Starting phenix.real_space_refine
on Wed Mar  4 12:30:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vf2_31946/03_2026/7vf2_31946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vf2_31946/03_2026/7vf2_31946.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vf2_31946/03_2026/7vf2_31946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vf2_31946/03_2026/7vf2_31946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vf2_31946/03_2026/7vf2_31946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vf2_31946/03_2026/7vf2_31946.cif"
  }
  resolution = 3.0
  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=   0.005 sd=   0.070
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: 4
    Type Number    sf(0)   Gaussians
     S      83      5.16       5
     C    8551      2.51       5
     N    2301      2.21       5
     O    2630      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 76 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: 13565
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1196, 9390
          Classifications: {'peptide': 1196}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1149}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1187
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 8, 'TRANS': 143}
    Chain: "C"
      Number of atoms: 1494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1494
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 3, 'TRANS': 180}
    Chain: "D"
      Number of atoms: 1494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1494
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 3, 'TRANS': 180}
  Time building chain proxies: 2.91, per 1000 atoms: 0.21
  Number of scatterers: 13565
  At special positions: 0
  Unit cell: (112.34, 115.62, 150.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      83     16.00
     O    2630      8.00
     N    2301      7.00
     C    8551      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: 1.12
  Conformation dependent library (CDL) restraints added in 489.3 milliseconds
  

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3300

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 3 sheets defined
      74.5% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 357 through 369
    Processing helix  chain 'A' and resid 374 through 390
      removed outlier: 3.899A  pdb=" N   ALA A 378 " --> pdb=" O   GLU A 374 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ALA A 381 " --> pdb=" O   GLY A 377 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LYS A 384 " --> pdb=" O   GLU A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 405
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 413 through 421
    Processing helix  chain 'A' and resid 426 through 439
    Processing helix  chain 'A' and resid 440 through 445
    Processing helix  chain 'A' and resid 451 through 468
      removed outlier: 3.570A  pdb=" N   GLN A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 456 " --> pdb=" O   ASN A 452 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 468 " --> pdb=" O   SER A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 480
      removed outlier: 3.878A  pdb=" N   GLY A 473 " --> pdb=" O   CYS A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 490
      removed outlier: 4.083A  pdb=" N   GLU A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 511
    Processing helix  chain 'A' and resid 513 through 522
    Processing helix  chain 'A' and resid 529 through 539
    Processing helix  chain 'A' and resid 543 through 579
      removed outlier: 3.688A  pdb=" N   LYS A 556 " --> pdb=" O   ALA A 552 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER A 579 " --> pdb=" O   GLU A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 640
    Processing helix  chain 'A' and resid 640 through 645
    Processing helix  chain 'A' and resid 668 through 679
      removed outlier: 4.074A  pdb=" N   ARG A 674 " --> pdb=" O   PRO A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 691
    Processing helix  chain 'A' and resid 691 through 697
      removed outlier: 3.963A  pdb=" N   HIS A 697 " --> pdb=" O   VAL A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 712
      removed outlier: 3.766A  pdb=" N   LEU A 701 " --> pdb=" O   HIS A 697 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL A 707 " --> pdb=" O   ALA A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 724
      removed outlier: 3.681A  pdb=" N   MET A 722 " --> pdb=" O   LEU A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 746
      removed outlier: 3.962A  pdb=" N   PHE A 738 " --> pdb=" O   ALA A 734 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU A 743 " --> pdb=" O   TYR A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 776
    Processing helix  chain 'A' and resid 789 through 801
    Processing helix  chain 'A' and resid 802 through 804
      No H-bonds generated for 'chain 'A' and resid 802 through 804'
    Processing helix  chain 'A' and resid 805 through 816
    Processing helix  chain 'A' and resid 822 through 833
    Processing helix  chain 'A' and resid 845 through 862
      removed outlier: 3.652A  pdb=" N   ASN A 849 " --> pdb=" O   SER A 845 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL A 859 " --> pdb=" O   ILE A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 882
      removed outlier: 3.934A  pdb=" N   GLU A 869 " --> pdb=" O   VAL A 865 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   GLN A 870 " --> pdb=" O   GLN A 866 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   HIS A 871 " --> pdb=" O   MET A 867 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   ALA A 873 " --> pdb=" O   GLU A 869 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   SER A 874 " --> pdb=" O   GLN A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 896
    Processing helix  chain 'A' and resid 897 through 899
      No H-bonds generated for 'chain 'A' and resid 897 through 899'
    Processing helix  chain 'A' and resid 907 through 918
    Processing helix  chain 'A' and resid 928 through 940
      removed outlier: 4.078A  pdb=" N   THR A 932 " --> pdb=" O   VAL A 928 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU A 937 " --> pdb=" O   ALA A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 966
      removed outlier: 3.775A  pdb=" N   VAL A 960 " --> pdb=" O   TRP A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 989
      removed outlier: 3.512A  pdb=" N   ILE A 973 " --> pdb=" O   MET A 969 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   VAL A 975 " --> pdb=" O   THR A 971 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   GLN A 985 " --> pdb=" O   SER A 981 " (cutoff:3.500A)
      Proline residue:  A 986  - end of helix
    Processing helix  chain 'A' and resid 995 through 1021
    Processing helix  chain 'A' and resid 1032 through 1045
      removed outlier: 3.962A  pdb=" N   THR A1039 " --> pdb=" O   SER A1035 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   MET A1042 " --> pdb=" O   VAL A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1070
