Starting phenix.real_space_refine
on Tue Mar  3 17:18:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kby_62234/03_2026/9kby_62234.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kby_62234/03_2026/9kby_62234.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kby_62234/03_2026/9kby_62234.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kby_62234/03_2026/9kby_62234.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kby_62234/03_2026/9kby_62234.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kby_62234/03_2026/9kby_62234.map"
  }
  resolution = 3.15
  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=  -0.063 sd=   0.354
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      65      5.49       5
     Mg      2      5.21       5
     S      31      5.16       5
     C    4387      2.51       5
     N    1246      2.21       5
     O    1518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7249
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 731, 5864
          Classifications: {'peptide': 731}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 699}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 1383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1383
          Classifications: {'RNA': 65}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 32, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 1, 'rna3p': 63}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.75, per 1000 atoms: 0.24
  Number of scatterers: 7249
  At special positions: 0
  Unit cell: (64.98, 83.79, 133.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      31     16.00
     P      65     15.00
     Mg      2     11.99
     O    1518      8.00
     N    1246      7.00
     C    4387      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: 0.84
  Conformation dependent library (CDL) restraints added in 249.9 milliseconds
  

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1394

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 5 sheets defined
      51.7% alpha, 13.8% beta
      27 base pairs and 38 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 776 through 780
    Processing helix  chain 'A' and resid 820 through 825
      removed outlier: 4.331A  pdb=" N   THR A 825 " --> pdb=" O   VAL A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 871
      removed outlier: 3.567A  pdb=" N   ARG A 856 " --> pdb=" O   ASN A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 922
    Processing helix  chain 'A' and resid 923 through 927
    Processing helix  chain 'A' and resid 953 through 957
      removed outlier: 3.705A  pdb=" N   LYS A 957 " --> pdb=" O   ILE A 953 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 953 through 957'
    Processing helix  chain 'A' and resid 992 through 999
      removed outlier: 4.031A  pdb=" N   TYR A 998 " --> pdb=" O   VAL A 994 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS A 999 " --> pdb=" O   GLU A 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1067
      removed outlier: 4.067A  pdb=" N   LEU A1067 " --> pdb=" O   SER A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1089
      removed outlier: 3.508A  pdb=" N   ARG A1074 " --> pdb=" O   SER A1070 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1091
      No H-bonds generated for 'chain 'A' and resid 1090 through 1091'
    Processing helix  chain 'A' and resid 1092 through 1098
    Processing helix  chain 'A' and resid 1099 through 1108
      removed outlier: 3.712A  pdb=" N   GLU A1105 " --> pdb=" O   HIS A1101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1141
      removed outlier: 4.023A  pdb=" N   VAL A1123 " --> pdb=" O   GLU A1119 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   LEU A1124 " --> pdb=" O   ARG A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1158
      removed outlier: 3.880A  pdb=" N   THR A1150 " --> pdb=" O   GLU A1146 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG A1151 " --> pdb=" O   GLY A1147 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   VAL A1156 " --> pdb=" O   ARG A1152 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASN A1158 " --> pdb=" O   SER A1154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1158 through 1168
      removed outlier: 3.580A  pdb=" N   LYS A1168 " --> pdb=" O   ARG A1164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1174
      removed outlier: 5.877A  pdb=" N   GLN A1172 " --> pdb=" O   LYS A1169 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A1173 " --> pdb=" O   ASN A1170 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR A1174 " --> pdb=" O   LEU A1171 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1169 through 1174'
    Processing helix  chain 'A' and resid 1233 through 1250
      removed outlier: 3.770A  pdb=" N   VAL A1239 " --> pdb=" O   ILE A1235 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A1243 " --> pdb=" O   VAL A1239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1251 through 1263
      removed outlier: 4.010A  pdb=" N   LYS A1257 " --> pdb=" O   LYS A1253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1270 through 1279
