Starting phenix.real_space_refine
on Wed Mar  4 08:45:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xw3_33490/03_2026/7xw3_33490.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xw3_33490/03_2026/7xw3_33490.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xw3_33490/03_2026/7xw3_33490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xw3_33490/03_2026/7xw3_33490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xw3_33490/03_2026/7xw3_33490.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xw3_33490/03_2026/7xw3_33490.cif"
  }
  resolution = 4.04
  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=   0.000 sd=   0.018
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      67      5.16       5
     C    7694      2.51       5
     N    2060      2.21       5
     O    2260      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 62 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: 12081
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1502, 12081
          Classifications: {'peptide': 1502}
          Link IDs: {'PTRANS': 89, 'TRANS': 1412}
          Chain breaks: 5
  Time building chain proxies: 2.34, per 1000 atoms: 0.19
  Number of scatterers: 12081
  At special positions: 0
  Unit cell: (101.384, 106.894, 160.892, 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      67     16.00
     O    2260      8.00
     N    2060      7.00
     C    7694      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 567.2 milliseconds
  

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2878

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 12 sheets defined
      43.7% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 50
      removed outlier: 4.268A  pdb=" N   GLU A  50 " --> pdb=" O   TYR A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 58
      removed outlier: 4.271A  pdb=" N   ALA A  55 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASP A  57 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 79
      removed outlier: 4.912A  pdb=" N   LEU A  76 " --> pdb=" O   PHE A  72 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU A  77 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 85
      removed outlier: 5.387A  pdb=" N   TYR A  83 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLN A  84 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 115
      removed outlier: 3.698A  pdb=" N   THR A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 133
      removed outlier: 3.873A  pdb=" N   TRP A 133 " --> pdb=" O   ASN A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 151 through 161
    Processing helix  chain 'A' and resid 176 through 182
      removed outlier: 3.544A  pdb=" N   LEU A 179 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 196
      removed outlier: 4.338A  pdb=" N   GLU A 188 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 231
    Processing helix  chain 'A' and resid 266 through 282
    Processing helix  chain 'A' and resid 295 through 313
    Processing helix  chain 'A' and resid 314 through 336
      removed outlier: 3.969A  pdb=" N   ALA A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLY A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   MET A 324 " --> pdb=" O   LYS A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 363
    Processing helix  chain 'A' and resid 374 through 385
      removed outlier: 3.748A  pdb=" N   ILE A 378 " --> pdb=" O   THR A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 466
    Processing helix  chain 'A' and resid 468 through 473
      removed outlier: 3.625A  pdb=" N   TYR A 473 " --> pdb=" O   PRO A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 510
      removed outlier: 3.669A  pdb=" N   ALA A 510 " --> pdb=" O   ARG A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 552
    Processing helix  chain 'A' and resid 567 through 588
      removed outlier: 4.429A  pdb=" N   SER A 571 " --> pdb=" O   ASP A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 638
      removed outlier: 3.770A  pdb=" N   ILE A 631 " --> pdb=" O   ILE A 627 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   CYS A 638 " --> pdb=" O   ILE A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 705
    Processing helix  chain 'A' and resid 754 through 758
    Processing helix  chain 'A' and resid 839 through 857
    Processing helix  chain 'A' and resid 893 through 903
      removed outlier: 3.745A  pdb=" N   MET A 897 " --> pdb=" O   ASP A 893 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   SER A 903 " --> pdb=" O   ASP A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 974
      removed outlier: 3.598A  pdb=" N   TYR A 971 " --> pdb=" O   THR A 967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1036
      No H-bonds generated for 'chain 'A' and resid 1034 through 1036'
    Processing helix  chain 'A' and resid 1044 through 1053
      removed outlier: 3.963A  pdb=" N   CYS A1053 " --> pdb=" O   ARG A1049 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1078
    Processing helix  chain 'A' and resid 1293 through 1302
      removed outlier: 3.748A  pdb=" N   ILE A1297 " --> pdb=" O   ASN A1293 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLN A1299 " --> pdb=" O   GLY A1295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1312 through 1333
      removed outlier: 3.894A  pdb=" N   MET A1317 " --> pdb=" O   GLU A1313 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU A1318 " --> pdb=" O   ARG A1314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1351