    Processing helix  chain 'A' and resid 1076 through 1080
    Processing helix  chain 'A' and resid 1082 through 1087
    Processing helix  chain 'A' and resid 1089 through 1100
    Processing helix  chain 'A' and resid 1108 through 1120
      removed outlier: 3.949A  pdb=" N   GLU A1118 " --> pdb=" O   ILE A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1152
      removed outlier: 3.513A  pdb=" N   ILE A1137 " --> pdb=" O   GLU A1133 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG A1144 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1154 through 1165
      removed outlier: 3.801A  pdb=" N   GLU A1160 " --> pdb=" O   LYS A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1184
      removed outlier: 3.935A  pdb=" N   VAL A1182 " --> pdb=" O   ARG A1178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1208
    Processing helix  chain 'A' and resid 1219 through 1234
    Processing helix  chain 'A' and resid 1235 through 1247
      removed outlier: 3.584A  pdb=" N   LEU A1245 " --> pdb=" O   ALA A1241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1253 through 1268
      removed outlier: 3.670A  pdb=" N   ALA A1257 " --> pdb=" O   ASP A1253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1275 through 1291
      removed outlier: 4.401A  pdb=" N   GLU A1281 " --> pdb=" O   GLN A1277 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   TYR A1282 " --> pdb=" O   GLN A1278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1308 through 1314
      removed outlier: 3.601A  pdb=" N   SER A1314 " --> pdb=" O   LEU A1310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1319 through 1336
      removed outlier: 3.687A  pdb=" N   SER A1325 " --> pdb=" O   GLU A1321 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU A1334 " --> pdb=" O   LEU A1330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1355
      removed outlier: 3.601A  pdb=" N   LEU A1344 " --> pdb=" O   SER A1340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1357 through 1369
    Processing helix  chain 'A' and resid 1373 through 1385
    Processing helix  chain 'A' and resid 1390 through 1406
    Processing helix  chain 'A' and resid 1434 through 1443
    Processing helix  chain 'A' and resid 1447 through 1461
    Processing helix  chain 'A' and resid 1468 through 1486
      removed outlier: 3.556A  pdb=" N   SER A1472 " --> pdb=" O   ASP A1468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1507 through 1514
    Processing helix  chain 'A' and resid 1525 through 1530
    Processing helix  chain 'A' and resid 1554 through 1559
      removed outlier: 4.388A  pdb=" N   LYS A1558 " --> pdb=" O   GLU A1554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1565 through 1575
      removed outlier: 3.868A  pdb=" N   PHE A1573 " --> pdb=" O   LEU A1569 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU A1574 " --> pdb=" O   GLU A1570 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER A1575 " --> pdb=" O   ARG A1571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1517 through 1521
      removed outlier: 4.200A  pdb=" N   LYS B1520 " --> pdb=" O   ALA B1517 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE B1521 " --> pdb=" O   LEU B1518 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1517 through 1521'
    Processing helix  chain 'B' and resid 1522 through 1531
    Processing helix  chain 'B' and resid 1533 through 1538
      removed outlier: 3.762A  pdb=" N   GLY B1538 " --> pdb=" O   LYS B1534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1538 through 1551
    Processing helix  chain 'B' and resid 1555 through 1561
    Processing helix  chain 'B' and resid 1567 through 1583
    Processing helix  chain 'B' and resid 1596 through 1608
    Processing helix  chain 'B' and resid 1626 through 1643
    Processing helix  chain 'C' and resid 65 through 98
    Processing helix  chain 'C' and resid 102 through 112
    Processing helix  chain 'C' and resid 114 through 146
    Processing helix  chain 'C' and resid 151 through 175
    Processing helix  chain 'C' and resid 176 through 243
    Processing helix  chain 'D' and resid 66 through 100
    Processing helix  chain 'D' and resid 104 through 109
    Processing helix  chain 'D' and resid 114 through 145
      removed outlier: 3.604A  pdb=" N   SER D 143 " --> pdb=" O   GLN D 139 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA D 144 " --> pdb=" O   ASN D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 148 through 178
      removed outlier: 3.634A  pdb=" N   GLN D 169 " --> pdb=" O   ILE D 165 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLN D 174 " --> pdb=" O   GLU D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 244
      removed outlier: 3.790A  pdb=" N   GLU D 203 " --> pdb=" O   SER D 199 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 657 through 658
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1126 through 1128
      removed outlier: 6.178A  pdb=" N   MET A1126 " --> pdb=" O   VAL A1519 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1549 through 1551

    902 hydrogen bonds defined for protein.
    2688 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2859
        1.33 -     1.45: 2695
        1.45 -     1.57: 8074
        1.57 -     1.69: 0
        1.69 -     1.81: 132
  Bond restraints: 13760
  Sorted by residual:
  bond pdb=" C   GLN A 647 "
       pdb=" N   GLN A 648 "
    ideal  model  delta    sigma   weight residual
    1.330  1.283  0.047 1.47e-02 4.63e+03 1.03e+01
  bond pdb=" N   ARG B1512 "
       pdb=" CA  ARG B1512 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.036 1.31e-02 5.83e+03 7.72e+00
  bond pdb=" N   LYS C 146 "
       pdb=" CA  LYS C 146 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.25e-02 6.40e+03 7.07e+00
  bond pdb=" C   TRP C 145 "
       pdb=" N   LYS C 146 "
    ideal  model  delta    sigma   weight residual
    1.333  1.366 -0.034 1.36e-02 5.41e+03 6.08e+00
  bond pdb=" N   GLU D 141 "
       pdb=" CA  GLU D 141 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.031 1.28e-02 6.10e+03 5.73e+00
  ... (remaining 13755 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 18136
        2.06 -     4.13: 389
        4.13 -     6.19: 48
        6.19 -     8.25: 7
        8.25 -    10.32: 2
  Bond angle restraints: 18582
  Sorted by residual:
  angle pdb=" N   ILE A1541 "
        pdb=" CA  ILE A1541 "
        pdb=" C   ILE A1541 "
      ideal   model   delta    sigma   weight residual
     113.47  105.93    7.54 1.01e+00 9.80e-01 5.58e+01
  angle pdb=" N   VAL A1274 "
        pdb=" CA  VAL A1274 "
        pdb=" C   VAL A1274 "
      ideal   model   delta    sigma   weight residual
     113.42  107.22    6.20 1.17e+00 7.31e-01 2.81e+01
  angle pdb=" CA  GLU B1513 "
        pdb=" C   GLU B1513 "
        pdb=" N   PRO B1514 "
      ideal   model   delta    sigma   weight residual
     118.75  123.54   -4.79 9.70e-01 1.06e+00 2.44e+01
  angle pdb=" N   ALA A 783 "
        pdb=" CA  ALA A 783 "
        pdb=" C   ALA A 783 "
      ideal   model   delta    sigma   weight residual
     113.38  107.55    5.83 1.23e+00 6.61e-01 2.24e+01