      removed outlier: 3.800A  pdb=" N   GLN A1274 " --> pdb=" O   SER A1270 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA A1276 " --> pdb=" O   GLN A1272 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   CYS A1277 " --> pdb=" O   VAL A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1280 through 1288
      Proline residue:  A1285  - end of helix
      removed outlier: 4.183A  pdb=" N   THR A1288 " --> pdb=" O   PRO A1285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1291 through 1300
      removed outlier: 4.208A  pdb=" N   LEU A1295 " --> pdb=" O   ASN A1291 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASN A1297 " --> pdb=" O   GLU A1293 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLN A1298 " --> pdb=" O   THR A1294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1305 through 1312
      removed outlier: 4.270A  pdb=" N   LEU A1309 " --> pdb=" O   HIS A1305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1326 through 1349
      removed outlier: 3.756A  pdb=" N   ASP A1334 " --> pdb=" O   GLU A1330 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ALA A1335 " --> pdb=" O   PHE A1331 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR A1342 " --> pdb=" O   ASP A1338 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   PHE A1345 " --> pdb=" O   MET A1341 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR A1347 " --> pdb=" O   SER A1343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1353 through 1365
      removed outlier: 3.601A  pdb=" N   ARG A1361 " --> pdb=" O   LEU A1357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1366 through 1378
      removed outlier: 4.481A  pdb=" N   ASN A1372 " --> pdb=" O   GLU A1368 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   VAL A1373 " --> pdb=" O   ALA A1369 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ALA A1374 " --> pdb=" O   LEU A1370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1379 through 1382
    Processing helix  chain 'A' and resid 1387 through 1399
      removed outlier: 3.575A  pdb=" N   HIS A1391 " --> pdb=" O   SER A1387 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU A1395 " --> pdb=" O   HIS A1391 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASP A1396 " --> pdb=" O   GLU A1392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1417 through 1435
      removed outlier: 4.510A  pdb=" N   GLY A1421 " --> pdb=" O   PRO A1417 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN A1422 " --> pdb=" O   LYS A1418 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A1424 " --> pdb=" O   LEU A1420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1438 through 1450
      removed outlier: 3.565A  pdb=" N   VAL A1442 " --> pdb=" O   ASN A1438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1462 through 1475
      removed outlier: 3.988A  pdb=" N   GLU A1466 " --> pdb=" O   SER A1462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1510 through 1530
      removed outlier: 3.689A  pdb=" N   THR A1524 " --> pdb=" O   GLN A1520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1536 through 1545
      removed outlier: 4.043A  pdb=" N   ASP A1540 " --> pdb=" O   HIS A1536 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   VAL A1541 " --> pdb=" O   PRO A1537 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A1542 " --> pdb=" O   LEU A1538 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 827 through 831
      removed outlier: 3.576A  pdb=" N   SER A 837 " --> pdb=" O   HIS A 802 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS A 841 " --> pdb=" O   MET A 798 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   SER A 794 " --> pdb=" O   SER A 845 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   VAL A 847 " --> pdb=" O   LEU A 792 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU A 792 " --> pdb=" O   VAL A 847 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   GLU A 849 " --> pdb=" O   VAL A 790 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   VAL A 790 " --> pdb=" O   GLU A 849 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   MET A 815 " --> pdb=" O   HIS A 793 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   PHE A 811 " --> pdb=" O   ILE A 797 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU A 899 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 943 through 946
      removed outlier: 3.643A  pdb=" N   GLY A 949 " --> pdb=" O   LEU A 946 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1043 through 1045
      removed outlier: 6.607A  pdb=" N   LEU A1012 " --> pdb=" O   ILE A 975 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ILE A 975 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ARG A1014 " --> pdb=" O   ALA A 973 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLN A 968 " --> pdb=" O   THR A 963 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   SER A 959 " --> pdb=" O   VAL A 972 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   LEU A 960 " --> pdb=" O   LYS A1053 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1478 through 1479
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1478 through 1479
      removed outlier: 3.534A  pdb=" N   VAL A1495 " --> pdb=" O   LEU A1502 " (cutoff:3.500A)

    255 hydrogen bonds defined for protein.
