Starting phenix.real_space_refine
on Wed Mar  4 11:53:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b52_12017/03_2026/7b52_12017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b52_12017/03_2026/7b52_12017.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b52_12017/03_2026/7b52_12017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b52_12017/03_2026/7b52_12017.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b52_12017/03_2026/7b52_12017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b52_12017/03_2026/7b52_12017.map"
  }
  resolution = 3.8
  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=   0.001 sd=   0.065
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      87      5.16       5
     C    8294      2.51       5
     N    2229      2.21       5
     O    2576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 97 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: 13186
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 13186
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1638, 13185
          Classifications: {'peptide': 1638}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 65}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 1589}
          Chain breaks: 19
          Unresolved non-hydrogen bonds: 266
          Unresolved non-hydrogen angles: 311
          Unresolved non-hydrogen dihedrals: 224
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASN:plan1': 9, 'GLN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 132
      Conformer: "B"
        Number of residues, atoms: 1638, 13185
          Classifications: {'peptide': 1638}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 65}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 1589}
          Chain breaks: 19
          Unresolved non-hydrogen bonds: 266
          Unresolved non-hydrogen angles: 311
          Unresolved non-hydrogen dihedrals: 224
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASN:plan1': 9, 'GLN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 132
          bond proxies already assigned to first conformer: 13455
  Time building chain proxies: 5.12, per 1000 atoms: 0.39
  Number of scatterers: 13186
  At special positions: 0
  Unit cell: (104.58, 134.46, 144.42, 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      87     16.00
     O    2576      8.00
     N    2229      7.00
     C    8294      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=27, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  52 " - pdb=" SG  CYS A 228 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  67 " - pdb=" SG  CYS A 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 305 " - pdb=" SG  CYS A 322 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 645 " - pdb=" SG  CYS A 734 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 771 " - pdb=" SG  CYS A 910 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 785 " - pdb=" SG  CYS A 803 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 799 " - pdb=" SG  CYS A 966 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 807 " - pdb=" SG  CYS A 964 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 975 " - pdb=" SG  CYS A1099 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 987 " - pdb=" SG  CYS A1005 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1149 " - pdb=" SG  CYS A1180 " distance=2.03
    Simple disulfide: pdb=" SG ACYS A1219 " - pdb=" SG  CYS A1418 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1230 " - pdb=" SG  CYS A1273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1251 " - pdb=" SG  CYS A1264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1344 " - pdb=" SG  CYS A1437 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1418 " - pdb=" SG BCYS A1219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1462 " - pdb=" SG  CYS A1546 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1476 " - pdb=" SG  CYS A1501 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1486 " - pdb=" SG  CYS A1576 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1505 " - pdb=" SG  CYS A1574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1596 " - pdb=" SG  CYS A1632 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1688 " - pdb=" SG  CYS A1782 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1689 " - pdb=" SG  CYS A1906 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1807 " - pdb=" SG  CYS A1909 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1821 " - pdb=" SG  CYS A1838 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1842 " - pdb=" SG  CYS A1961 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1896 " - pdb=" SG  CYS A1907 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 612.8 milliseconds
  

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3098

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 2 sheets defined
      54.2% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 16
      removed outlier: 4.060A  pdb=" N   TYR A  14 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 29
      removed outlier: 3.990A  pdb=" N   LEU A  27 " --> pdb=" O   LYS A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 99 through 104
      removed outlier: 3.578A  pdb=" N   GLU A 103 " --> pdb=" O   PRO A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 111
    Processing helix  chain 'A' and resid 120 through 141
      removed outlier: 4.075A  pdb=" N   PHE A 124 " --> pdb=" O   ASP A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 168
    Processing helix  chain 'A' and resid 176 through 194
      removed outlier: 4.010A  pdb=" N   ASN A 182 " --> pdb=" O   ASN A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 200
    Processing helix  chain 'A' and resid 206 through 227
      removed outlier: 5.447A  pdb=" N   GLN A 220 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   LYS A 221 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
    Processing helix  chain 'A' and resid 274 through 298
    Processing helix  chain 'A' and resid 319 through 349
      removed outlier: 4.234A  pdb=" N   LYS A 323 " --> pdb=" O   CYS A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 3.853A  pdb=" N   ASN A 354 " --> pdb=" O   TYR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 378
      removed outlier: 3.892A  pdb=" N   PHE A 373 " --> pdb=" O   TYR A 369 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU A 378 " --> pdb=" O   PHE A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 391