  angle pdb=" N   SER A1444 "
        pdb=" CA  SER A1444 "
        pdb=" C   SER A1444 "
      ideal   model   delta    sigma   weight residual
     114.75  109.41    5.34 1.26e+00 6.30e-01 1.80e+01
  ... (remaining 18577 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7715
       17.96 -    35.92: 661
       35.92 -    53.88: 124
       53.88 -    71.84: 42
       71.84 -    89.80: 39
  Dihedral angle restraints: 8581
    sinusoidal: 3540
      harmonic: 5041
  Sorted by residual:
  dihedral pdb=" CA  HIS A1463 "
           pdb=" C   HIS A1463 "
           pdb=" N   SER A1464 "
           pdb=" CA  SER A1464 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.51  -23.49     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  LYS A1251 "
           pdb=" C   LYS A1251 "
           pdb=" N   GLY A1252 "
           pdb=" CA  GLY A1252 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.65  -21.35     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  LYS A1465 "
           pdb=" C   LYS A1465 "
           pdb=" N   ASP A1466 "
           pdb=" CA  ASP A1466 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.75  -21.25     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 8578 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1579
       0.041 -    0.081: 479
       0.081 -    0.122: 110
       0.122 -    0.162: 13
       0.162 -    0.203: 5
  Chirality restraints: 2186
  Sorted by residual:
  chirality pdb=" CA  GLU D 136 "
            pdb=" N   GLU D 136 "
            pdb=" C   GLU D 136 "
            pdb=" CB  GLU D 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ARG B1639 "
            pdb=" N   ARG B1639 "
            pdb=" C   ARG B1639 "
            pdb=" CB  ARG B1639 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.84e-01
  chirality pdb=" CA  GLU B1513 "
            pdb=" N   GLU B1513 "
            pdb=" C   GLU B1513 "
            pdb=" CB  GLU B1513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.67e-01
  ... (remaining 2183 not shown)

  Planarity restraints: 2386
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 669 "    0.036 5.00e-02 4.00e+02   5.39e-02 4.65e+00
        pdb=" N   PRO A 670 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 670 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 670 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C  67 "   -0.008 2.00e-02 2.50e+03   1.62e-02 2.64e+00
        pdb=" C   GLN C  67 "    0.028 2.00e-02 2.50e+03
        pdb=" O   GLN C  67 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLU C  68 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 148 "    0.024 5.00e-02 4.00e+02   3.66e-02 2.14e+00
        pdb=" N   PRO D 149 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO D 149 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D 149 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2383 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 176
        2.66 -     3.22: 13487
        3.22 -     3.78: 21777
        3.78 -     4.34: 29896
        4.34 -     4.90: 48636
  Nonbonded interactions: 113972
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 148 "
            pdb=" OG  SER C 151 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OD2 ASP A1206 "
            pdb=" OG1 THR A1222 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" O   ASP A 508 "
            pdb=" OG  SER A 512 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OE1 GLU A1311 "
            pdb=" OG  SER A1503 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" O   ILE A 511 "
            pdb=" OH  TYR A 675 "
     model   vdw
     2.176 3.040
  ... (remaining 113967 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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=0.00 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:             2.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     12.530
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
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      :  0.004   0.047  13760  Z= 0.210
  Angle     :  0.729  10.315  18582  Z= 0.439
  Chirality :  0.041   0.203   2186
  Planarity :  0.004   0.054   2386
  Dihedral  : 15.876  89.804   5281
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.82 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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: -2.72 (0.17), residues: 1704
  helix: -1.44 (0.13), residues: 1221
  sheet:  None (None), residues: 0
  loop : -2.35 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1144 
 TYR   0.010   0.001   TYR D 193 
 PHE   0.012   0.001   PHE A1453 
 TRP   0.008   0.001   TRP B1500 
 HIS   0.005   0.001   HIS A1376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (13760)
  covalent geometry    : angle       0.72889 (18582)
  hydrogen bonds       : bond        0.12313 (  902)
  hydrogen bonds       : angle       5.67959 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 217
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A 1217 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7839 (tp40)
REVERT: A 1259 ILE cc_start: 0.8804 (tp) cc_final: 0.8559 (tp)
REVERT: A 1483 MET cc_start: 0.8347 (mpp) cc_final: 0.7976 (mpt)
REVERT: B 1513 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7446 (tm-30)
REVERT: B 1514 PRO cc_start: 0.8866 (Cg_exo) cc_final: 0.8394 (Cg_endo)
REVERT: C   78 MET cc_start: 0.8123 (tpt) cc_final: 0.7902 (tpt)
REVERT: C  233 ARG cc_start: 0.8674 (ttm170) cc_final: 0.8387 (mtt90)
REVERT: D   78 MET cc_start: 0.8476 (ptm) cc_final: 0.8258 (pp-130)
REVERT: D  236 LEU cc_start: 0.6454 (tt) cc_final: 0.6006 (mt)
  outliers start: 4
  outliers final: 1
  residues processed: 220
  average time/residue: 0.6524
  time to fit residues: 155.5929
Evaluate side-chains
  140 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 138
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1513 GLU
Chi-restraints excluded: chain C residue   94 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    0.3980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 419 GLN
A 430 GLN
A 455 GLN
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 GLN
A 558 HIS
A 636 HIS
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 766 GLN
A 797 HIS
A 823 GLN
A 917 GLN
A 951 GLN
A 962 GLN
A1041 HIS
A1142 ASN
** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1152 HIS
A1175 HIS
A1261 GLN
** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1357 HIS
A1440 GLN
A1463 HIS
A1510 ASN
C  74 ASN
C  85 GLN
C 137 GLN
C 152 GLN
C 219 GLN
C 228 GLN
D 118 ASN
D 137 GLN
D 174 GLN
D 201 GLN
D 240 GLN

Total number of N/Q/H flips: 32

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.145178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.094651 restraints weight = 20131.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.95
r_work: 0.3238 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13760  Z= 0.211
  Angle     :  0.675  11.922  18582  Z= 0.335
  Chirality :  0.042   0.171   2186
  Planarity :  0.004   0.055   2386
  Dihedral  :  5.494  73.469   1816