    723 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      69 hydrogen bonds
      138 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      38 stacking parallelities
  Total time for adding SS restraints: 1.36

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.19 -     1.53: 7230
        1.53 -     1.88: 306
        1.88 -     2.22: 0
        2.22 -     2.56: 0
        2.56 -     2.91: 1
  Bond restraints: 7537
  Sorted by residual:
  bond pdb=" C   ASN A1458 "
       pdb=" N   GLN A1460 "
    ideal  model  delta    sigma   weight residual
    1.334  2.906 -1.572 1.42e-02 4.96e+03 1.23e+04
  bond pdb=" C   GLN A1460 "
       pdb=" O   GLN A1460 "
    ideal  model  delta    sigma   weight residual
    1.235  1.192  0.043 1.22e-02 6.72e+03 1.22e+01
  bond pdb=" N   ILE A1461 "
       pdb=" CA  ILE A1461 "
    ideal  model  delta    sigma   weight residual
    1.458  1.503 -0.045 1.41e-02 5.03e+03 1.03e+01
  bond pdb=" N   ILE A1464 "
       pdb=" CA  ILE A1464 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.55e+00
  bond pdb=" N   PRO A 785 "
       pdb=" CD  PRO A 785 "
    ideal  model  delta    sigma   weight residual
    1.473  1.438  0.035 1.40e-02 5.10e+03 6.09e+00
  ... (remaining 7532 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.99: 10506
        8.99 -    17.99: 1
       17.99 -    26.98: 0
       26.98 -    35.97: 0
       35.97 -    44.96: 2
  Bond angle restraints: 10509
  Sorted by residual:
  angle pdb=" O   ASN A1458 "
        pdb=" C   ASN A1458 "
        pdb=" N   GLN A1460 "
      ideal   model   delta    sigma   weight residual
     122.46   82.00   40.46 1.19e+00 7.06e-01 1.16e+03
  angle pdb=" C   ASN A1458 "
        pdb=" N   GLN A1460 "
        pdb=" CA  GLN A1460 "
      ideal   model   delta    sigma   weight residual
     121.72  166.68  -44.96 1.54e+00 4.22e-01 8.53e+02
  angle pdb=" CA  ASN A1458 "
        pdb=" C   ASN A1458 "
        pdb=" N   GLN A1460 "
      ideal   model   delta    sigma   weight residual
     115.10  131.32  -16.22 1.26e+00 6.30e-01 1.66e+02
  angle pdb=" N   ASN A1458 "
        pdb=" CA  ASN A1458 "
        pdb=" C   ASN A1458 "
      ideal   model   delta    sigma   weight residual
     108.56  100.10    8.46 1.74e+00 3.30e-01 2.37e+01
  angle pdb=" N   VAL A1266 "
        pdb=" CA  VAL A1266 "
        pdb=" C   VAL A1266 "
      ideal   model   delta    sigma   weight residual
     113.71  109.36    4.35 9.50e-01 1.11e+00 2.10e+01
  ... (remaining 10504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.19: 4245
       29.19 -    58.37: 299
       58.37 -    87.56: 78
       87.56 -   116.74: 2
      116.74 -   145.93: 1
  Dihedral angle restraints: 4625
    sinusoidal: 2484
      harmonic: 2141
  Sorted by residual:
  dihedral pdb=" O4'   C B  60 "
           pdb=" C1'   C B  60 "
           pdb=" N1    C B  60 "
           pdb=" C2    C B  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -14.07 -145.93     1      1.50e+01 4.44e-03 7.80e+01
  dihedral pdb=" CA  HIS A1190 "
           pdb=" C   HIS A1190 "
           pdb=" N   PRO A1191 "
           pdb=" CA  PRO A1191 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.07  -24.93     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  PHE A 814 "
           pdb=" C   PHE A 814 "
           pdb=" N   MET A 815 "
           pdb=" CA  MET A 815 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.10   20.90     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 4622 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1044
       0.053 -    0.106: 175
       0.106 -    0.159: 21
       0.159 -    0.212: 4
       0.212 -    0.265: 2
  Chirality restraints: 1246
  Sorted by residual:
  chirality pdb=" CA  SER A1457 "
            pdb=" N   SER A1457 "
            pdb=" C   SER A1457 "
            pdb=" CB  SER A1457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  GLN A1460 "
            pdb=" N   GLN A1460 "
            pdb=" C   GLN A1460 "
            pdb=" CB  GLN A1460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" C3'   A B  62 "
            pdb=" C4'   A B  62 "
            pdb=" O3'   A B  62 "
            pdb=" C2'   A B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.68    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1243 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A1458 "    0.164 2.00e-02 2.50e+03   2.07e-01 4.30e+02
        pdb=" C   ASN A1458 "   -0.353 2.00e-02 2.50e+03
        pdb=" O   ASN A1458 "    0.132 2.00e-02 2.50e+03
        pdb=" N   GLN A1460 "    0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1457 "    0.019 2.00e-02 2.50e+03   4.08e-02 1.67e+01
        pdb=" C   SER A1457 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   SER A1457 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ASN A1458 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A1460 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.26e+00