      removed outlier: 5.487A  pdb=" N   LYS A1349 " --> pdb=" O   TYR A1345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1352 through 1361
      removed outlier: 3.777A  pdb=" N   ARG A1358 " --> pdb=" O   CYS A1354 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU A1359 " --> pdb=" O   ASN A1355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1364 through 1369
      removed outlier: 3.595A  pdb=" N   MET A1369 " --> pdb=" O   PRO A1366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1375 through 1380
      removed outlier: 3.502A  pdb=" N   ASN A1379 " --> pdb=" O   ASP A1375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1446 through 1452
      removed outlier: 4.120A  pdb=" N   ILE A1450 " --> pdb=" O   ASP A1446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1556 through 1587
      removed outlier: 4.234A  pdb=" N   ALA A1560 " --> pdb=" O   ASP A1556 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY A1568 " --> pdb=" O   GLU A1564 " (cutoff:3.500A)
      removed outlier: 8.734A  pdb=" N   GLU A1576 " --> pdb=" O   THR A1572 " (cutoff:3.500A)
      removed outlier: 10.132A  pdb=" N   ARG A1577 " --> pdb=" O   SER A1573 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ALA A1578 " --> pdb=" O   CYS A1574 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LEU A1586 " --> pdb=" O   PHE A1582 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   GLY A1587 " --> pdb=" O   LEU A1583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1595 through 1601
      removed outlier: 3.533A  pdb=" N   ARG A1599 " --> pdb=" O   LYS A1595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1656 through 1668
      removed outlier: 4.418A  pdb=" N   ASN A1668 " --> pdb=" O   SER A1664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1680 through 1688
      removed outlier: 4.344A  pdb=" N   PHE A1687 " --> pdb=" O   LEU A1683 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR A1688 " --> pdb=" O   LEU A1684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1701 through 1722
      removed outlier: 3.759A  pdb=" N   ALA A1710 " --> pdb=" O   PHE A1706 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   ILE A1711 " --> pdb=" O   LEU A1707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1741 through 1752
    Processing helix  chain 'A' and resid 1762 through 1778
      removed outlier: 3.955A  pdb=" N   PHE A1766 " --> pdb=" O   SER A1762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1792 through 1801
    Processing helix  chain 'A' and resid 1807 through 1823
      removed outlier: 3.564A  pdb=" N   ILE A1811 " --> pdb=" O   ALA A1807 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   SER A1823 " --> pdb=" O   ILE A1819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1826 through 1846
      removed outlier: 3.981A  pdb=" N   VAL A1830 " --> pdb=" O   SER A1826 " (cutoff:3.500A)
      Proline residue:  A1836  - end of helix
      Proline residue:  A1840  - end of helix
    Processing helix  chain 'A' and resid 1852 through 1861
    Processing helix  chain 'A' and resid 1896 through 1916
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
      removed outlier: 3.685A  pdb=" N   THR A  60 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLY A 204 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A 203 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99
      removed outlier: 5.514A  pdb=" N   PHE A  98 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 256
      removed outlier: 5.844A  pdb=" N   SER A 558 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   CYS A 251 " --> pdb=" O   SER A 558 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 560 " --> pdb=" O   CYS A 251 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ILE A 253 " --> pdb=" O   TYR A 560 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   MET A 562 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 534 " --> pdb=" O   ASN A 559 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU A 563 " --> pdb=" O   ARG A 536 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE A 445 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   GLY A 444 " --> pdb=" O   LEU A 516 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ALA A 518 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ILE A 446 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 589 through 590
    Processing sheet with id=AA5, first strand: chain 'A' and resid 652 through 657
    Processing sheet with id=AA6, first strand: chain 'A' and resid 746 through 750
      removed outlier: 4.133A  pdb=" N   GLN A 747 " --> pdb=" O   ILE A1554 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ILE A1554 " --> pdb=" O   GLN A 747 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 805 through 806
      removed outlier: 3.617A  pdb=" N   THR A 806 " --> pdb=" O   TYR A 769 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE A 836 " --> pdb=" O   CYS A 768 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU A 770 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   SER A 834 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
      removed outlier: 8.638A  pdb=" N   VAL A 772 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   LYS A 832 " --> pdb=" O   VAL A 772 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 777