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.29 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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: -1.04 (0.19), residues: 1704
  helix: -0.16 (0.14), residues: 1224
  sheet:  None (None), residues: 0
  loop : -1.83 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  72 
 TYR   0.013   0.002   TYR A 739 
 PHE   0.015   0.002   PHE A1533 
 TRP   0.008   0.001   TRP A1532 
 HIS   0.004   0.001   HIS A1363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (13760)
  covalent geometry    : angle       0.67485 (18582)
  hydrogen bonds       : bond        0.04013 (  902)
  hydrogen bonds       : angle       4.39136 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 148
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A  664 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7533 (pp20)
REVERT: A  867 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.7954 (ptp)
REVERT: A  987 TRP cc_start: 0.8355 (t-100) cc_final: 0.8116 (t-100)
REVERT: A 1217 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7993 (tp40)
REVERT: A 1402 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7058 (mmt-90)
REVERT: A 1483 MET cc_start: 0.8632 (mpp) cc_final: 0.7724 (mpt)
REVERT: A 1524 MET cc_start: 0.8672 (tpp) cc_final: 0.8360 (tpp)
REVERT: B 1513 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7543 (tp30)
REVERT: B 1606 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7719 (mp10)
REVERT: C   68 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8609 (tp30)
REVERT: C   78 MET cc_start: 0.8002 (tpt) cc_final: 0.7741 (tpt)
REVERT: C  136 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8078 (mm-30)
REVERT: C  241 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8482 (tm-30)
REVERT: D   72 ARG cc_start: 0.8486 (mtm110) cc_final: 0.8079 (mtm-85)
REVERT: D   78 MET cc_start: 0.8826 (ptm) cc_final: 0.8418 (pp-130)
REVERT: D   89 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8069 (pp20)
REVERT: D  236 LEU cc_start: 0.6122 (tt) cc_final: 0.5691 (mt)
  outliers start: 33
  outliers final: 7
  residues processed: 170
  average time/residue: 0.5415
  time to fit residues: 101.8132
Evaluate side-chains
  143 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 GLU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1330 LEU
Chi-restraints excluded: chain A residue 1364 LEU
Chi-restraints excluded: chain B residue 1513 GLU
Chi-restraints excluded: chain B residue 1539 SER
Chi-restraints excluded: chain B residue 1606 GLN
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain D residue   92 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 140 optimal weight:    9.9990
   chunk 92 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 157 optimal weight:    2.9990
   chunk 131 optimal weight:   30.0000
   chunk 84 optimal weight:    5.9990
   chunk 138 optimal weight:    0.9980
   chunk 152 optimal weight:   10.0000
   chunk 108 optimal weight:   20.0000
   chunk 151 optimal weight:    0.4980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 789 HIS
** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1507 HIS
C  95 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.147150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.097999 restraints weight = 20188.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.90
r_work: 0.3286 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13760  Z= 0.138
  Angle     :  0.586  10.615  18582  Z= 0.292
  Chirality :  0.039   0.146   2186
  Planarity :  0.004   0.051   2386
  Dihedral  :  5.062  62.221   1814
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.58 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 (0.20), residues: 1704
  helix:  0.64 (0.14), residues: 1216
  sheet:  None (None), residues: 0
  loop : -1.51 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  72 
 TYR   0.011   0.001   TYR D 239 
 PHE   0.012   0.001   PHE A1533 
 TRP   0.007   0.001   TRP B1500 
 HIS   0.003   0.001   HIS A1376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (13760)
  covalent geometry    : angle       0.58608 (18582)
  hydrogen bonds       : bond        0.03538 (  902)
  hydrogen bonds       : angle       4.06922 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 141
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7828 (t0) cc_final: 0.7048 (p0)
REVERT: A  780 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7255 (mtm110)
REVERT: A  831 TYR cc_start: 0.8164 (t80) cc_final: 0.7915 (t80)
REVERT: A  867 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.7746 (ptp)
REVERT: A  917 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8010 (mm110)
REVERT: A  987 TRP cc_start: 0.8320 (t-100) cc_final: 0.8092 (t-100)
REVERT: A 1217 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8033 (tp40)
REVERT: A 1259 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8370 (tp)
REVERT: A 1402 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7068 (mmm-85)
REVERT: A 1483 MET cc_start: 0.8628 (mpp) cc_final: 0.7738 (mpt)
REVERT: B 1513 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7373 (tp30)
REVERT: B 1514 PRO cc_start: 0.8932 (Cg_exo) cc_final: 0.8508 (Cg_endo)
REVERT: B 1606 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7633 (mp10)
REVERT: C  136 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8054 (mm-30)
REVERT: C  241 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8393 (tm-30)
REVERT: D   78 MET cc_start: 0.8801 (ptm) cc_final: 0.8402 (pp-130)
REVERT: D   89 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8121 (pp20)
REVERT: D  108 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8583 (tp)
REVERT: D  163 MET cc_start: 0.8968 (ttp) cc_final: 0.8625 (tpp)
REVERT: D  206 ASP cc_start: 0.8514 (m-30) cc_final: 0.8245 (m-30)
REVERT: D  236 LEU cc_start: 0.6181 (tt) cc_final: 0.5791 (mt)
  outliers start: 42
  outliers final: 8
  residues processed: 168
  average time/residue: 0.5441
  time to fit residues: 100.8911
Evaluate side-chains
  143 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ASN
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1259 ILE
Chi-restraints excluded: chain A residue 1491 LEU
Chi-restraints excluded: chain A residue 1548 VAL
Chi-restraints excluded: chain B residue 1513 GLU
Chi-restraints excluded: chain B residue 1539 SER
Chi-restraints excluded: chain B residue 1606 GLN
Chi-restraints excluded: chain B residue 1608 VAL
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  108 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 145 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 140 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 142 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 985 GLN
** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1336 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 = 0.4078 r_free = 0.4078 target = 0.143463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.095471 restraints weight = 20090.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.75
r_work: 0.3271 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13760  Z= 0.195
  Angle     :  0.619  10.850  18582  Z= 0.302