        pdb=" C   GLN A1460 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   GLN A1460 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ILE A1461 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 89
        2.64 -     3.20: 6085
        3.20 -     3.77: 11032
        3.77 -     4.33: 15211
        4.33 -     4.90: 24422
  Nonbonded interactions: 56839
  Sorted by model distance:
  nonbonded pdb=" OP1   C B  22 "
            pdb="MG    MG A1802 "
     model   vdw
     2.069 2.170
  nonbonded pdb=" OE1 GLN A1240 "
            pdb="MG    MG A1801 "
     model   vdw
     2.143 2.170
  nonbonded pdb=" OG  SER A 966 "
            pdb=" O2'   U B  69 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER A1535 "
            pdb=" OE1 GLU A1539 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" ND2 ASN A1510 "
            pdb=" OP1   C B  42 "
     model   vdw
     2.284 3.120
  ... (remaining 56834 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.190
  Find NCS groups from input model:        0.030
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
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      :  0.018   1.572   7537  Z= 1.290
  Angle     :  0.866  44.965  10509  Z= 0.575
  Chirality :  0.042   0.265   1246
  Planarity :  0.007   0.207   1092
  Dihedral  : 19.150 145.931   3231
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.04 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 17.85 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.30), residues: 717
  helix: -1.27 (0.28), residues: 299
  sheet:  0.31 (0.54), residues: 91
  loop : -0.62 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1282 
 TYR   0.017   0.001   TYR A 965 
 PHE   0.012   0.001   PHE A 971 
 TRP   0.013   0.001   TRP A1476 
 HIS   0.003   0.001   HIS A1086 

Details of bonding type rmsd
  covalent geometry    : bond        0.01845 ( 7537)
  covalent geometry    : angle       0.86605 (10509)
  hydrogen bonds       : bond        0.28299 (  322)
  hydrogen bonds       : angle       8.30982 (  861)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  956 VAL cc_start: 0.8703 (t) cc_final: 0.8473 (p)
  outliers start: 5
  outliers final: 1
  residues processed: 138
  average time/residue: 0.1218
  time to fit residues: 20.9113
Evaluate side-chains
  105 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1457 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
A1007 HIS
A1020 HIS
A1190 HIS
A1399 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.087465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.077105 restraints weight = 19045.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.00
r_work: 0.3120 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7537  Z= 0.147
  Angle     :  0.610   8.251  10509  Z= 0.316
  Chirality :  0.039   0.179   1246
  Planarity :  0.004   0.028   1092
  Dihedral  : 18.094 147.874   1795
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.89 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.79 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.29), residues: 719
  helix: -0.33 (0.27), residues: 321
  sheet:  0.70 (0.53), residues: 100
  loop : -0.94 (0.33), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1512 
 TYR   0.012   0.002   TYR A 796 
 PHE   0.021   0.002   PHE A1432 
 TRP   0.018   0.002   TRP A1476 
 HIS   0.005   0.001   HIS A1007 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7537)
  covalent geometry    : angle       0.60995 (10509)
  hydrogen bonds       : bond        0.04995 (  322)
  hydrogen bonds       : angle       4.69933 (  861)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  956 VAL cc_start: 0.8934 (t) cc_final: 0.8681 (p)
REVERT: A 1157 VAL cc_start: 0.8042 (t) cc_final: 0.7771 (p)
  outliers start: 17
  outliers final: 7
  residues processed: 109
  average time/residue: 0.0991
  time to fit residues: 14.0263
Evaluate side-chains
  101 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  967 LYS
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1270 SER
Chi-restraints excluded: chain A residue 1278 ILE
Chi-restraints excluded: chain A residue 1493 LEU
Chi-restraints excluded: chain A residue 1504 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 19 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0970
   chunk 8 optimal weight:    0.0570
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.3496

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.086359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.075628 restraints weight = 18737.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.99
r_work: 0.3089 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7537  Z= 0.121