      removed outlier: 3.673A  pdb=" N   VAL A 776 " --> pdb=" O   THR A 826 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLY A 823 " --> pdb=" O   THR A 820 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR A 820 " --> pdb=" O   GLY A 823 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 801 through 802
    Processing sheet with id=AB1, first strand: chain 'A' and resid 865 through 867
      removed outlier: 3.711A  pdb=" N   GLU A 866 " --> pdb=" O   VAL A1386 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A1386 " --> pdb=" O   GLU A 866 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 988 through 991
      removed outlier: 5.702A  pdb=" N   ASP A 991 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   VAL A 947 " --> pdb=" O   ASP A 991 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE A 945 " --> pdb=" O   ILE A 932 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   VAL A 931 " --> pdb=" O   HIS A1041 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1878 through 1881
      removed outlier: 3.611A  pdb=" N   VAL A1878 " --> pdb=" O   GLY A1894 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A1894 " --> pdb=" O   VAL A1878 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLY A1892 " --> pdb=" O   VAL A1880 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1275 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: 2.18

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2063
        1.32 -     1.44: 3116
        1.44 -     1.57: 7070
        1.57 -     1.69: 0
        1.69 -     1.82: 95
  Bond restraints: 12344
  Sorted by residual:
  bond pdb=" N   ARG A 763 "
       pdb=" CA  ARG A 763 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 7.00e-03 2.04e+04 1.88e+01
  bond pdb=" C   VAL A 129 "
       pdb=" O   VAL A 129 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.23e-02 6.61e+03 1.28e+01
  bond pdb=" N   VAL A 113 "
       pdb=" CA  VAL A 113 "
    ideal  model  delta    sigma   weight residual
    1.456  1.500 -0.044 1.30e-02 5.92e+03 1.13e+01
  bond pdb=" N   ILE A 813 "
       pdb=" CA  ILE A 813 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.031 9.10e-03 1.21e+04 1.13e+01
  bond pdb=" N   GLN A 488 "
       pdb=" CA  GLN A 488 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.04e-02 9.25e+03 1.12e+01
  ... (remaining 12339 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 15541
        2.38 -     4.77: 1050
        4.77 -     7.15: 102
        7.15 -     9.53: 14
        9.53 -    11.91: 5
  Bond angle restraints: 16712
  Sorted by residual:
  angle pdb=" N   ILE A  73 "
        pdb=" CA  ILE A  73 "
        pdb=" C   ILE A  73 "
      ideal   model   delta    sigma   weight residual
     113.43  103.09   10.34 1.09e+00 8.42e-01 9.00e+01
  angle pdb=" N   PRO A1376 "
        pdb=" CA  PRO A1376 "
        pdb=" C   PRO A1376 "
      ideal   model   delta    sigma   weight residual
     110.70  121.51  -10.81 1.22e+00 6.72e-01 7.85e+01
  angle pdb=" N   THR A  71 "
        pdb=" CA  THR A  71 "
        pdb=" C   THR A  71 "
      ideal   model   delta    sigma   weight residual
     111.28  103.06    8.22 1.09e+00 8.42e-01 5.69e+01
  angle pdb=" N   MET A1346 "
        pdb=" CA  MET A1346 "
        pdb=" C   MET A1346 "
      ideal   model   delta    sigma   weight residual
     112.72  103.16    9.56 1.28e+00 6.10e-01 5.58e+01
  angle pdb=" N   ASN A1455 "
        pdb=" CA  ASN A1455 "
        pdb=" C   ASN A1455 "
      ideal   model   delta    sigma   weight residual
     112.87  105.22    7.65 1.20e+00 6.94e-01 4.07e+01
  ... (remaining 16707 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 6709
       17.66 -    35.32: 681
       35.32 -    52.98: 124
       52.98 -    70.64: 53
       70.64 -    88.29: 27
  Dihedral angle restraints: 7594
    sinusoidal: 3153
      harmonic: 4441
  Sorted by residual:
  dihedral pdb=" C   ASP A1753 "
           pdb=" N   ASP A1753 "
           pdb=" CA  ASP A1753 "
           pdb=" CB  ASP A1753 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.23   18.63     0      2.50e+00 1.60e-01 5.56e+01
  dihedral pdb=" N   ASP A1753 "
           pdb=" C   ASP A1753 "
           pdb=" CA  ASP A1753 "
           pdb=" CB  ASP A1753 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.98  -17.18     0      2.50e+00 1.60e-01 4.72e+01
  dihedral pdb=" C   TYR A1752 "
           pdb=" N   TYR A1752 "
           pdb=" CA  TYR A1752 "
           pdb=" CB  TYR A1752 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.92   13.32     0      2.50e+00 1.60e-01 2.84e+01
  ... (remaining 7591 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 1754
       0.139 -    0.279: 103
       0.279 -    0.418: 7
       0.418 -    0.558: 1
       0.558 -    0.697: 1
  Chirality restraints: 1866
  Sorted by residual:
  chirality pdb=" CA  ASP A1753 "
            pdb=" N   ASP A1753 "
            pdb=" C   ASP A1753 "
            pdb=" CB  ASP A1753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.81    0.70 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" CA  PHE A  72 "
            pdb=" N   PHE A  72 "
            pdb=" C   PHE A  72 "
            pdb=" CB  PHE A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.27e+00
  chirality pdb=" CA  TYR A1752 "
            pdb=" N   TYR A1752 "
            pdb=" C   TYR A1752 "
            pdb=" CB  TYR A1752 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.83e+00
  ... (remaining 1863 not shown)

  Planarity restraints: 2158
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 553 "   -0.021 2.00e-02 2.50e+03   4.31e-02 1.86e+01