  Chirality :  0.040   0.151   2186
  Planarity :  0.004   0.052   2386
  Dihedral  :  4.921  56.487   1814
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.52 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.28 (0.20), residues: 1704
  helix:  0.79 (0.14), residues: 1225
  sheet:  None (None), residues: 0
  loop : -1.26 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  72 
 TYR   0.018   0.001   TYR D 239 
 PHE   0.014   0.001   PHE A1573 
 TRP   0.009   0.001   TRP A1532 
 HIS   0.004   0.001   HIS A1363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (13760)
  covalent geometry    : angle       0.61874 (18582)
  hydrogen bonds       : bond        0.03564 (  902)
  hydrogen bonds       : angle       4.02004 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 146
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7732 (t0) cc_final: 0.6950 (p0)
REVERT: A  664 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7690 (pp20)
REVERT: A  780 ARG cc_start: 0.7466 (mtm110) cc_final: 0.7196 (mtm110)
REVERT: A  831 TYR cc_start: 0.8222 (t80) cc_final: 0.7932 (t80)
REVERT: A  867 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.7815 (ptp)
REVERT: A  917 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8037 (mm110)
REVERT: A  987 TRP cc_start: 0.8348 (t-100) cc_final: 0.8127 (t-100)
REVERT: A 1217 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8050 (tp40)
REVERT: A 1259 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8393 (tp)
REVERT: A 1402 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7066 (mmm-85)
REVERT: A 1458 LYS cc_start: 0.8401 (tptt) cc_final: 0.8120 (tptt)
REVERT: B 1513 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7379 (tp30)
REVERT: B 1514 PRO cc_start: 0.8961 (Cg_exo) cc_final: 0.8543 (Cg_endo)
REVERT: B 1606 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7660 (mp10)
REVERT: C  136 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8109 (mm-30)
REVERT: C  233 ARG cc_start: 0.8668 (ttm170) cc_final: 0.8441 (mtm-85)
REVERT: C  241 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: D   78 MET cc_start: 0.8833 (ptm) cc_final: 0.8409 (pp-130)
REVERT: D   89 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8156 (pp20)
REVERT: D  108 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8653 (tp)
REVERT: D  112 MET cc_start: 0.8711 (mmp) cc_final: 0.8353 (mmp)
REVERT: D  163 MET cc_start: 0.8947 (ttp) cc_final: 0.8610 (tpp)
REVERT: D  206 ASP cc_start: 0.8519 (m-30) cc_final: 0.8253 (m-30)
REVERT: D  236 LEU cc_start: 0.6141 (tt) cc_final: 0.5763 (mt)
  outliers start: 46
  outliers final: 13
  residues processed: 179
  average time/residue: 0.5783
  time to fit residues: 113.4006
Evaluate side-chains
  159 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  805 ASN
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1185 CYS
Chi-restraints excluded: chain A residue 1259 ILE
Chi-restraints excluded: chain A residue 1313 LEU
Chi-restraints excluded: chain A residue 1520 LEU
Chi-restraints excluded: chain A residue 1548 VAL
Chi-restraints excluded: chain B residue 1513 GLU
Chi-restraints excluded: chain B residue 1539 SER
Chi-restraints excluded: chain B residue 1606 GLN
Chi-restraints excluded: chain B residue 1608 VAL
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  108 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 125 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 134 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 86 optimal weight:    0.4980
   chunk 103 optimal weight:    7.9990
   chunk 124 optimal weight:    0.6980
   chunk 106 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 998 HIS
** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.147191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.097619 restraints weight = 20229.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.89
r_work: 0.3312 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13760  Z= 0.123
  Angle     :  0.570  11.380  18582  Z= 0.279
  Chirality :  0.038   0.159   2186
  Planarity :  0.003   0.051   2386
  Dihedral  :  4.682  49.511   1814
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.95 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.75 (0.20), residues: 1704
  helix:  1.15 (0.15), residues: 1224
  sheet:  None (None), residues: 0
  loop : -1.11 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 162 
 TYR   0.010   0.001   TYR A 739 
 PHE   0.012   0.001   PHE A 738 
 TRP   0.007   0.001   TRP A1532 
 HIS   0.003   0.001   HIS A1376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (13760)
  covalent geometry    : angle       0.57017 (18582)
  hydrogen bonds       : bond        0.03296 (  902)
  hydrogen bonds       : angle       3.86755 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 154
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7906 (t)
REVERT: A  426 ASP cc_start: 0.7682 (t0) cc_final: 0.6909 (p0)
REVERT: A  780 ARG cc_start: 0.7514 (mtm110) cc_final: 0.7303 (mtm110)
REVERT: A  831 TYR cc_start: 0.8226 (t80) cc_final: 0.7873 (t80)
REVERT: A  867 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.7696 (ptp)
REVERT: A  917 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8077 (mm110)
REVERT: A  987 TRP cc_start: 0.8371 (t-100) cc_final: 0.8168 (t-100)
REVERT: A 1259 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8400 (tp)
REVERT: A 1402 ARG cc_start: 0.7915 (mtp85) cc_final: 0.6964 (mmm-85)
REVERT: A 1458 LYS cc_start: 0.8428 (tptt) cc_final: 0.8153 (tptt)
REVERT: A 1483 MET cc_start: 0.8671 (mpp) cc_final: 0.7802 (mpt)
REVERT: B 1513 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7635 (tp30)
REVERT: B 1606 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7647 (mp10)
REVERT: C  136 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8071 (mm-30)
REVERT: C  241 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: D   78 MET cc_start: 0.8818 (ptm) cc_final: 0.8380 (pp-130)
REVERT: D   89 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8187 (pp20)
REVERT: D  108 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8602 (tp)
REVERT: D  163 MET cc_start: 0.8943 (ttp) cc_final: 0.8633 (tpp)
REVERT: D  206 ASP cc_start: 0.8458 (m-30) cc_final: 0.8188 (m-30)
REVERT: D  236 LEU cc_start: 0.6136 (tt) cc_final: 0.5754 (mt)
  outliers start: 41
  outliers final: 15
  residues processed: 183
  average time/residue: 0.6073
  time to fit residues: 121.5118
Evaluate side-chains
  159 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  805 ASN
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  908 ILE
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1259 ILE
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1520 LEU
Chi-restraints excluded: chain A residue 1548 VAL
Chi-restraints excluded: chain A residue 1549 LYS
Chi-restraints excluded: chain B residue 1513 GLU
Chi-restraints excluded: chain B residue 1539 SER
Chi-restraints excluded: chain B residue 1606 GLN
Chi-restraints excluded: chain B residue 1608 VAL