  Angle     :  0.555   7.660  10509  Z= 0.283
  Chirality :  0.037   0.159   1246
  Planarity :  0.004   0.029   1092
  Dihedral  : 18.037 146.916   1794
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.48 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.04 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.30), residues: 719
  helix:  0.41 (0.28), residues: 316
  sheet:  0.71 (0.52), residues: 100
  loop : -0.89 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1512 
 TYR   0.012   0.001   TYR A 965 
 PHE   0.033   0.002   PHE A 813 
 TRP   0.013   0.002   TRP A1476 
 HIS   0.003   0.001   HIS A1391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7537)
  covalent geometry    : angle       0.55523 (10509)
  hydrogen bonds       : bond        0.04644 (  322)
  hydrogen bonds       : angle       4.39443 (  861)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 11
  residues processed: 116
  average time/residue: 0.1002
  time to fit residues: 15.1630
Evaluate side-chains
  102 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  849 GLU
Chi-restraints excluded: chain A residue  911 SER
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1126 ASP
Chi-restraints excluded: chain A residue 1278 ILE
Chi-restraints excluded: chain A residue 1379 LEU
Chi-restraints excluded: chain A residue 1480 ILE
Chi-restraints excluded: chain A residue 1493 LEU
Chi-restraints excluded: chain A residue 1504 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 63 optimal weight:    0.3980
   chunk 42 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0270
   chunk 62 optimal weight:    0.0870
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1529 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.085112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.074497 restraints weight = 18902.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.01
r_work: 0.3066 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7537  Z= 0.119
  Angle     :  0.549   7.784  10509  Z= 0.280
  Chirality :  0.037   0.153   1246
  Planarity :  0.004   0.033   1092
  Dihedral  : 18.059 149.780   1794
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.17 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.70 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.30), residues: 719
  helix:  0.65 (0.29), residues: 318
  sheet:  1.14 (0.58), residues: 83
  loop : -0.94 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1135 
 TYR   0.008   0.001   TYR A 970 
 PHE   0.043   0.002   PHE A 813 
 TRP   0.012   0.001   TRP A1476 
 HIS   0.003   0.001   HIS A1113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7537)
  covalent geometry    : angle       0.54879 (10509)
  hydrogen bonds       : bond        0.04208 (  322)
  hydrogen bonds       : angle       4.25860 (  861)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  815 MET cc_start: 0.6911 (ptp) cc_final: 0.6643 (ptp)
REVERT: A 1013 LEU cc_start: 0.7097 (mt) cc_final: 0.6788 (tp)
REVERT: A 1048 GLU cc_start: 0.8325 (tp30) cc_final: 0.8028 (tp30)
  outliers start: 23
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1019
  time to fit residues: 14.8666
Evaluate side-chains
  109 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  849 GLU
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1043 ILE
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1105 GLU
Chi-restraints excluded: chain A residue 1126 ASP
Chi-restraints excluded: chain A residue 1273 VAL
Chi-restraints excluded: chain A residue 1278 ILE
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1379 LEU
Chi-restraints excluded: chain A residue 1493 LEU
Chi-restraints excluded: chain A residue 1501 CYS
Chi-restraints excluded: chain A residue 1526 LEU
Chi-restraints excluded: chain A residue 1539 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A1007 HIS
** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.081713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.070988 restraints weight = 18840.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 1.99
r_work: 0.2992 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7537  Z= 0.152
  Angle     :  0.600   7.183  10509  Z= 0.306
  Chirality :  0.039   0.171   1246
  Planarity :  0.004   0.038   1092
  Dihedral  : 18.130 160.909   1794
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.17 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.46 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.29), residues: 719
  helix:  0.31 (0.28), residues: 320
  sheet:  0.78 (0.53), residues: 97
  loop : -1.01 (0.32), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1512 
 TYR   0.021   0.002   TYR A1326 
 PHE   0.039   0.002   PHE A 813 
 TRP   0.016   0.002   TRP A1476 
 HIS   0.004   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7537)