        pdb=" C   ALA A 553 "    0.075 2.00e-02 2.50e+03
        pdb=" O   ALA A 553 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ARG A 554 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A1667 "   -0.019 2.00e-02 2.50e+03   3.93e-02 1.55e+01
        pdb=" C   GLU A1667 "    0.068 2.00e-02 2.50e+03
        pdb=" O   GLU A1667 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ASN A1668 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A1778 "   -0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   GLU A1778 "    0.059 2.00e-02 2.50e+03
        pdb=" O   GLU A1778 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   LYS A1779 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 2155 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1908
        2.75 -     3.29: 12432
        3.29 -     3.83: 19617
        3.83 -     4.36: 23741
        4.36 -     4.90: 38336
  Nonbonded interactions: 96034
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 319 "
            pdb=" NZ  LYS A 320 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" O   HIS A 145 "
            pdb=" NE2 GLN A 146 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" O   HIS A 856 "
            pdb=" NH2 ARG A 944 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" N   GLU A 188 "
            pdb=" OE1 GLU A 188 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   SER A1287 "
            pdb=" OG  SER A1287 "
     model   vdw
     2.256 3.040
  ... (remaining 96029 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.610
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.450
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6348
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      :  0.009   0.119  12344  Z= 0.541
  Angle     :  1.242  11.914  16712  Z= 0.820
  Chirality :  0.074   0.697   1866
  Planarity :  0.007   0.078   2158
  Dihedral  : 16.199  88.294   4716
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.39 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 10.78 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.09 (0.18), residues: 1490
  helix: -2.80 (0.16), residues: 615
  sheet: -3.97 (0.38), residues: 120
  loop : -2.36 (0.20), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 821 
 TYR   0.031   0.003   TYR A1546 
 PHE   0.055   0.003   PHE A1812 
 TRP   0.024   0.004   TRP A 133 
 HIS   0.014   0.003   HIS A1325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00947 (12344)
  covalent geometry    : angle       1.24208 (16712)
  hydrogen bonds       : bond        0.17665 (  441)
  hydrogen bonds       : angle       7.68490 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.8192 (m-70)
REVERT: A  324 MET cc_start: -0.0902 (mmm) cc_final: -0.1320 (mmm)
REVERT: A  713 MET cc_start: 0.2126 (ptm) cc_final: 0.1452 (ptm)
REVERT: A  747 GLN cc_start: 0.7972 (mt0) cc_final: 0.7592 (mp10)
REVERT: A  842 MET cc_start: 0.7944 (mmt) cc_final: 0.7238 (mmt)
REVERT: A 1090 ARG cc_start: 0.3420 (OUTLIER) cc_final: 0.2659 (tmt170)
REVERT: A 1559 ILE cc_start: 0.7451 (tp) cc_final: 0.7233 (tp)
REVERT: A 1860 MET cc_start: 0.3830 (tpt) cc_final: 0.2510 (mtt)
  outliers start: 34
  outliers final: 11
  residues processed: 179
  average time/residue: 0.1134
  time to fit residues: 28.7865
Evaluate side-chains
  119 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    5.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN
A  65 ASN
A  84 GLN
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 249 GLN
A 356 HIS
A 362 HIS
A 588 ASN
A 628 ASN
A 885 ASN
A1004 HIS
A1028 GLN
A1041 HIS
A1339 HIS
A1355 ASN
A1668 ASN
A1727 HIS
A1780 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.189845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.155923 restraints weight = 29667.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.155601 restraints weight = 25324.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.156979 restraints weight = 21996.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.158256 restraints weight = 15069.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.158559 restraints weight = 13966.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6242
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12344  Z= 0.146
  Angle     :  0.654   7.670  16712  Z= 0.350
  Chirality :  0.044   0.169   1866
  Planarity :  0.005   0.047   2158
  Dihedral  :  6.156  25.991   1653
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.36 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.47 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.20), residues: 1490
  helix: -1.11 (0.20), residues: 628
  sheet: -3.31 (0.38), residues: 144
  loop : -1.98 (0.21), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1049 
 TYR   0.022   0.002   TYR A1757 
 PHE   0.019   0.002   PHE A1812 
 TRP   0.007   0.001   TRP A1831 
 HIS   0.007   0.001   HIS A 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (12344)
  covalent geometry    : angle       0.65412 (16712)
  hydrogen bonds       : bond        0.04680 (  441)
  hydrogen bonds       : angle       5.19004 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 154
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 HIS cc_start: 0.6385 (m-70) cc_final: 0.5887 (m90)
REVERT: A  163 TYR cc_start: 0.6676 (m-80) cc_final: 0.6209 (m-10)
REVERT: A  494 MET cc_start: 0.6844 (ptt) cc_final: 0.6037 (ptt)
REVERT: A  559 ASN cc_start: 0.7250 (t0) cc_final: 0.6915 (t0)
REVERT: A  707 GLU cc_start: 0.7219 (pt0) cc_final: 0.6967 (pp20)