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  108 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 137 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 162 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   chunk 56 optimal weight:    0.6980
   chunk 41 optimal weight:   30.0000
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1336 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 = 0.4058 r_free = 0.4058 target = 0.143697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.094246 restraints weight = 20258.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.89
r_work: 0.3215 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  13760  Z= 0.192
  Angle     :  0.625  12.656  18582  Z= 0.302
  Chirality :  0.040   0.163   2186
  Planarity :  0.004   0.052   2386
  Dihedral  :  4.629  45.923   1814
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.59 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.83 (0.20), residues: 1704
  helix:  1.18 (0.15), residues: 1223
  sheet:  None (None), residues: 0
  loop : -1.01 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B1551 
 TYR   0.009   0.001   TYR A 739 
 PHE   0.016   0.001   PHE A1573 
 TRP   0.013   0.001   TRP A1532 
 HIS   0.003   0.001   HIS A1363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 (13760)
  covalent geometry    : angle       0.62462 (18582)
  hydrogen bonds       : bond        0.03431 (  902)
  hydrogen bonds       : angle       3.86904 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 147
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A  423 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7879 (t)
REVERT: A  426 ASP cc_start: 0.7652 (t0) cc_final: 0.6889 (p0)
REVERT: A  664 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7613 (pp20)
REVERT: A  780 ARG cc_start: 0.7429 (mtm110) cc_final: 0.7206 (mtm110)
REVERT: A  831 TYR cc_start: 0.8150 (t80) cc_final: 0.7793 (t80)
REVERT: A  867 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.7777 (ptp)
REVERT: A  902 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7649 (mtm180)
REVERT: A  917 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8069 (mm110)
REVERT: A 1259 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8313 (tp)
REVERT: A 1402 ARG cc_start: 0.7851 (mtp85) cc_final: 0.6934 (mmm-85)
REVERT: A 1458 LYS cc_start: 0.8428 (tptt) cc_final: 0.8203 (tptt)
REVERT: A 1483 MET cc_start: 0.8712 (mpp) cc_final: 0.7821 (mpt)
REVERT: B 1606 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7564 (mp10)
REVERT: B 1611 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7243 (tp30)
REVERT: C  136 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8076 (mm-30)
REVERT: C  233 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8366 (mtt90)
REVERT: C  241 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: D   78 MET cc_start: 0.8858 (ptm) cc_final: 0.8407 (pp-130)
REVERT: D   89 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8223 (pp20)
REVERT: D  163 MET cc_start: 0.8937 (ttp) cc_final: 0.8603 (tpp)
REVERT: D  206 ASP cc_start: 0.8498 (m-30) cc_final: 0.8246 (m-30)
REVERT: D  236 LEU cc_start: 0.6081 (tt) cc_final: 0.5709 (mt)
  outliers start: 49
  outliers final: 17
  residues processed: 179
  average time/residue: 0.6020
  time to fit residues: 118.0490
Evaluate side-chains
  166 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  664 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  805 ASN
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  902 ARG
Chi-restraints excluded: chain A residue  908 ILE
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1001 THR
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1185 CYS
Chi-restraints excluded: chain A residue 1259 ILE
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1520 LEU
Chi-restraints excluded: chain A residue 1548 VAL
Chi-restraints excluded: chain B residue 1539 SER
Chi-restraints excluded: chain B residue 1606 GLN
Chi-restraints excluded: chain B residue 1608 VAL
Chi-restraints excluded: chain B residue 1611 GLU
Chi-restraints excluded: chain D residue   92 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 28 optimal weight:    0.1980
   chunk 141 optimal weight:    1.9990
   chunk 107 optimal weight:   30.0000
   chunk 161 optimal weight:    5.9990
   chunk 145 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 95 optimal weight:    0.6980
   chunk 40 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0470
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1336 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.146088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.097672 restraints weight = 20090.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.86
r_work: 0.3265 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  13760  Z= 0.115
  Angle     :  0.581  13.501  18582  Z= 0.282
  Chirality :  0.038   0.174   2186
  Planarity :  0.003   0.051   2386
  Dihedral  :  4.243  18.559   1811
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.28 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  1.17 (0.20), residues: 1704
  helix:  1.45 (0.15), residues: 1225
  sheet:  None (None), residues: 0
  loop : -0.95 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B1551 
 TYR   0.010   0.001   TYR A 739 
 PHE   0.013   0.001   PHE C 120 
 TRP   0.006   0.001   TRP B1500 
 HIS   0.002   0.001   HIS A1376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13760)
  covalent geometry    : angle       0.58065 (18582)
  hydrogen bonds       : bond        0.03156 (  902)
  hydrogen bonds       : angle       3.73574 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 149
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7585 (t0) cc_final: 0.6832 (p0)
REVERT: A  831 TYR cc_start: 0.8178 (t80) cc_final: 0.7824 (t80)
REVERT: A  867 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.7889 (ptp)
REVERT: A  902 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7577 (mtm110)
REVERT: A  917 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8061 (mm110)
REVERT: A 1255 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7295 (ptt90)
REVERT: A 1259 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8288 (tp)
REVERT: A 1402 ARG cc_start: 0.7783 (mtp85) cc_final: 0.6924 (mmm-85)
REVERT: A 1458 LYS cc_start: 0.8459 (tptt) cc_final: 0.8240 (tptt)
REVERT: A 1483 MET cc_start: 0.8696 (mpp) cc_final: 0.7867 (mpt)
REVERT: B 1513 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7593 (tp30)
REVERT: B 1606 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7711 (mp10)
REVERT: C  136 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8131 (mm-30)
REVERT: C  233 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8418 (mtt90)
REVERT: C  241 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: D   78 MET cc_start: 0.8839 (ptm) cc_final: 0.8365 (pp-130)
REVERT: D   89 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8238 (pp20)
REVERT: D  163 MET cc_start: 0.8933 (ttp) cc_final: 0.8572 (tpp)
REVERT: D  206 ASP cc_start: 0.8423 (m-30) cc_final: 0.8171 (m-30)
REVERT: D  236 LEU cc_start: 0.6115 (tt) cc_final: 0.5673 (mt)
REVERT: D  239 TYR cc_start: 0.6426 (t80) cc_final: 0.6053 (t80)
  outliers start: 34
