( 1785)

*********************** 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
  139 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8653 (p0) cc_final: 0.8298 (p0)
REVERT: A  213 MET cc_start: 0.8159 (ttp) cc_final: 0.7752 (ppp)
REVERT: A  230 PHE cc_start: 0.7197 (t80) cc_final: 0.6873 (t80)
REVERT: A  245 MET cc_start: 0.9269 (ttm) cc_final: 0.8912 (tpp)
REVERT: A  282 MET cc_start: 0.8598 (mmp) cc_final: 0.8243 (mmp)
REVERT: A  290 ARG cc_start: 0.8780 (tpt170) cc_final: 0.8059 (tpt90)
REVERT: A  370 ASN cc_start: 0.9393 (m-40) cc_final: 0.9043 (m110)
REVERT: A  559 LEU cc_start: 0.9669 (mm) cc_final: 0.9434 (mm)
REVERT: A  572 MET cc_start: 0.8302 (mpp) cc_final: 0.7893 (mpp)
REVERT: A  573 ASP cc_start: 0.8156 (t70) cc_final: 0.7573 (t0)
REVERT: A  954 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8743 (tm-30)
REVERT: A  989 ASP cc_start: 0.8724 (t70) cc_final: 0.8491 (t70)
REVERT: A 1037 PHE cc_start: 0.8300 (t80) cc_final: 0.8015 (t80)
REVERT: A 1050 GLU cc_start: 0.8709 (pt0) cc_final: 0.8357 (pt0)
REVERT: A 1105 MET cc_start: 0.8596 (ttm) cc_final: 0.8061 (ttp)
REVERT: A 1141 MET cc_start: 0.9058 (tmm) cc_final: 0.8595 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0802
  time to fit residues: 15.5589
Evaluate side-chains
  108 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0470
   chunk 69 optimal weight:    7.9990
   chunk 55 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    0.9282

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.094931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.081432 restraints weight = 31018.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.083548 restraints weight = 16575.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.084988 restraints weight = 10455.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.085917 restraints weight = 7405.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.086649 restraints weight = 5822.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.5640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7726  Z= 0.137
  Angle     :  0.549   9.735  10554  Z= 0.296
  Chirality :  0.040   0.206   1302
  Planarity :  0.003   0.027   1344
  Dihedral  :  9.373  89.473   1242
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.26), residues: 1119
  helix:  2.56 (0.19), residues: 728
  sheet:  0.90 (0.59), residues: 60
  loop :  0.16 (0.36), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 252 
 TYR   0.007   0.001   TYR A1077 
 PHE   0.015   0.001   PHE A1030 
 TRP   0.008   0.001   TRP A 362 
 HIS   0.005   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7726)
  covalent geometry    : angle       0.54923 (10554)
  hydrogen bonds       : bond        0.06298 (  613)
  hydrogen bonds       : angle       3.76223 ( 1785)

*********************** 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
  142 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8684 (p0) cc_final: 0.8295 (p0)
REVERT: A  213 MET cc_start: 0.8108 (ttp) cc_final: 0.7709 (ppp)
REVERT: A  245 MET cc_start: 0.9228 (ttm) cc_final: 0.8885 (tpp)
REVERT: A  282 MET cc_start: 0.8505 (mmp) cc_final: 0.8266 (mmt)
REVERT: A  290 ARG cc_start: 0.8751 (tpt170) cc_final: 0.7989 (tpt90)
REVERT: A  370 ASN cc_start: 0.9395 (m-40) cc_final: 0.9051 (m110)
REVERT: A  559 LEU cc_start: 0.9677 (mm) cc_final: 0.9440 (mm)
REVERT: A  572 MET cc_start: 0.8195 (mpp) cc_final: 0.7857 (mpp)
REVERT: A  573 ASP cc_start: 0.8150 (t70) cc_final: 0.7547 (t0)
REVERT: A 1037 PHE cc_start: 0.8267 (t80) cc_final: 0.7960 (t80)
REVERT: A 1050 GLU cc_start: 0.8752 (pt0) cc_final: 0.8419 (pt0)
REVERT: A 1105 MET cc_start: 0.8578 (ttm) cc_final: 0.8059 (ttp)
REVERT: A 1141 MET cc_start: 0.9080 (tmm) cc_final: 0.8652 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0752
  time to fit residues: 15.3291
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  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.095341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.082002 restraints weight = 31234.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.084113 restraints weight = 16647.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.085537 restraints weight = 10439.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.086512 restraints weight = 7406.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.087197 restraints weight = 5796.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.5845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7726  Z= 0.134
  Angle     :  0.541   7.281  10554  Z= 0.291
  Chirality :  0.039   0.171   1302
  Planarity :  0.004   0.080   1344
  Dihedral  :  8.925  83.029   1242
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.26), residues: 1119
  helix:  2.60 (0.19), residues: 724
  sheet:  0.99 (0.60), residues: 60
  loop :  0.27 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 252 
 TYR   0.007   0.001   TYR A1077 
 PHE   0.021   0.001   PHE A 316 
 TRP   0.008   0.001   TRP A1093 
 HIS   0.004   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7726)
  covalent geometry    : angle       0.54062 (10554)
  hydrogen bonds       : bond        0.06038 (  613)
  hydrogen bonds       : angle       3.71544 ( 1785)