REVERT: A  713 MET cc_start: 0.3031 (ppp) cc_final: 0.2558 (ppp)
REVERT: A  842 MET cc_start: 0.8145 (mmt) cc_final: 0.7412 (mmt)
REVERT: A 1333 CYS cc_start: 0.8312 (m) cc_final: 0.7647 (t)
REVERT: A 1359 LEU cc_start: 0.7113 (tp) cc_final: 0.6813 (tt)
REVERT: A 1860 MET cc_start: 0.4043 (tpt) cc_final: 0.2594 (mtt)
  outliers start: 3
  outliers final: 1
  residues processed: 156
  average time/residue: 0.1054
  time to fit residues: 23.6072
Evaluate side-chains
  95 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 147 optimal weight:   30.0000
   chunk 17 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 95 optimal weight:    0.4980
   chunk 103 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 488 GLN
A 493 GLN
A 850 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.187643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.154533 restraints weight = 31592.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.152800 restraints weight = 31942.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.154696 restraints weight = 26037.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.155349 restraints weight = 17385.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.155794 restraints weight = 17092.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.4227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6366
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12344  Z= 0.152
  Angle     :  0.629   7.013  16712  Z= 0.332
  Chirality :  0.044   0.157   1866
  Planarity :  0.005   0.054   2158
  Dihedral  :  5.635  30.778   1653
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.77 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  4.14 %
    Favored  : 95.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.04 (0.21), residues: 1490
  helix: -0.47 (0.20), residues: 623
  sheet: -3.16 (0.41), residues: 120
  loop : -1.80 (0.21), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 587 
 TYR   0.026   0.002   TYR A 186 
 PHE   0.029   0.002   PHE A1812 
 TRP   0.010   0.001   TRP A1831 
 HIS   0.006   0.001   HIS A1727 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12344)
  covalent geometry    : angle       0.62859 (16712)
  hydrogen bonds       : bond        0.04471 (  441)
  hydrogen bonds       : angle       4.82428 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  559 ASN cc_start: 0.6805 (t0) cc_final: 0.6581 (t0)
REVERT: A  707 GLU cc_start: 0.7403 (pt0) cc_final: 0.7098 (pp20)
REVERT: A  842 MET cc_start: 0.8061 (mmt) cc_final: 0.7342 (mmt)
REVERT: A 1021 LYS cc_start: 0.5701 (mmtt) cc_final: 0.4579 (tttt)
REVERT: A 1069 GLU cc_start: 0.6942 (tp30) cc_final: 0.6679 (tm-30)
REVERT: A 1333 CYS cc_start: 0.8159 (m) cc_final: 0.7574 (t)
REVERT: A 1860 MET cc_start: 0.4417 (tpt) cc_final: 0.2608 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0909
  time to fit residues: 19.2187
Evaluate side-chains
  95 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 124 optimal weight:    0.8980
   chunk 147 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0060
   chunk 34 optimal weight:    7.9990
   chunk 120 optimal weight:    0.2980
   chunk 1 optimal weight:    0.6980
   chunk 134 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 488 GLN
A 493 GLN
A 532 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.186335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.157936 restraints weight = 32169.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.157550 restraints weight = 41360.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.158807 restraints weight = 37056.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.159007 restraints weight = 23937.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.159843 restraints weight = 22196.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6182
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12344  Z= 0.116
  Angle     :  0.569   7.338  16712  Z= 0.299
  Chirality :  0.042   0.153   1866
  Planarity :  0.005   0.049   2158
  Dihedral  :  5.191  27.503   1653
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.30 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.18 %
    Favored  : 96.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.21), residues: 1490
  helix:  0.01 (0.21), residues: 624
  sheet: -2.78 (0.44), residues: 107
  loop : -1.69 (0.22), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 587 
 TYR   0.016   0.001   TYR A 972 
 PHE   0.022   0.001   PHE A 347 
 TRP   0.012   0.002   TRP A1024 
 HIS   0.011   0.001   HIS A1449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (12344)
  covalent geometry    : angle       0.56856 (16712)
  hydrogen bonds       : bond        0.03807 (  441)
  hydrogen bonds       : angle       4.51397 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 MET cc_start: 0.2531 (ppp) cc_final: 0.2267 (ppp)
REVERT: A  842 MET cc_start: 0.7951 (mmt) cc_final: 0.7325 (mmt)
REVERT: A 1359 LEU cc_start: 0.7047 (tp) cc_final: 0.6626 (tt)
REVERT: A 1860 MET cc_start: 0.4579 (tpt) cc_final: 0.2689 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0836
  time to fit residues: 18.2155
Evaluate side-chains
  96 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 109 optimal weight:    0.3980
   chunk 88 optimal weight:    0.0070
   chunk 114 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 125 optimal weight:    0.9990
   chunk 133 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 488 GLN
A 532 ASN