  outliers final: 14
  residues processed: 174
  average time/residue: 0.6188
  time to fit residues: 117.7469
Evaluate side-chains
  156 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  805 ASN
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  902 ARG
Chi-restraints excluded: chain A residue  908 ILE
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1185 CYS
Chi-restraints excluded: chain A residue 1255 ARG
Chi-restraints excluded: chain A residue 1259 ILE
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1520 LEU
Chi-restraints excluded: chain A residue 1548 VAL
Chi-restraints excluded: chain B residue 1498 VAL
Chi-restraints excluded: chain B residue 1513 GLU
Chi-restraints excluded: chain B residue 1539 SER
Chi-restraints excluded: chain B residue 1606 GLN
Chi-restraints excluded: chain B residue 1608 VAL
Chi-restraints excluded: chain D residue   92 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 112 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    0.3980
   chunk 55 optimal weight:    1.9990
   chunk 128 optimal weight:    3.9990
   chunk 138 optimal weight:    1.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** 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 = 0.4051 r_free = 0.4051 target = 0.143301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.094402 restraints weight = 20126.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.85
r_work: 0.3214 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  13760  Z= 0.181
  Angle     :  0.626  14.971  18582  Z= 0.300
  Chirality :  0.040   0.191   2186
  Planarity :  0.004   0.051   2386
  Dihedral  :  4.274  18.861   1811
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.40 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  1.12 (0.20), residues: 1704
  helix:  1.41 (0.15), residues: 1222
  sheet:  None (None), residues: 0
  loop : -0.93 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 233 
 TYR   0.010   0.001   TYR A 914 
 PHE   0.023   0.001   PHE A1573 
 TRP   0.010   0.001   TRP A1532 
 HIS   0.003   0.001   HIS A1363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (13760)
  covalent geometry    : angle       0.62632 (18582)
  hydrogen bonds       : bond        0.03315 (  902)
  hydrogen bonds       : angle       3.77015 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 138
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7569 (t0) cc_final: 0.6855 (p0)
REVERT: A  664 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7684 (pp20)
REVERT: A  831 TYR cc_start: 0.8206 (t80) cc_final: 0.7861 (t80)
REVERT: A  867 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8038 (ptp)
REVERT: A  902 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7650 (mtm110)
REVERT: A  917 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8112 (mm110)
REVERT: A 1255 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7354 (ptt90)
REVERT: A 1259 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8346 (tp)
REVERT: A 1402 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7063 (mmm-85)
REVERT: A 1458 LYS cc_start: 0.8486 (tptt) cc_final: 0.8255 (tptt)
REVERT: B 1606 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7588 (mp10)
REVERT: C  136 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: C  241 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8361 (tm-30)
REVERT: D   78 MET cc_start: 0.8845 (ptm) cc_final: 0.8383 (pp-130)
REVERT: D   89 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8294 (pp20)
REVERT: D  163 MET cc_start: 0.8943 (ttp) cc_final: 0.8585 (tpp)
REVERT: D  206 ASP cc_start: 0.8473 (m-30) cc_final: 0.8226 (m-30)
REVERT: D  236 LEU cc_start: 0.6120 (tt) cc_final: 0.5800 (tp)
REVERT: D  239 TYR cc_start: 0.6417 (t80) cc_final: 0.6079 (t80)
  outliers start: 37
  outliers final: 17
  residues processed: 165
  average time/residue: 0.5954
  time to fit residues: 108.0415
Evaluate side-chains
  159 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  805 ASN
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  902 ARG
Chi-restraints excluded: chain A residue  908 ILE
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1185 CYS
Chi-restraints excluded: chain A residue 1255 ARG
Chi-restraints excluded: chain A residue 1259 ILE
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1520 LEU
Chi-restraints excluded: chain A residue 1548 VAL
Chi-restraints excluded: chain B residue 1498 VAL
Chi-restraints excluded: chain B residue 1518 LEU
Chi-restraints excluded: chain B residue 1539 SER
Chi-restraints excluded: chain B residue 1606 GLN
Chi-restraints excluded: chain B residue 1608 VAL
Chi-restraints excluded: chain D residue   92 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 59 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 137 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** 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 = 0.4073 r_free = 0.4073 target = 0.145220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.096640 restraints weight = 20144.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.85
r_work: 0.3252 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13760  Z= 0.129
  Angle     :  0.612  15.199  18582  Z= 0.290
  Chirality :  0.038   0.181   2186
  Planarity :  0.004   0.048   2386
  Dihedral  :  4.206  18.563   1811
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.66 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  1.28 (0.20), residues: 1704
  helix:  1.53 (0.15), residues: 1226
  sheet:  None (None), residues: 0
  loop : -0.87 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 233 
 TYR   0.011   0.001   TYR A 914 
 PHE   0.013   0.001   PHE C 120 
 TRP   0.007   0.001   TRP A1532 
 HIS   0.002   0.001   HIS A1376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (13760)
  covalent geometry    : angle       0.61151 (18582)
  hydrogen bonds       : bond        0.03193 (  902)
  hydrogen bonds       : angle       3.71229 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7472 (t0) cc_final: 0.6792 (p0)
REVERT: A  664 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7711 (pp20)
REVERT: A  831 TYR cc_start: 0.8217 (t80) cc_final: 0.7840 (t80)
REVERT: A  867 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.7968 (ptp)
REVERT: A  902 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7671 (mtm110)
REVERT: A  917 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8102 (mm110)
REVERT: A 1255 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7284 (ptt90)
REVERT: A 1259 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8315 (tp)
REVERT: A 1402 ARG cc_start: 0.7747 (mtp85) cc_final: 0.6884 (mmm-85)
REVERT: A 1458 LYS cc_start: 0.8512 (tptt) cc_final: 0.8278 (tptt)
REVERT: A 1483 MET cc_start: 0.8706 (mpp) cc_final: 0.7796 (mpt)
REVERT: B 1513 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7642 (tp30)
REVERT: B 1606 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7747 (mp10)
REVERT: C  136 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8082 (mm-30)
REVERT: C  241 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: D   78 MET cc_start: 0.8815 (ptm) cc_final: 0.8356 (pp-130)