      removed outlier: 3.812A  pdb=" N   LYS A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASP A 391 " --> pdb=" O   TYR A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 575
      removed outlier: 3.850A  pdb=" N   ALA A 575 " --> pdb=" O   GLU A 572 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 572 through 575'
    Processing helix  chain 'A' and resid 609 through 632
    Processing helix  chain 'A' and resid 642 through 659
      removed outlier: 3.661A  pdb=" N   LYS A 646 " --> pdb=" O   GLU A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 684
      removed outlier: 3.663A  pdb=" N   LYS A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 714
      removed outlier: 4.719A  pdb=" N   TRP A 711 " --> pdb=" O   LEU A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 725
    Processing helix  chain 'A' and resid 757 through 780
      removed outlier: 4.626A  pdb=" N   TRP A 766 " --> pdb=" O   PHE A 762 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   ASN A 769 " --> pdb=" O   GLU A 765 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ASP A 780 " --> pdb=" O   ALA A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 785
    Processing helix  chain 'A' and resid 803 through 816
    Processing helix  chain 'A' and resid 830 through 851
      removed outlier: 3.546A  pdb=" N   ARG A 851 " --> pdb=" O   GLU A 847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 890
    Processing helix  chain 'A' and resid 896 through 905
      removed outlier: 3.616A  pdb=" N   TYR A 900 " --> pdb=" O   THR A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 977
      removed outlier: 3.665A  pdb=" N   THR A 974 " --> pdb=" O   THR A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1026 through 1053
      removed outlier: 3.992A  pdb=" N   THR A1030 " --> pdb=" O   GLY A1026 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE A1032 " --> pdb=" O   ASP A1028 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLN A1048 " --> pdb=" O   TYR A1044 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A1049 " --> pdb=" O   GLN A1045 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A1053 " --> pdb=" O   TYR A1049 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1126
      removed outlier: 3.550A  pdb=" N   LYS A1106 " --> pdb=" O   LEU A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1142 through 1157
      removed outlier: 3.550A  pdb=" N   PHE A1146 " --> pdb=" O   SER A1142 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   TYR A1153 " --> pdb=" O   CYS A1149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1171 through 1180
      removed outlier: 3.760A  pdb=" N   PHE A1175 " --> pdb=" O   ASP A1171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1200
      removed outlier: 3.960A  pdb=" N   SER A1192 " --> pdb=" O   GLU A1188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1271
    Processing helix  chain 'A' and resid 1274 through 1278
      removed outlier: 3.560A  pdb=" N   LEU A1277 " --> pdb=" O   VAL A1274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1292 through 1317
    Processing helix  chain 'A' and resid 1342 through 1359
      removed outlier: 3.625A  pdb=" N   LEU A1359 " --> pdb=" O   LYS A1355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1368 through 1381
      removed outlier: 3.785A  pdb=" N   LEU A1372 " --> pdb=" O   HIS A1368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1400 through 1427
      removed outlier: 4.435A  pdb=" N   ARG A1410 " --> pdb=" O   LYS A1406 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   GLU A1411 " --> pdb=" O   GLY A1407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1444 through 1447
    Processing helix  chain 'A' and resid 1448 through 1476
    Processing helix  chain 'A' and resid 1499 through 1530
      removed outlier: 4.116A  pdb=" N   GLN A1517 " --> pdb=" O   SER A1513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1534 through 1543
    Processing helix  chain 'A' and resid 1559 through 1564
    Processing helix  chain 'A' and resid 1567 through 1572
      removed outlier: 3.657A  pdb=" N   SER A1572 " --> pdb=" O   ASP A1569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1625 through 1630
    Processing helix  chain 'A' and resid 1635 through 1644
      removed outlier: 4.407A  pdb=" N   ILE A1639 " --> pdb=" O   GLU A1635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1649 through 1674
      removed outlier: 4.050A  pdb=" N   GLU A1653 " --> pdb=" O   LYS A1649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1679 through 1703
    Processing helix  chain 'A' and resid 1710 through 1725
      removed outlier: 3.990A  pdb=" N   TYR A1715 " --> pdb=" O   GLU A1711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1730 through 1741
    Processing helix  chain 'A' and resid 1755 through 1776
      removed outlier: 4.987A  pdb=" N   TRP A1761 " --> pdb=" O   ARG A1757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1793 through 1821
      removed outlier: 3.635A  pdb=" N   GLU A1815 " --> pdb=" O   THR A1811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1838 through 1867
      Proline residue:  A1851  - end of helix
      removed outlier: 3.733A  pdb=" N   ILE A1854 " --> pdb=" O   ASN A1850 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU A1855 " --> pdb=" O   PRO A1851 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TRP A1856 " --> pdb=" O   LYS A1852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1887 through 1894
    Processing helix  chain 'A' and resid 1941 through 1948
      removed outlier: 4.283A  pdb=" N   ASN A1948 " --> pdb=" O   ASN A1944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1951 through 1984
      removed outlier: 3.629A  pdb=" N   ALA A1956 " --> pdb=" O   LYS A1952 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   HIS A1957 " --> pdb=" O   LYS A1953 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   MET A1959 " --> pdb=" O   SER A1955 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   LYS A1960 " --> pdb=" O   ALA A1956 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 569 through 570
    Processing sheet with id=AA2, first strand: chain 'A' and resid 923 through 925

    614 hydrogen bonds defined for protein.