  covalent geometry    : angle       0.59970 (10509)
  hydrogen bonds       : bond        0.04961 (  322)
  hydrogen bonds       : angle       4.40868 (  861)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A 1075 MET cc_start: 0.8810 (tpp) cc_final: 0.7932 (ttm)
REVERT: A 1139 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8092 (mt)
REVERT: A 1465 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.8002 (tttm)
  outliers start: 23
  outliers final: 14
  residues processed: 107
  average time/residue: 0.1006
  time to fit residues: 13.9287
Evaluate side-chains
  105 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  849 GLU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  950 CYS
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1126 ASP
Chi-restraints excluded: chain A residue 1139 LEU
Chi-restraints excluded: chain A residue 1229 TRP
Chi-restraints excluded: chain A residue 1270 SER
Chi-restraints excluded: chain A residue 1278 ILE
Chi-restraints excluded: chain A residue 1379 LEU
Chi-restraints excluded: chain A residue 1465 LYS
Chi-restraints excluded: chain A residue 1480 ILE
Chi-restraints excluded: chain A residue 1493 LEU
Chi-restraints excluded: chain A residue 1539 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 18 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A1007 HIS
** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.080212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.069519 restraints weight = 18744.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.99
r_work: 0.2960 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7537  Z= 0.175
  Angle     :  0.640   7.506  10509  Z= 0.326
  Chirality :  0.040   0.171   1246
  Planarity :  0.005   0.042   1092
  Dihedral  : 18.200 168.832   1794
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.17 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.12 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.29), residues: 719
  helix:  0.08 (0.27), residues: 317
  sheet:  0.70 (0.52), residues: 97
  loop : -1.04 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 856 
 TYR   0.013   0.002   TYR A1326 
 PHE   0.028   0.002   PHE A 813 
 TRP   0.017   0.002   TRP A1476 
 HIS   0.005   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 7537)
  covalent geometry    : angle       0.63962 (10509)
  hydrogen bonds       : bond        0.05259 (  322)
  hydrogen bonds       : angle       4.53526 (  861)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A 1139 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8289 (mt)
REVERT: A 1281 ARG cc_start: 0.7285 (mmp-170) cc_final: 0.6876 (mpt-90)
  outliers start: 23
  outliers final: 15
  residues processed: 105
  average time/residue: 0.1026
  time to fit residues: 13.7161
Evaluate side-chains
  99 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  849 GLU
Chi-restraints excluded: chain A residue  911 SER
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  950 CYS
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1126 ASP
Chi-restraints excluded: chain A residue 1139 LEU
Chi-restraints excluded: chain A residue 1229 TRP
Chi-restraints excluded: chain A residue 1270 SER
Chi-restraints excluded: chain A residue 1278 ILE
Chi-restraints excluded: chain A residue 1379 LEU
Chi-restraints excluded: chain A residue 1480 ILE
Chi-restraints excluded: chain A residue 1493 LEU
Chi-restraints excluded: chain A residue 1539 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    0.0770
   chunk 5 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0770
   chunk 23 optimal weight:    0.0040
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.2908

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

Flipped N/Q/H residues before XYZ refinement:
A1007 HIS
** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.082891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.072240 restraints weight = 18673.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.00
r_work: 0.3022 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.4493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7537  Z= 0.116
  Angle     :  0.561   7.438  10509  Z= 0.288
  Chirality :  0.037   0.155   1246
  Planarity :  0.004   0.040   1092
  Dihedral  : 18.220 169.093   1794
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.62 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 20.88 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.30), residues: 719
  helix:  0.49 (0.28), residues: 325
  sheet:  0.69 (0.52), residues: 97
  loop : -1.03 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1135 
 TYR   0.013   0.001   TYR A 965 
 PHE   0.048   0.002   PHE A1131 
 TRP   0.012   0.001   TRP A1476 
 HIS   0.004   0.001   HIS A1190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7537)