*********************** 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
  140 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8693 (p0) cc_final: 0.8289 (p0)
REVERT: A  213 MET cc_start: 0.8090 (ttp) cc_final: 0.7717 (ppp)
REVERT: A  230 PHE cc_start: 0.6852 (t80) cc_final: 0.6203 (t80)
REVERT: A  245 MET cc_start: 0.9224 (ttm) cc_final: 0.8859 (tpp)
REVERT: A  282 MET cc_start: 0.8457 (mmp) cc_final: 0.8176 (mmt)
REVERT: A  290 ARG cc_start: 0.8706 (tpt170) cc_final: 0.7970 (tpt90)
REVERT: A  572 MET cc_start: 0.8216 (mpp) cc_final: 0.8015 (mpp)
REVERT: A  573 ASP cc_start: 0.8196 (t70) cc_final: 0.7556 (t0)
REVERT: A  954 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8809 (tm-30)
REVERT: A 1037 PHE cc_start: 0.8280 (t80) cc_final: 0.7934 (t80)
REVERT: A 1041 SER cc_start: 0.8412 (p) cc_final: 0.8127 (p)
REVERT: A 1050 GLU cc_start: 0.8741 (pt0) cc_final: 0.8390 (pt0)
REVERT: A 1105 MET cc_start: 0.8601 (ttm) cc_final: 0.8071 (ttp)
REVERT: A 1141 MET cc_start: 0.9076 (tmm) cc_final: 0.8622 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0734
  time to fit residues: 14.8535
Evaluate side-chains
  106 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0980
   chunk 82 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 84 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 110 optimal weight:    0.2980
   chunk 94 optimal weight:    8.9990
   chunk 56 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3750 r_free = 0.3750 target = 0.095968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.082564 restraints weight = 31455.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.084721 restraints weight = 16647.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.086147 restraints weight = 10427.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.087081 restraints weight = 7392.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.087813 restraints weight = 5792.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.6051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7726  Z= 0.130
  Angle     :  0.538   7.174  10554  Z= 0.289
  Chirality :  0.039   0.203   1302
  Planarity :  0.003   0.027   1344
  Dihedral  :  8.512  76.716   1242
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.74 (0.26), residues: 1119
  helix:  2.61 (0.19), residues: 727
  sheet:  0.95 (0.60), residues: 60
  loop :  0.18 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 348 
 TYR   0.008   0.001   TYR A1077 
 PHE   0.022   0.001   PHE A 317 
 TRP   0.008   0.001   TRP A 240 
 HIS   0.004   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 7726)
  covalent geometry    : angle       0.53765 (10554)
  hydrogen bonds       : bond        0.05897 (  613)
  hydrogen bonds       : angle       3.63024 ( 1785)

*********************** 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
  140 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8646 (p0) cc_final: 0.8218 (p0)
REVERT: A  213 MET cc_start: 0.8073 (ttp) cc_final: 0.7723 (ppp)
REVERT: A  245 MET cc_start: 0.9299 (ttm) cc_final: 0.8767 (tpp)
REVERT: A  282 MET cc_start: 0.8376 (mmp) cc_final: 0.8117 (mmt)
REVERT: A  290 ARG cc_start: 0.8618 (tpt170) cc_final: 0.7909 (tpt90)
REVERT: A  572 MET cc_start: 0.8168 (mpp) cc_final: 0.7952 (mpp)
REVERT: A  573 ASP cc_start: 0.8174 (t70) cc_final: 0.7545 (t0)
REVERT: A  954 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8783 (tm-30)
REVERT: A 1037 PHE cc_start: 0.8227 (t80) cc_final: 0.7876 (t80)
REVERT: A 1050 GLU cc_start: 0.8725 (pt0) cc_final: 0.8390 (pt0)
REVERT: A 1105 MET cc_start: 0.8473 (ttm) cc_final: 0.8037 (ttp)
REVERT: A 1141 MET cc_start: 0.9055 (tmm) cc_final: 0.8571 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0740
  time to fit residues: 14.9562
Evaluate side-chains
  108 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.0670
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 109 optimal weight:    0.1980
   chunk 53 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.5920

-------------------------------------------------------------------------------
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 = 0.3747 r_free = 0.3747 target = 0.095855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.082468 restraints weight = 31300.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.084622 restraints weight = 16708.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.086073 restraints weight = 10510.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.087031 restraints weight = 7433.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.087736 restraints weight = 5809.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.6207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7726  Z= 0.126
  Angle     :  0.541   7.547  10554  Z= 0.285
  Chirality :  0.039   0.169   1302
  Planarity :  0.003   0.027   1344
  Dihedral  :  8.153  72.192   1242
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.76 (0.26), residues: 1119
  helix:  2.63 (0.19), residues: 723
  sheet:  0.47 (0.58), residues: 68
  loop :  0.33 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 348 
 TYR   0.007   0.001   TYR A1077 
 PHE   0.011   0.001   PHE A 509 
 TRP   0.009   0.001   TRP A 240 
 HIS   0.004   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 7726)
  covalent geometry    : angle       0.54072 (10554)
  hydrogen bonds       : bond        0.05727 (  613)
  hydrogen bonds       : angle       3.59055 ( 1785)