    1800 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: 2.09

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4294
        1.35 -     1.47: 3298
        1.47 -     1.59: 5760
        1.59 -     1.72: 0
        1.72 -     1.84: 105
  Bond restraints: 13457
  Sorted by residual:
  bond pdb=" C   LEU A 236 "
       pdb=" N   ILE A 237 "
    ideal  model  delta    sigma   weight residual
    1.329  1.301  0.028 1.69e-02 3.50e+03 2.76e+00
  bond pdb=" N   ASP A  31 "
       pdb=" CA  ASP A  31 "
    ideal  model  delta    sigma   weight residual
    1.456  1.434  0.021 1.48e-02 4.57e+03 2.05e+00
  bond pdb=" C   SER A 951 "
       pdb=" N   PRO A 952 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 2.34e-02 1.83e+03 1.97e+00
  bond pdb=" CB  TYR A 655 "
       pdb=" CG  TYR A 655 "
    ideal  model  delta    sigma   weight residual
    1.512  1.483  0.029 2.20e-02 2.07e+03 1.75e+00
  bond pdb=" N   ASP A 891 "
       pdb=" CA  ASP A 891 "
    ideal  model  delta    sigma   weight residual
    1.460  1.484 -0.023 1.83e-02 2.99e+03 1.62e+00
  ... (remaining 13452 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 17472
        1.97 -     3.94: 551
        3.94 -     5.90: 91
        5.90 -     7.87: 10
        7.87 -     9.84: 9
  Bond angle restraints: 18133
  Sorted by residual:
  angle pdb=" N   GLN A1758 "
        pdb=" CA  GLN A1758 "
        pdb=" C   GLN A1758 "
      ideal   model   delta    sigma   weight residual
     113.18  106.45    6.73 1.33e+00 5.65e-01 2.56e+01
  angle pdb=" C   THR A 146 "
        pdb=" N   ASN A 147 "
        pdb=" CA  ASN A 147 "
      ideal   model   delta    sigma   weight residual
     121.70  129.19   -7.49 1.80e+00 3.09e-01 1.73e+01
  angle pdb=" N   GLU A 504 "
        pdb=" CA  GLU A 504 "
        pdb=" C   GLU A 504 "
      ideal   model   delta    sigma   weight residual
     110.53  115.74   -5.21 1.32e+00 5.74e-01 1.55e+01
  angle pdb=" N   GLY A1621 "
        pdb=" CA  GLY A1621 "
        pdb=" C   GLY A1621 "
      ideal   model   delta    sigma   weight residual
     115.08  109.05    6.03 1.54e+00 4.22e-01 1.54e+01
  angle pdb=" N   TYR A1366 "
        pdb=" CA  TYR A1366 "
        pdb=" C   TYR A1366 "
      ideal   model   delta    sigma   weight residual
     110.80  102.48    8.32 2.13e+00 2.20e-01 1.53e+01
  ... (remaining 18128 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 7367
       17.90 -    35.80: 684
       35.80 -    53.70: 96
       53.70 -    71.60: 26
       71.60 -    89.50: 21
  Dihedral angle restraints: 8194
    sinusoidal: 3384
      harmonic: 4810
  Sorted by residual:
  dihedral pdb=" CB  CYS A 771 "
           pdb=" SG  CYS A 771 "
           pdb=" SG  CYS A 910 "
           pdb=" CB  CYS A 910 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.65   81.35     1      1.00e+01 1.00e-02 8.16e+01
  dihedral pdb=" CB  CYS A1149 "
           pdb=" SG  CYS A1149 "
           pdb=" SG  CYS A1180 "
           pdb=" CB  CYS A1180 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.90  -77.90     1      1.00e+01 1.00e-02 7.59e+01
  dihedral pdb=" CA  GLN A 965 "
           pdb=" C   GLN A 965 "
           pdb=" N   CYS A 966 "
           pdb=" CA  CYS A 966 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.00  -43.00     0      5.00e+00 4.00e-02 7.40e+01
  ... (remaining 8191 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1441
       0.050 -    0.101: 393
       0.101 -    0.151: 46
       0.151 -    0.202: 3
       0.202 -    0.252: 1
  Chirality restraints: 1884
  Sorted by residual:
  chirality pdb=" CA  SER A 951 "
            pdb=" N   SER A 951 "
            pdb=" C   SER A 951 "
            pdb=" CB  SER A 951 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  GLU A1541 "
            pdb=" N   GLU A1541 "
            pdb=" C   GLU A1541 "
            pdb=" CB  GLU A1541 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" CB  ILE A1165 "
            pdb=" CA  ILE A1165 "
            pdb=" CG1 ILE A1165 "
            pdb=" CG2 ILE A1165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.79e-01
  ... (remaining 1881 not shown)

  Planarity restraints: 2343
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 560 "   -0.027 2.00e-02 2.50e+03   2.72e-02 1.86e+01
        pdb=" CG  TRP A 560 "    0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 560 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 560 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 560 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 560 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 560 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 560 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 560 "   -0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 560 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 766 "    0.020 2.00e-02 2.50e+03   3.87e-02 1.50e+01
        pdb=" C   TRP A 766 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   TRP A 766 "    0.025 2.00e-02 2.50e+03
        pdb=" N   VAL A 767 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 890 "   -0.014 2.00e-02 2.50e+03   2.77e-02 7.66e+00
        pdb=" C   ILE A 890 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ILE A 890 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ASP A 891 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 2340 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 300
        2.61 -     3.18: 13719
        3.18 -     3.75: 22258
        3.75 -     4.33: 29935