  covalent geometry    : angle       0.56125 (10509)
  hydrogen bonds       : bond        0.04034 (  322)
  hydrogen bonds       : angle       4.23701 (  861)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1139 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8307 (mt)
  outliers start: 16
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1029
  time to fit residues: 12.7823
Evaluate side-chains
  96 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  849 GLU
Chi-restraints excluded: chain A residue  911 SER
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  950 CYS
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1139 LEU
Chi-restraints excluded: chain A residue 1229 TRP
Chi-restraints excluded: chain A residue 1270 SER
Chi-restraints excluded: chain A residue 1278 ILE
Chi-restraints excluded: chain A residue 1480 ILE
Chi-restraints excluded: chain A residue 1493 LEU
Chi-restraints excluded: chain A residue 1539 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 46 optimal weight:    0.0060
   chunk 78 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
A1007 HIS
A1178 GLN
** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.080195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.069558 restraints weight = 18991.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 2.00
r_work: 0.2963 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   7537  Z= 0.167
  Angle     :  0.635   7.600  10509  Z= 0.324
  Chirality :  0.040   0.171   1246
  Planarity :  0.004   0.040   1092
  Dihedral  : 18.229 173.695   1794
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.59 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.88 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.29), residues: 719
  helix:  0.19 (0.27), residues: 317
  sheet:  0.66 (0.52), residues: 97
  loop : -1.02 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1282 
 TYR   0.014   0.002   TYR A 796 
 PHE   0.040   0.002   PHE A1131 
 TRP   0.017   0.002   TRP A1476 
 HIS   0.004   0.001   HIS A1190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 7537)
  covalent geometry    : angle       0.63521 (10509)
  hydrogen bonds       : bond        0.05071 (  322)
  hydrogen bonds       : angle       4.46672 (  861)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A 1139 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8368 (mt)
  outliers start: 18
  outliers final: 15
  residues processed: 95
  average time/residue: 0.1062
  time to fit residues: 12.9850
Evaluate side-chains
  97 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  849 GLU
Chi-restraints excluded: chain A residue  911 SER
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  950 CYS
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1105 GLU
Chi-restraints excluded: chain A residue 1126 ASP
Chi-restraints excluded: chain A residue 1139 LEU
Chi-restraints excluded: chain A residue 1229 TRP
Chi-restraints excluded: chain A residue 1270 SER
Chi-restraints excluded: chain A residue 1278 ILE
Chi-restraints excluded: chain A residue 1480 ILE
Chi-restraints excluded: chain A residue 1493 LEU
Chi-restraints excluded: chain A residue 1504 VAL
Chi-restraints excluded: chain A residue 1539 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 31 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 14 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A1007 HIS
** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.081808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.071255 restraints weight = 18528.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 1.96
r_work: 0.3001 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.4768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7537  Z= 0.129
  Angle     :  0.584   7.555  10509  Z= 0.302
  Chirality :  0.038   0.160   1246
  Planarity :  0.004   0.040   1092
  Dihedral  : 18.256 175.837   1794
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.89 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.48 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.30), residues: 719
  helix:  0.44 (0.28), residues: 317
  sheet:  0.57 (0.51), residues: 97
  loop : -1.00 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1282 
 TYR   0.015   0.002   TYR A 965 
 PHE   0.022   0.002   PHE A 813 
 TRP   0.014   0.001   TRP A1476 
 HIS   0.004   0.001   HIS A1190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7537)
  covalent geometry    : angle       0.58419 (10509)
  hydrogen bonds       : bond        0.04306 (  322)
  hydrogen bonds       : angle       4.27242 (  861)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A 1139 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8453 (mt)
  outliers start: 17
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1059
  time to fit residues: 12.8226