REVERT: D   89 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8234 (pp20)
REVERT: D  163 MET cc_start: 0.8934 (ttp) cc_final: 0.8587 (tpp)
REVERT: D  206 ASP cc_start: 0.8453 (m-30) cc_final: 0.8205 (m-30)
REVERT: D  236 LEU cc_start: 0.6109 (tt) cc_final: 0.5759 (tp)
REVERT: D  239 TYR cc_start: 0.6451 (t80) cc_final: 0.6035 (t80)
  outliers start: 34
  outliers final: 21
  residues processed: 165
  average time/residue: 0.6063
  time to fit residues: 109.5887
Evaluate side-chains
  163 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  805 ASN
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  902 ARG
Chi-restraints excluded: chain A residue  908 ILE
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1185 CYS
Chi-restraints excluded: chain A residue 1186 ASP
Chi-restraints excluded: chain A residue 1255 ARG
Chi-restraints excluded: chain A residue 1259 ILE
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1364 LEU
Chi-restraints excluded: chain A residue 1520 LEU
Chi-restraints excluded: chain A residue 1548 VAL
Chi-restraints excluded: chain B residue 1498 VAL
Chi-restraints excluded: chain B residue 1513 GLU
Chi-restraints excluded: chain B residue 1518 LEU
Chi-restraints excluded: chain B residue 1539 SER
Chi-restraints excluded: chain B residue 1606 GLN
Chi-restraints excluded: chain B residue 1608 VAL
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  111 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0270
   chunk 84 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 159 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 129 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0470
   chunk 155 optimal weight:    0.7980
   chunk 167 optimal weight:    5.9990
   overall best weight:    0.9740

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** 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 = 0.4071 r_free = 0.4071 target = 0.144918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.095781 restraints weight = 20135.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.87
r_work: 0.3239 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  13760  Z= 0.147
  Angle     :  0.623  15.893  18582  Z= 0.298
  Chirality :  0.039   0.172   2186
  Planarity :  0.004   0.060   2386
  Dihedral  :  4.192  18.666   1811
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.66 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  1.31 (0.20), residues: 1704
  helix:  1.54 (0.15), residues: 1227
  sheet:  None (None), residues: 0
  loop : -0.85 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 233 
 TYR   0.010   0.001   TYR A 914 
 PHE   0.028   0.001   PHE A1573 
 TRP   0.013   0.001   TRP A1532 
 HIS   0.002   0.001   HIS A1150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13760)
  covalent geometry    : angle       0.62305 (18582)
  hydrogen bonds       : bond        0.03213 (  902)
  hydrogen bonds       : angle       3.72432 ( 2688)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7374 (t0) cc_final: 0.6684 (p0)
REVERT: A  664 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7687 (pp20)
REVERT: A  831 TYR cc_start: 0.8174 (t80) cc_final: 0.7801 (t80)
REVERT: A  867 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.7973 (ptp)
REVERT: A  902 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7692 (mtm110)
REVERT: A  917 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8052 (mm110)
REVERT: A 1255 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7275 (ptt90)
REVERT: A 1259 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8298 (tp)
REVERT: A 1402 ARG cc_start: 0.7714 (mtp85) cc_final: 0.6836 (mmm-85)
REVERT: A 1458 LYS cc_start: 0.8497 (tptt) cc_final: 0.8267 (tptt)
REVERT: A 1483 MET cc_start: 0.8703 (mpp) cc_final: 0.7772 (mpt)
REVERT: B 1513 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7638 (tp30)
REVERT: B 1606 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7722 (mp10)
REVERT: C  136 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8085 (mm-30)
REVERT: D   78 MET cc_start: 0.8827 (ptm) cc_final: 0.8364 (pp-130)
REVERT: D   89 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8286 (pp20)
REVERT: D  163 MET cc_start: 0.8937 (ttp) cc_final: 0.8586 (tpp)
REVERT: D  206 ASP cc_start: 0.8440 (m-30) cc_final: 0.8190 (m-30)
REVERT: D  236 LEU cc_start: 0.6050 (tt) cc_final: 0.5743 (tp)
REVERT: D  239 TYR cc_start: 0.6444 (t80) cc_final: 0.6069 (t80)
  outliers start: 33
  outliers final: 20
  residues processed: 161
  average time/residue: 0.5885
  time to fit residues: 104.1659
Evaluate side-chains
  159 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  805 ASN
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  902 ARG
Chi-restraints excluded: chain A residue  908 ILE
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1185 CYS
Chi-restraints excluded: chain A residue 1255 ARG
Chi-restraints excluded: chain A residue 1259 ILE
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1364 LEU
Chi-restraints excluded: chain A residue 1520 LEU
Chi-restraints excluded: chain A residue 1548 VAL
Chi-restraints excluded: chain B residue 1498 VAL
Chi-restraints excluded: chain B residue 1513 GLU
Chi-restraints excluded: chain B residue 1518 LEU
Chi-restraints excluded: chain B residue 1539 SER
Chi-restraints excluded: chain B residue 1606 GLN
Chi-restraints excluded: chain B residue 1608 VAL
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  111 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 133 optimal weight:    0.9990
   chunk 164 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 111 optimal weight:    0.0010
   chunk 4 optimal weight:    7.9990
   chunk 139 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 68 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 713 GLN
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 240 GLN
C 241 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.145709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.097042 restraints weight = 20258.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.87
r_work: 0.3259 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13760  Z= 0.124
  Angle     :  0.604  15.796  18582  Z= 0.290
  Chirality :  0.038   0.168   2186
  Planarity :  0.004   0.053   2386
  Dihedral  :  4.131  18.413   1811
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 19.92 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  1.45 (0.20), residues: 1704
  helix:  1.65 (0.15), residues: 1225
  sheet:  None (None), residues: 0
  loop : -0.79 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 233 
 TYR   0.011   0.001   TYR A 914 
 PHE   0.017   0.001   PHE C 147 
 TRP   0.008   0.001   TRP A1532 
 HIS   0.002   0.001   HIS A 789 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (13760)
  covalent geometry    : angle       0.60435 (18582)
  hydrogen bonds       : bond        0.03129 (  902)
  hydrogen bonds       : angle       3.70250 ( 2688)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4357.49 seconds
wall clock time: 75 minutes 5.42 seconds (4505.42 seconds total)