        4.33 -     4.90: 45762
  Nonbonded interactions: 111974
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 688 "
            pdb=" OG  SER A 702 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O   THR A 895 "
            pdb=" OG  SER A 899 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" OH  TYR A 842 "
            pdb=" O   LEU A 894 "
     model   vdw
     2.058 3.040
  nonbonded pdb=" O   GLU A 573 "
            pdb=" NH2 ARG A 841 "
     model   vdw
     2.098 3.120
  nonbonded pdb=" O   ASN A1027 "
            pdb=" OG1 THR A1030 "
     model   vdw
     2.115 3.040
  ... (remaining 111969 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=0.50 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:             5.610
  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:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.230
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13484  Z= 0.203
  Angle     :  0.848   9.840  18187  Z= 0.497
  Chirality :  0.043   0.252   1884
  Planarity :  0.005   0.062   2343
  Dihedral  : 14.200  89.497   5015
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 24.35
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 16.40 %
    Favored  : 83.42 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.57 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.38 %

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: -2.23 (0.20), residues: 1598
  helix:  0.15 (0.18), residues: 820
  sheet: -4.87 (1.00), residues: 10
  loop : -3.45 (0.20), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 191 
 TYR   0.028   0.002   TYR A 655 
 PHE   0.020   0.002   PHE A 373 
 TRP   0.072   0.003   TRP A 560 
 HIS   0.006   0.002   HIS A1709 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (13457)
  covalent geometry    : angle       0.84493 (18133)
  SS BOND              : bond        0.00370 (   27)
  SS BOND              : angle       1.55681 (   54)
  hydrogen bonds       : bond        0.15045 (  614)
  hydrogen bonds       : angle       5.87822 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.9081 (mpp) cc_final: 0.8819 (mpp)
REVERT: A 1783 MET cc_start: 0.8976 (tpp) cc_final: 0.8675 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 27
  average time/residue: 0.1258
  time to fit residues: 5.6483
Evaluate side-chains
  22 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.0470
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0020
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.6090

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
A 182 ASN
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 845 HIS
A 903 ASN
A1039 ASN
A1048 GLN
A1143 ASN
A1498 GLN
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1674 ASN
A1857 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.033192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.025668 restraints weight = 164361.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.026431 restraints weight = 103643.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.026974 restraints weight = 74841.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.027346 restraints weight = 59277.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.027588 restraints weight = 50049.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13484  Z= 0.152
  Angle     :  0.776  10.048  18187  Z= 0.410
  Chirality :  0.044   0.200   1884
  Planarity :  0.005   0.085   2343
  Dihedral  :  6.447  41.370   1761
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 14.33 %
    Favored  : 85.42 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.24 %
    Favored  : 95.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.93 (0.20), residues: 1598
  helix:  0.32 (0.18), residues: 829
  sheet: -4.44 (1.04), residues: 10
  loop : -3.25 (0.20), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 191 
 TYR   0.023   0.002   TYR A 351 
 PHE   0.015   0.002   PHE A1454 
 TRP   0.032   0.002   TRP A 283 
 HIS   0.006   0.001   HIS A 888 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (13457)
  covalent geometry    : angle       0.77384 (18133)
  SS BOND              : bond        0.00328 (   27)
  SS BOND              : angle       1.27439 (   54)
  hydrogen bonds       : bond        0.05031 (  614)
  hydrogen bonds       : angle       4.61750 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.9004 (mpp) cc_final: 0.8667 (mpp)
REVERT: A 1272 LEU cc_start: 0.8664 (tp) cc_final: 0.8452 (tp)
REVERT: A 1764 MET cc_start: 0.9522 (mmm) cc_final: 0.9248 (mmt)
REVERT: A 1783 MET cc_start: 0.8837 (tpp) cc_final: 0.8541 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 27
  average time/residue: 0.1030
  time to fit residues: 4.8753
Evaluate side-chains
  25 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1601 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 141 optimal weight:    3.9990
   chunk 162 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 146 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 157 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 GLN
A 903 ASN
A 955 ASN
A1143 ASN
A1542 ASN
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.031774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.024362 restraints weight = 174407.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.025112 restraints weight = 108708.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.025631 restraints weight = 78476.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.025990 restraints weight = 62034.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.026220 restraints weight = 52403.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  13484  Z= 0.271