*********************** 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
  143 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.8603 (p0) cc_final: 0.8149 (p0)
REVERT: A  213 MET cc_start: 0.8052 (ttp) cc_final: 0.7704 (ppp)
REVERT: A  245 MET cc_start: 0.9279 (ttm) cc_final: 0.8627 (tpp)
REVERT: A  282 MET cc_start: 0.8287 (mmp) cc_final: 0.8087 (mmt)
REVERT: A  290 ARG cc_start: 0.8564 (tpt170) cc_final: 0.7843 (tpt90)
REVERT: A  573 ASP cc_start: 0.8198 (t70) cc_final: 0.7567 (t0)
REVERT: A  954 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8770 (tm-30)
REVERT: A  995 VAL cc_start: 0.9080 (p) cc_final: 0.8802 (p)
REVERT: A 1037 PHE cc_start: 0.8215 (t80) cc_final: 0.7864 (t80)
REVERT: A 1105 MET cc_start: 0.8454 (ttm) cc_final: 0.8021 (ttp)
REVERT: A 1141 MET cc_start: 0.9005 (tmm) cc_final: 0.8526 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0682
  time to fit residues: 14.2868
Evaluate side-chains
  113 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 100 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 92 optimal weight:   20.0000
   chunk 10 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.4382

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3716 r_free = 0.3716 target = 0.095789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.082262 restraints weight = 32629.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.084368 restraints weight = 17802.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.085780 restraints weight = 11374.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.086717 restraints weight = 8192.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.087247 restraints weight = 6426.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.6303

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= 0.149
  Angle     :  0.584  13.160  10554  Z= 0.308
  Chirality :  0.040   0.170   1302
  Planarity :  0.003   0.026   1344
  Dihedral  :  7.804  67.575   1242
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.26), residues: 1119
  helix:  2.63 (0.19), residues: 718
  sheet:  1.05 (0.60), residues: 60
  loop :  0.07 (0.36), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 154 
 TYR   0.008   0.001   TYR A 305 
 PHE   0.016   0.001   PHE A 158 
 TRP   0.021   0.001   TRP A1093 
 HIS   0.004   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7726)
  covalent geometry    : angle       0.58395 (10554)
  hydrogen bonds       : bond        0.05962 (  613)
  hydrogen bonds       : angle       3.75507 ( 1785)

********************** 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
  136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 MET cc_start: 0.8882 (mmm) cc_final: 0.7993 (mmt)
REVERT: A  190 ASN cc_start: 0.8580 (p0) cc_final: 0.8132 (p0)
REVERT: A  193 ASP cc_start: 0.8686 (p0) cc_final: 0.8221 (t0)
REVERT: A  213 MET cc_start: 0.8004 (ttp) cc_final: 0.7664 (ppp)
REVERT: A  245 MET cc_start: 0.9271 (ttm) cc_final: 0.8650 (tpp)
REVERT: A  282 MET cc_start: 0.8341 (mmp) cc_final: 0.8139 (mmt)
REVERT: A  290 ARG cc_start: 0.8612 (tpt170) cc_final: 0.7882 (tpt90)
REVERT: A  573 ASP cc_start: 0.8222 (t70) cc_final: 0.7630 (t0)
REVERT: A  954 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8785 (tm-30)
REVERT: A 1037 PHE cc_start: 0.8263 (t80) cc_final: 0.7899 (t80)
REVERT: A 1041 SER cc_start: 0.8288 (p) cc_final: 0.8035 (p)
REVERT: A 1122 SER cc_start: 0.8809 (m) cc_final: 0.8604 (p)
REVERT: A 1141 MET cc_start: 0.9023 (tmm) cc_final: 0.8492 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0607
  time to fit residues: 12.2928
Evaluate side-chains
  108 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3712 r_free = 0.3712 target = 0.095140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.080348 restraints weight = 31203.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.082473 restraints weight = 17162.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.083944 restraints weight = 11025.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.084940 restraints weight = 7983.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.085475 restraints weight = 6275.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.6390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7726  Z= 0.162
  Angle     :  0.598  15.101  10554  Z= 0.318
  Chirality :  0.040   0.171   1302
  Planarity :  0.003   0.026   1344
  Dihedral  :  7.479  65.426   1242
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.25), residues: 1119
  helix:  2.52 (0.19), residues: 721
  sheet:  1.38 (0.65), residues: 46
  loop : -0.08 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 348 
 TYR   0.008   0.001   TYR A 162 
 PHE   0.028   0.002   PHE A 230 
 TRP   0.018   0.001   TRP A1093 
 HIS   0.006   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 7726)
  covalent geometry    : angle       0.59819 (10554)
  hydrogen bonds       : bond        0.06201 (  613)
  hydrogen bonds       : angle       3.86853 ( 1785)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1330.24 seconds
wall clock time: 23 minutes 41.62 seconds (1421.62 seconds total)