A1353 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.187188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.157970 restraints weight = 32223.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.157083 restraints weight = 36524.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.158400 restraints weight = 32290.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.158873 restraints weight = 21367.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.159308 restraints weight = 20919.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6204
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12344  Z= 0.107
  Angle     :  0.561   7.464  16712  Z= 0.291
  Chirality :  0.042   0.153   1866
  Planarity :  0.005   0.048   2158
  Dihedral  :  4.956  25.733   1653
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.36 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.99 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.21), residues: 1490
  helix:  0.16 (0.21), residues: 633
  sheet: -2.61 (0.45), residues: 93
  loop : -1.65 (0.22), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 944 
 TYR   0.014   0.001   TYR A 914 
 PHE   0.021   0.001   PHE A 347 
 TRP   0.006   0.001   TRP A1048 
 HIS   0.009   0.001   HIS A1449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (12344)
  covalent geometry    : angle       0.56118 (16712)
  hydrogen bonds       : bond        0.03614 (  441)
  hydrogen bonds       : angle       4.33804 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  559 ASN cc_start: 0.6590 (t0) cc_final: 0.6167 (t0)
REVERT: A  713 MET cc_start: 0.3014 (ppp) cc_final: 0.2740 (ppp)
REVERT: A 1860 MET cc_start: 0.4700 (tpt) cc_final: 0.2763 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0816
  time to fit residues: 17.4571
Evaluate side-chains
  94 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 130 optimal weight:    0.6980
   chunk 24 optimal weight:   20.0000
   chunk 111 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 127 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 488 GLN
A 532 ASN
A1353 ASN
A1580 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.186410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.153440 restraints weight = 31712.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.152154 restraints weight = 30750.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.153842 restraints weight = 26680.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.154325 restraints weight = 18328.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.154689 restraints weight = 17995.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6264
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12344  Z= 0.108
  Angle     :  0.559   8.047  16712  Z= 0.289
  Chirality :  0.042   0.162   1866
  Planarity :  0.005   0.050   2158
  Dihedral  :  4.799  27.071   1653
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.16 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.44 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.22), residues: 1490
  helix:  0.26 (0.21), residues: 636
  sheet: -2.72 (0.44), residues: 97
  loop : -1.51 (0.22), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 944 
 TYR   0.015   0.001   TYR A 186 
 PHE   0.030   0.001   PHE A 280 
 TRP   0.006   0.001   TRP A1048 
 HIS   0.004   0.001   HIS A1449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (12344)
  covalent geometry    : angle       0.55931 (16712)
  hydrogen bonds       : bond        0.03571 (  441)
  hydrogen bonds       : angle       4.27612 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  559 ASN cc_start: 0.6916 (t0) cc_final: 0.6437 (t0)
REVERT: A  713 MET cc_start: 0.2919 (ppp) cc_final: 0.2702 (ppp)
REVERT: A 1774 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7803 (pm20)
REVERT: A 1860 MET cc_start: 0.4433 (tpt) cc_final: 0.2573 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0808
  time to fit residues: 16.2453
Evaluate side-chains
  92 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 66 optimal weight:    0.3980
   chunk 80 optimal weight:    6.9990
   chunk 75 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 126 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0980
   chunk 132 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 488 GLN
A 532 ASN
A1660 ASN
A1767 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.187313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.158446 restraints weight = 32065.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.157209 restraints weight = 37783.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.158952 restraints weight = 34916.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.159119 restraints weight = 22597.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.159979 restraints weight = 21628.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6153
moved from start:          0.4556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12344  Z= 0.107
  Angle     :  0.559   8.047  16712  Z= 0.289
  Chirality :  0.042   0.156   1866
  Planarity :  0.005   0.050   2158
  Dihedral  :  4.640  26.716   1653
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.03 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.22), residues: 1490
  helix:  0.38 (0.21), residues: 629
  sheet: -2.77 (0.43), residues: 107
  loop : -1.32 (0.22), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 944 
 TYR   0.018   0.001   TYR A 186 
 PHE   0.021   0.001   PHE A 347 
 TRP   0.006   0.001   TRP A1048 