  Angle     :  0.793  10.612  18187  Z= 0.423
  Chirality :  0.045   0.203   1884
  Planarity :  0.005   0.055   2343
  Dihedral  :  6.436  40.364   1761
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 19.86
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.27 %
    Favored  : 84.61 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  7.07 %
    Favored  : 92.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.99 (0.20), residues: 1598
  helix:  0.32 (0.18), residues: 831
  sheet: -4.82 (1.07), residues: 10
  loop : -3.34 (0.20), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 191 
 TYR   0.018   0.002   TYR A 351 
 PHE   0.020   0.002   PHE A1031 
 TRP   0.033   0.002   TRP A 283 
 HIS   0.009   0.002   HIS A1709 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 (13457)
  covalent geometry    : angle       0.79081 (18133)
  SS BOND              : bond        0.00454 (   27)
  SS BOND              : angle       1.30908 (   54)
  hydrogen bonds       : bond        0.05049 (  614)
  hydrogen bonds       : angle       4.69354 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1764 MET cc_start: 0.9483 (mmm) cc_final: 0.9282 (mmt)
REVERT: A 1783 MET cc_start: 0.8811 (tpp) cc_final: 0.8565 (tpp)
  outliers start: 4
  outliers final: 1
  residues processed: 26
  average time/residue: 0.1018
  time to fit residues: 4.7553
Evaluate side-chains
  23 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1445 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 129 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 153 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 139 optimal weight:    0.1980
   chunk 140 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 205 GLN
A 903 ASN
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.033004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.025489 restraints weight = 165355.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.026251 restraints weight = 104369.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.026775 restraints weight = 75815.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.027143 restraints weight = 60226.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.027407 restraints weight = 50929.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13484  Z= 0.138
  Angle     :  0.711  10.001  18187  Z= 0.374
  Chirality :  0.042   0.174   1884
  Planarity :  0.004   0.051   2343
  Dihedral  :  6.173  40.725   1761
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.95 %
    Favored  : 85.98 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  7.77 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.71 (0.21), residues: 1598
  helix:  0.63 (0.18), residues: 807
  sheet:  None (None), residues: 0
  loop : -3.24 (0.20), residues: 791

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 191 
 TYR   0.034   0.001   TYR A  14 
 PHE   0.012   0.002   PHE A1031 
 TRP   0.026   0.002   TRP A 283 
 HIS   0.006   0.001   HIS A 888 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (13457)
  covalent geometry    : angle       0.71000 (18133)
  SS BOND              : bond        0.00280 (   27)
  SS BOND              : angle       1.09406 (   54)
  hydrogen bonds       : bond        0.04542 (  614)
  hydrogen bonds       : angle       4.33157 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1764 MET cc_start: 0.9474 (mmm) cc_final: 0.9248 (mmt)
REVERT: A 1783 MET cc_start: 0.8796 (tpp) cc_final: 0.8555 (tpp)
  outliers start: 8
  outliers final: 4
  residues processed: 36
  average time/residue: 0.0991
  time to fit residues: 6.1299
Evaluate side-chains
  30 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue 1105 GLU
Chi-restraints excluded: chain A residue 1601 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 140 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 104 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 115 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 193 ASN
A 845 HIS
A 903 ASN
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1847 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.032923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.025496 restraints weight = 166968.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.026221 restraints weight = 106067.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.026738 restraints weight = 77540.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.027093 restraints weight = 61845.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.027333 restraints weight = 52510.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13484  Z= 0.140
  Angle     :  0.702  10.633  18187  Z= 0.368
  Chirality :  0.041   0.176   1884
  Planarity :  0.004   0.053   2343
  Dihedral  :  5.980  39.743   1761
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.64 %
    Favored  : 86.30 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  9.19 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.65 (0.21), residues: 1598
  helix:  0.69 (0.18), residues: 815
  sheet: -4.37 (1.04), residues: 10
  loop : -3.23 (0.20), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 834 
 TYR   0.014   0.001   TYR A 351 
 PHE   0.017   0.002   PHE A 276 
 TRP   0.064   0.002   TRP A 560 
 HIS   0.005   0.001   HIS A 888 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (13457)