Evaluate side-chains
  96 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  849 GLU
Chi-restraints excluded: chain A residue  911 SER
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  950 CYS
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1139 LEU
Chi-restraints excluded: chain A residue 1229 TRP
Chi-restraints excluded: chain A residue 1270 SER
Chi-restraints excluded: chain A residue 1278 ILE
Chi-restraints excluded: chain A residue 1480 ILE
Chi-restraints excluded: chain A residue 1493 LEU
Chi-restraints excluded: chain A residue 1501 CYS
Chi-restraints excluded: chain A residue 1504 VAL
Chi-restraints excluded: chain A residue 1539 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 49 optimal weight:    0.3980
   chunk 73 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 831 HIS
A1007 HIS
** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.080252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.069749 restraints weight = 18519.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.97
r_work: 0.2966 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.4897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7537  Z= 0.158
  Angle     :  0.628   7.940  10509  Z= 0.324
  Chirality :  0.039   0.169   1246
  Planarity :  0.004   0.041   1092
  Dihedral  : 18.290 179.098   1794
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.59 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.03 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.29), residues: 719
  helix:  0.20 (0.27), residues: 317
  sheet:  0.60 (0.51), residues: 97
  loop : -1.04 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1289 
 TYR   0.016   0.002   TYR A 965 
 PHE   0.023   0.002   PHE A 813 
 TRP   0.021   0.002   TRP A1476 
 HIS   0.004   0.001   HIS A1190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7537)
  covalent geometry    : angle       0.62825 (10509)
  hydrogen bonds       : bond        0.04924 (  322)
  hydrogen bonds       : angle       4.39868 (  861)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A 1139 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8470 (mt)
  outliers start: 19
  outliers final: 18
  residues processed: 95
  average time/residue: 0.0985
  time to fit residues: 12.2431
Evaluate side-chains
  97 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  780 LYS
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  849 GLU
Chi-restraints excluded: chain A residue  911 SER
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  950 CYS
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1060 ASP
Chi-restraints excluded: chain A residue 1105 GLU
Chi-restraints excluded: chain A residue 1112 CYS
Chi-restraints excluded: chain A residue 1139 LEU
Chi-restraints excluded: chain A residue 1229 TRP
Chi-restraints excluded: chain A residue 1270 SER
Chi-restraints excluded: chain A residue 1278 ILE
Chi-restraints excluded: chain A residue 1480 ILE
Chi-restraints excluded: chain A residue 1493 LEU
Chi-restraints excluded: chain A residue 1501 CYS
Chi-restraints excluded: chain A residue 1504 VAL
Chi-restraints excluded: chain A residue 1539 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 22 optimal weight:    0.4980
   chunk 37 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 71 optimal weight:    0.1980
   chunk 11 optimal weight:    0.0170
   chunk 3 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.3218

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

Flipped N/Q/H residues before XYZ refinement:
A 831 HIS
A1007 HIS
** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.082787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.072150 restraints weight = 18401.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.96
r_work: 0.3019 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7537  Z= 0.116
  Angle     :  0.565   7.932  10509  Z= 0.293
  Chirality :  0.037   0.154   1246
  Planarity :  0.004   0.040   1092
  Dihedral  : 18.285 179.055   1794
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.20 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 21.33 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.30), residues: 719
  helix:  0.55 (0.28), residues: 323
  sheet:  0.52 (0.50), residues: 97
  loop : -1.17 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1282 
 TYR   0.017   0.002   TYR A 965 
 PHE   0.024   0.002   PHE A 813 
 TRP   0.017   0.001   TRP A1476 
 HIS   0.004   0.001   HIS A1190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7537)
  covalent geometry    : angle       0.56518 (10509)
  hydrogen bonds       : bond        0.03967 (  322)
  hydrogen bonds       : angle       4.16722 (  861)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1892.12 seconds
wall clock time: 33 minutes 2.36 seconds (1982.36 seconds total)