 HIS   0.004   0.001   HIS A 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (12344)
  covalent geometry    : angle       0.55855 (16712)
  hydrogen bonds       : bond        0.03473 (  441)
  hydrogen bonds       : angle       4.27455 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 HIS cc_start: 0.5932 (t-90) cc_final: 0.5532 (t-90)
REVERT: A  190 MET cc_start: 0.8312 (mmm) cc_final: 0.8035 (mtm)
REVERT: A  559 ASN cc_start: 0.6894 (t0) cc_final: 0.6445 (t0)
REVERT: A  773 ILE cc_start: 0.6815 (mt) cc_final: 0.5988 (mm)
REVERT: A 1069 GLU cc_start: 0.6779 (tp30) cc_final: 0.6573 (tm-30)
REVERT: A 1860 MET cc_start: 0.4401 (tpt) cc_final: 0.2519 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0835
  time to fit residues: 17.8406
Evaluate side-chains
  93 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 104 optimal weight:    0.0980
   chunk 14 optimal weight:    0.4980
   chunk 9 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0000
   chunk 52 optimal weight:    7.9990
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    0.1980
   chunk 148 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0570
   overall best weight:    0.1702

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 488 GLN
A 532 ASN
A1767 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.189888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.163319 restraints weight = 32140.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.163313 restraints weight = 38045.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.164648 restraints weight = 34512.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.164537 restraints weight = 23472.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.165375 restraints weight = 22172.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.4406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
moved from start:          0.4924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12344  Z= 0.096
  Angle     :  0.549   8.366  16712  Z= 0.282
  Chirality :  0.041   0.148   1866
  Planarity :  0.004   0.051   2158
  Dihedral  :  4.394  23.853   1653
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.76 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.22), residues: 1490
  helix:  0.60 (0.22), residues: 630
  sheet: -2.39 (0.46), residues: 97
  loop : -1.25 (0.22), residues: 763

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 996 
 TYR   0.014   0.001   TYR A 186 
 PHE   0.019   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A1380 
 HIS   0.003   0.001   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 (12344)
  covalent geometry    : angle       0.54912 (16712)
  hydrogen bonds       : bond        0.03172 (  441)
  hydrogen bonds       : angle       4.11655 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 HIS cc_start: 0.5901 (t-90) cc_final: 0.5437 (t-90)
REVERT: A  559 ASN cc_start: 0.6493 (t0) cc_final: 0.6073 (t0)
REVERT: A  773 ILE cc_start: 0.6633 (mt) cc_final: 0.5881 (mm)
REVERT: A  837 MET cc_start: 0.7401 (tpp) cc_final: 0.6928 (tpp)
REVERT: A  842 MET cc_start: 0.7868 (mmt) cc_final: 0.7319 (mmt)
REVERT: A 1069 GLU cc_start: 0.6751 (tp30) cc_final: 0.6378 (tm-30)
REVERT: A 1391 LYS cc_start: 0.8371 (mmtm) cc_final: 0.7894 (tppt)
REVERT: A 1860 MET cc_start: 0.4120 (tpt) cc_final: 0.2181 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0901
  time to fit residues: 19.2832
Evaluate side-chains
  93 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 114 optimal weight:    0.5980
   chunk 129 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 145 optimal weight:    0.0370
   chunk 38 optimal weight:   10.0000
   chunk 86 optimal weight:    5.9990
   chunk 146 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 147 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.3062

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 488 GLN
A 532 ASN
A 548 GLN
A 982 ASN
A1668 ASN
A1767 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.185198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.158743 restraints weight = 31995.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.162361 restraints weight = 40386.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.161912 restraints weight = 26457.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.162388 restraints weight = 21020.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.162595 restraints weight = 19502.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6117
moved from start:          0.4887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12344  Z= 0.149
  Angle     :  0.627   8.900  16712  Z= 0.319
  Chirality :  0.044   0.183   1866
  Planarity :  0.005   0.050   2158
  Dihedral  :  4.773  32.014   1653
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.63 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.10 (0.22), residues: 1490
  helix:  0.26 (0.21), residues: 635
  sheet: -2.96 (0.45), residues: 98
  loop : -1.24 (0.22), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 137 
 TYR   0.019   0.002   TYR A1570 
 PHE   0.025   0.002   PHE A 347 
 TRP   0.014   0.002   TRP A 138 
 HIS   0.006   0.001   HIS A1727 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (12344)
  covalent geometry    : angle       0.62746 (16712)
  hydrogen bonds       : bond        0.03966 (  441)
  hydrogen bonds       : angle       4.43645 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  559 ASN cc_start: 0.6352 (t0) cc_final: 0.5960 (t0)