  covalent geometry    : angle       0.70048 (18133)
  SS BOND              : bond        0.00280 (   27)
  SS BOND              : angle       1.03728 (   54)
  hydrogen bonds       : bond        0.04370 (  614)
  hydrogen bonds       : angle       4.29230 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: A  655 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8915 (m-80)
REVERT: A 1445 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8743 (p0)
REVERT: A 1764 MET cc_start: 0.9476 (mmm) cc_final: 0.9253 (mmt)
REVERT: A 1783 MET cc_start: 0.8744 (tpp) cc_final: 0.8542 (tpp)
  outliers start: 7
  outliers final: 2
  residues processed: 36
  average time/residue: 0.0995
  time to fit residues: 6.2201
Evaluate side-chains
  29 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue 1445 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 119 optimal weight:    9.9990
   chunk 71 optimal weight:    0.3980
   chunk 92 optimal weight:    5.9990
   chunk 141 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0570
   chunk 49 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 90 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.0300

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

Flipped N/Q/H residues before XYZ refinement:
A 903 ASN
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.033012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.025579 restraints weight = 165559.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.026319 restraints weight = 104439.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.026841 restraints weight = 75890.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.027184 restraints weight = 60361.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.027455 restraints weight = 51352.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13484  Z= 0.134
  Angle     :  0.690  11.126  18187  Z= 0.362
  Chirality :  0.041   0.173   1884
  Planarity :  0.004   0.052   2343
  Dihedral  :  5.862  39.998   1761
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.52 %
    Favored  : 86.42 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.26 %
    Favored  : 90.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.63 (0.21), residues: 1598
  helix:  0.73 (0.18), residues: 814
  sheet: -4.16 (1.04), residues: 10
  loop : -3.23 (0.20), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 104 
 TYR   0.013   0.001   TYR A 351 
 PHE   0.012   0.001   PHE A1031 
 TRP   0.036   0.002   TRP A 560 
 HIS   0.004   0.001   HIS A 888 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (13457)
  covalent geometry    : angle       0.68909 (18133)
  SS BOND              : bond        0.00258 (   27)
  SS BOND              : angle       1.02033 (   54)
  hydrogen bonds       : bond        0.04263 (  614)
  hydrogen bonds       : angle       4.22826 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  655 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8912 (m-80)
REVERT: A 1445 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8699 (p0)
REVERT: A 1783 MET cc_start: 0.8738 (tpp) cc_final: 0.8510 (tpp)
  outliers start: 8
  outliers final: 3
  residues processed: 34
  average time/residue: 0.0983
  time to fit residues: 5.8421
Evaluate side-chains
  29 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue 1365 ILE
Chi-restraints excluded: chain A residue 1445 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 97 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 78 optimal weight:    9.9990
   chunk 162 optimal weight:    0.7980
   chunk 36 optimal weight:    8.9990
   chunk 150 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 903 ASN
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.032783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.025453 restraints weight = 165590.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.026182 restraints weight = 103708.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.026709 restraints weight = 75208.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.027076 restraints weight = 59522.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.027319 restraints weight = 50261.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13484  Z= 0.146
  Angle     :  0.689  11.492  18187  Z= 0.361
  Chirality :  0.041   0.270   1884
  Planarity :  0.004   0.052   2343
  Dihedral  :  5.771  39.325   1761
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.39 %
    Favored  : 86.55 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  9.89 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.55 (0.21), residues: 1598
  helix:  0.80 (0.18), residues: 814
  sheet: -4.20 (1.00), residues: 10
  loop : -3.21 (0.20), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 104 
 TYR   0.013   0.001   TYR A 981 
 PHE   0.013   0.001   PHE A1031 
 TRP   0.026   0.002   TRP A 560 
 HIS   0.004   0.001   HIS A1709 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (13457)
  covalent geometry    : angle       0.68819 (18133)
  SS BOND              : bond        0.00283 (   27)
  SS BOND              : angle       0.98253 (   54)
  hydrogen bonds       : bond        0.04194 (  614)
  hydrogen bonds       : angle       4.21328 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  655 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8917 (m-80)
REVERT: A 1365 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8359 (tp)
REVERT: A 1445 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8655 (p0)
REVERT: A 1764 MET cc_start: 0.9554 (mmm) cc_final: 0.9336 (mmt)
  outliers start: 7
  outliers final: 3
  residues processed: 32
  average time/residue: 0.0944
  time to fit residues: 5.3613
Evaluate side-chains
  31 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue 1365 ILE
Chi-restraints excluded: chain A residue 1445 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   chunk 87 optimal weight:    9.9990
   chunk 122 optimal weight:    8.9990
   chunk 126 optimal weight:    0.7980
   chunk 105 optimal weight:    6.9990
   chunk 145 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1857 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.033148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.025868 restraints weight = 165610.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.026581 restraints weight = 105251.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.027091 restraints weight = 77041.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.027447 restraints weight = 61498.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.027683 restraints weight = 52247.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3063
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3063 r_free = 0.3063    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3063 r_free = 0.3063    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3063
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13484  Z= 0.130
  Angle     :  0.676   9.186  18187  Z= 0.354
  Chirality :  0.041   0.266   1884
  Planarity :  0.004   0.051   2343
  Dihedral  :  5.668  39.652   1761
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.45 %
    Favored  : 86.48 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.96 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.50 (0.21), residues: 1598
  helix:  0.83 (0.18), residues: 815
  sheet: -4.05 (1.00), residues: 10
  loop : -3.17 (0.20), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 104 
 TYR   0.013   0.001   TYR A1891 
 PHE   0.010   0.001   PHE A1031 
 TRP   0.024   0.002   TRP A 283 
 HIS   0.003   0.001   HIS A 888 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (13457)
  covalent geometry    : angle       0.67520 (18133)
  SS BOND              : bond        0.00242 (   27)
  SS BOND              : angle       0.95124 (   54)
  hydrogen bonds       : bond        0.04074 (  614)
  hydrogen bonds       : angle       4.15745 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 26
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  655 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8789 (m-80)
REVERT: A 1357 MET cc_start: 0.9664 (tmm) cc_final: 0.9391 (tmm)
REVERT: A 1373 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8701 (mm-40)
REVERT: A 1445 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8575 (p0)
REVERT: A 1764 MET cc_start: 0.9543 (mmm) cc_final: 0.9303 (mmt)
REVERT: A 1941 ASP cc_start: 0.8762 (p0) cc_final: 0.8431 (p0)
  outliers start: 12
  outliers final: 7
  residues processed: 38
  average time/residue: 0.1003
  time to fit residues: 6.4542
Evaluate side-chains
  35 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 25
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  895 THR
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1365 ILE
Chi-restraints excluded: chain A residue 1373 GLN
Chi-restraints excluded: chain A residue 1445 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 158 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 108 optimal weight:    3.9990
   chunk 150 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 123 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.032809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.025434 restraints weight = 168675.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.026185 restraints weight = 105887.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.026713 restraints weight = 76672.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.027076 restraints weight = 60753.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.027335 restraints weight = 51394.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13484  Z= 0.152
  Angle     :  0.690   9.552  18187  Z= 0.363
  Chirality :  0.042   0.254   1884
  Planarity :  0.004   0.051   2343
  Dihedral  :  5.640  38.875   1761
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.20 %
    Favored  : 86.73 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 10.18 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.49 (0.21), residues: 1598
  helix:  0.84 (0.18), residues: 814
  sheet: -4.16 (0.99), residues: 10
  loop : -3.16 (0.20), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 104 
 TYR   0.012   0.001   TYR A 351 
 PHE   0.013   0.001   PHE A1031 
 TRP   0.024   0.002   TRP A 283 
 HIS   0.005   0.001   HIS A1709 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13457)
  covalent geometry    : angle       0.68642 (18133)
  SS BOND              : bond        0.00311 (   27)
  SS BOND              : angle       1.49797 (   54)
  hydrogen bonds       : bond        0.04164 (  614)
  hydrogen bonds       : angle       4.25791 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 25
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  655 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8899 (m-80)
REVERT: A 1357 MET cc_start: 0.9672 (tmm) cc_final: 0.9384 (tmm)
REVERT: A 1365 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8380 (tp)