REVERT: A  646 PHE cc_start: 0.5715 (m-10) cc_final: 0.5513 (m-10)
REVERT: A  773 ILE cc_start: 0.6750 (mt) cc_final: 0.6319 (pt)
REVERT: A  837 MET cc_start: 0.7424 (tpp) cc_final: 0.6945 (tpp)
REVERT: A  842 MET cc_start: 0.7745 (mmt) cc_final: 0.7144 (mmt)
REVERT: A  897 MET cc_start: 0.8059 (ptm) cc_final: 0.7665 (ttp)
REVERT: A 1069 GLU cc_start: 0.6734 (tp30) cc_final: 0.6440 (tm-30)
REVERT: A 1073 GLN cc_start: 0.7912 (pm20) cc_final: 0.7708 (pm20)
REVERT: A 1391 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7867 (tppt)
REVERT: A 1860 MET cc_start: 0.4306 (tpt) cc_final: 0.2445 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0862
  time to fit residues: 16.2994
Evaluate side-chains
  87 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 44 optimal weight:   20.0000
   chunk 116 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0170
   chunk 67 optimal weight:    4.9990
   chunk 74 optimal weight:    0.2980
   chunk 134 optimal weight:    0.5980
   chunk 140 optimal weight:    0.9980
   overall best weight:    0.5820

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 488 GLN
A 532 ASN
A 548 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.187051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.159602 restraints weight = 32188.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.158963 restraints weight = 40997.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.159784 restraints weight = 38726.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.162145 restraints weight = 27107.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.162096 restraints weight = 20188.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.4363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.5137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12344  Z= 0.109
  Angle     :  0.589   9.090  16712  Z= 0.300
  Chirality :  0.042   0.220   1866
  Planarity :  0.005   0.051   2158
  Dihedral  :  4.580  27.541   1653
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.09 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.22), residues: 1490
  helix:  0.36 (0.21), residues: 637
  sheet: -2.82 (0.42), residues: 107
  loop : -1.18 (0.23), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 137 
 TYR   0.018   0.001   TYR A 186 
 PHE   0.025   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 138 
 HIS   0.004   0.001   HIS A1727 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (12344)
  covalent geometry    : angle       0.58905 (16712)
  hydrogen bonds       : bond        0.03530 (  441)
  hydrogen bonds       : angle       4.29652 ( 1275)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 SER cc_start: 0.7899 (m) cc_final: 0.7629 (t)
REVERT: A  559 ASN cc_start: 0.6431 (t0) cc_final: 0.6045 (t0)
REVERT: A  773 ILE cc_start: 0.6611 (mt) cc_final: 0.6225 (mm)
REVERT: A  837 MET cc_start: 0.7466 (tpp) cc_final: 0.7001 (tpp)
REVERT: A  842 MET cc_start: 0.7692 (mmt) cc_final: 0.7268 (mmt)
REVERT: A  897 MET cc_start: 0.8020 (ptm) cc_final: 0.7576 (ttp)
REVERT: A 1069 GLU cc_start: 0.6612 (tp30) cc_final: 0.6253 (tm-30)
REVERT: A 1391 LYS cc_start: 0.8419 (mmtm) cc_final: 0.7902 (tppt)
REVERT: A 1453 ILE cc_start: 0.5152 (mp) cc_final: 0.4752 (tp)
REVERT: A 1860 MET cc_start: 0.4087 (tpt) cc_final: 0.2134 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0886
  time to fit residues: 17.3398
Evaluate side-chains
  90 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 33 optimal weight:    0.0770
   chunk 112 optimal weight:    0.0980
   chunk 93 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   chunk 94 optimal weight:   10.0000
   chunk 95 optimal weight:    2.9990
   chunk 110 optimal weight:    0.0270
   chunk 127 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 108 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.2596

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 488 GLN
A 532 ASN
** A1767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.189361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.161472 restraints weight = 32329.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.160436 restraints weight = 35923.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.161775 restraints weight = 31380.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.161858 restraints weight = 22087.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.162112 restraints weight = 23629.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6113
moved from start:          0.5441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12344  Z= 0.100
  Angle     :  0.569   8.859  16712  Z= 0.290
  Chirality :  0.041   0.146   1866
  Planarity :  0.004   0.049   2158
  Dihedral  :  4.287  21.194   1653
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.16 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.22), residues: 1490
  helix:  0.64 (0.22), residues: 623
  sheet: -2.82 (0.42), residues: 107
  loop : -1.09 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 137 
 TYR   0.018   0.001   TYR A1570 
 PHE   0.022   0.001   PHE A 347 
 TRP   0.009   0.001   TRP A 138 
 HIS   0.004   0.001   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (12344)
  covalent geometry    : angle       0.56905 (16712)
  hydrogen bonds       : bond        0.03279 (  441)
  hydrogen bonds       : angle       4.21874 ( 1275)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1711.99 seconds
wall clock time: 30 minutes 31.37 seconds (1831.37 seconds total)