REVERT: A 1373 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8740 (mm-40)
REVERT: A 1445 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8583 (p0)
REVERT: A 1764 MET cc_start: 0.9549 (mmm) cc_final: 0.9308 (mmt)
REVERT: A 1941 ASP cc_start: 0.8779 (p0) cc_final: 0.8481 (p0)
  outliers start: 10
  outliers final: 6
  residues processed: 35
  average time/residue: 0.1014
  time to fit residues: 6.1691
Evaluate side-chains
  34 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 24
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  895 THR
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1365 ILE
Chi-restraints excluded: chain A residue 1373 GLN
Chi-restraints excluded: chain A residue 1445 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 141 optimal weight:    8.9990
   chunk 138 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0670
   chunk 130 optimal weight:    6.9990
   chunk 74 optimal weight:    0.0670
   chunk 51 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0570
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.4174

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

Flipped N/Q/H residues before XYZ refinement:
A 879 GLN
A1601 ASN
** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.033595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.026157 restraints weight = 165189.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.026885 restraints weight = 105787.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.027405 restraints weight = 77728.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.027768 restraints weight = 62133.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.028008 restraints weight = 52814.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13484  Z= 0.125
  Angle     :  0.686   9.564  18187  Z= 0.357
  Chirality :  0.042   0.253   1884
  Planarity :  0.004   0.051   2343
  Dihedral  :  5.556  39.386   1761
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.39 %
    Favored  : 86.55 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 10.46 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.47 (0.21), residues: 1598
  helix:  0.83 (0.18), residues: 814
  sheet: -3.98 (0.98), residues: 10
  loop : -3.13 (0.20), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 104 
 TYR   0.016   0.001   TYR A 981 
 PHE   0.011   0.001   PHE A 159 
 TRP   0.023   0.002   TRP A 283 
 HIS   0.004   0.001   HIS A1305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (13457)
  covalent geometry    : angle       0.68348 (18133)
  SS BOND              : bond        0.00233 (   27)
  SS BOND              : angle       1.30223 (   54)
  hydrogen bonds       : bond        0.04094 (  614)
  hydrogen bonds       : angle       4.16858 ( 1800)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  655 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8655 (m-80)
REVERT: A 1357 MET cc_start: 0.9684 (tmm) cc_final: 0.9405 (tmm)
REVERT: A 1764 MET cc_start: 0.9558 (mmm) cc_final: 0.9311 (mmt)
REVERT: A 1941 ASP cc_start: 0.8714 (p0) cc_final: 0.8437 (p0)
  outliers start: 7
  outliers final: 5
  residues processed: 33
  average time/residue: 0.1075
  time to fit residues: 6.2959
Evaluate side-chains
  31 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue 1601 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 134 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 150 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0050
   chunk 16 optimal weight:    7.9990
   chunk 151 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0980
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A1601 ASN
** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1672 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.033800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.026471 restraints weight = 169101.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.027218 restraints weight = 106942.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.027749 restraints weight = 77863.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.028111 restraints weight = 61982.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.028366 restraints weight = 52634.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3085
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3085
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13484  Z= 0.122
  Angle     :  0.684   9.236  18187  Z= 0.356
  Chirality :  0.042   0.252   1884
  Planarity :  0.004   0.052   2343
  Dihedral  :  5.469  38.625   1761
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 12.77 %
    Favored  : 87.17 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 10.32 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.43 (0.21), residues: 1598
  helix:  0.88 (0.18), residues: 813
  sheet: -4.08 (0.97), residues: 10
  loop : -3.12 (0.20), residues: 775

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 104 
 TYR   0.011   0.001   TYR A 351 
 PHE   0.011   0.001   PHE A 159 
 TRP   0.022   0.001   TRP A 283 
 HIS   0.003   0.001   HIS A 888 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (13457)
  covalent geometry    : angle       0.68225 (18133)
  SS BOND              : bond        0.00230 (   27)
  SS BOND              : angle       1.21782 (   54)
  hydrogen bonds       : bond        0.04038 (  614)
  hydrogen bonds       : angle       4.17288 ( 1800)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2586.11 seconds
wall clock time: 45 minutes 46.02 seconds (2746.02 seconds total)