Starting phenix.real_space_refine
on Thu Jul 31 11:19:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b52_12017/07_2025/7b52_12017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b52_12017/07_2025/7b52_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b52_12017/07_2025/7b52_12017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b52_12017/07_2025/7b52_12017.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b52_12017/07_2025/7b52_12017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b52_12017/07_2025/7b52_12017.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8}
          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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 132
          bond proxies already assigned to first conformer: 13455
  Time building chain proxies: 14.28, per 1000 atoms: 1.08
  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: 3.12
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.28
  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: 3.79

  Time building geometry restraints manager: 3.77 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:             4.990
  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:          0.530
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     37.170
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.100
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.960
-------------------------------------------------------------------------------
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 : 24.47
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.072   0.003   TRP A 560 
 HIS   0.006   0.002   HIS A1709 
 PHE   0.020   0.002   PHE A 373 
 TYR   0.028   0.002   TYR A 655 
 ARG   0.014   0.001   ARG A 191 

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

*********************** 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  : 1.606 
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: 0.2700
  time to fit residues: 12.6434
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  : 1.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:    9.9990
   chunk 123 optimal weight:    0.0670
   chunk 68 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 127 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 148 optimal weight:    4.9990
   overall best weight:    1.6126

-------------------------------------------------------------------------------
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 275 GLN
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 = 0.3276 r_free = 0.3276 target = 0.032614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.025223 restraints weight = 161871.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.025956 restraints weight = 102395.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.026462 restraints weight = 74028.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13484  Z= 0.173
  Angle     :  0.777  10.162  18187  Z= 0.413
  Chirality :  0.044   0.206   1884
  Planarity :  0.005   0.082   2343
  Dihedral  :  6.513  41.171   1761
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 14.71 %
    Favored  : 85.04 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.21), residues: 1598
  helix:  0.31 (0.18), residues: 829
  sheet: -4.59 (1.08), residues: 10
  loop : -3.28 (0.20), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 283 
 HIS   0.006   0.001   HIS A 888 
 PHE   0.015   0.002   PHE A1031 
 TYR   0.024   0.002   TYR A 351 
 ARG   0.006   0.001   ARG A 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05233 (  614)
  hydrogen bonds       : angle       4.72828 ( 1800)
  SS BOND              : bond        0.00379 (   27)
  SS BOND              : angle       1.30788 (   54)
  covalent geometry    : bond        0.00364 (13457)
  covalent geometry    : angle       0.77507 (18133)

*********************** 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  : 1.759 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.9018 (mpp) cc_final: 0.8680 (mpp)
REVERT: A 1764 MET cc_start: 0.9500 (mmm) cc_final: 0.9208 (mmt)
REVERT: A 1783 MET cc_start: 0.8934 (tpp) cc_final: 0.8621 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 27
  average time/residue: 0.2784
  time to fit residues: 13.6402
Evaluate side-chains
  24 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 1.750 
-------------------------------------------------------------------------------
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 117 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0170
   chunk 90 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 99 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 143 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 162 optimal weight:    0.8980
   overall best weight:    2.1824

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 845 HIS
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.032459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.025010 restraints weight = 168402.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.025740 restraints weight = 105898.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.026256 restraints weight = 76962.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2991
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2991 r_free = 0.2991    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2991 r_free = 0.2991    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2991
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1293

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= 0.177
  Angle     :  0.736  10.138  18187  Z= 0.390
  Chirality :  0.043   0.192   1884
  Planarity :  0.004   0.051   2343
  Dihedral  :  6.317  40.682   1761
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 16.51
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.83 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  6.86 %
    Favored  : 92.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.21), residues: 1598
  helix:  0.40 (0.18), residues: 831
  sheet: -4.53 (1.07), residues: 10
  loop : -3.27 (0.20), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 283 
 HIS   0.006   0.001   HIS A1709 
 PHE   0.015   0.002   PHE A1031 
 TYR   0.018   0.002   TYR A 351 
 ARG   0.006   0.000   ARG A 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04830 (  614)
  hydrogen bonds       : angle       4.52233 ( 1800)
  SS BOND              : bond        0.00370 (   27)
  SS BOND              : angle       1.21405 (   54)
  covalent geometry    : bond        0.00374 (13457)
  covalent geometry    : angle       0.73431 (18133)

*********************** 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: 3
    poor density    : 24
  time to evaluate  : 3.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1783 MET cc_start: 0.8836 (tpp) cc_final: 0.8593 (tpp)
  outliers start: 3
  outliers final: 1
  residues processed: 27
  average time/residue: 0.2861
  time to fit residues: 13.9919
Evaluate side-chains
  24 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 1.562 
-------------------------------------------------------------------------------
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 114 optimal weight:   10.0000
   chunk 153 optimal weight:    3.9990
   chunk 138 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 130 optimal weight:    6.9990
   chunk 6 optimal weight:   20.0000
   chunk 135 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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**
A1143 ASN
** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1847 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.032331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.024952 restraints weight = 170223.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.025712 restraints weight = 106585.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.026238 restraints weight = 76924.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2976
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2976
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13484  Z= 0.173
  Angle     :  0.720  10.370  18187  Z= 0.380
  Chirality :  0.042   0.184   1884
  Planarity :  0.004   0.050   2343
  Dihedral  :  6.174  40.362   1761
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 14.58 %
    Favored  : 85.36 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.13 %
    Favored  : 91.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.21), residues: 1598
  helix:  0.50 (0.18), residues: 831
  sheet: -4.47 (1.08), residues: 10
  loop : -3.30 (0.20), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 283 
 HIS   0.005   0.001   HIS A1709 
 PHE   0.016   0.002   PHE A1031 
 TYR   0.016   0.001   TYR A 351 
 ARG   0.005   0.000   ARG A 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04553 (  614)
  hydrogen bonds       : angle       4.39727 ( 1800)
  SS BOND              : bond        0.00352 (   27)
  SS BOND              : angle       1.13710 (   54)
  covalent geometry    : bond        0.00366 (13457)
  covalent geometry    : angle       0.71853 (18133)

*********************** 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
  32 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 3.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1783 MET cc_start: 0.8817 (tpp) cc_final: 0.8587 (tpp)
  outliers start: 7
  outliers final: 4
  residues processed: 32
  average time/residue: 0.3533
  time to fit residues: 20.7712
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  : 1.248 
-------------------------------------------------------------------------------
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 1445 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 137 optimal weight:    0.0970
   chunk 87 optimal weight:   10.0000
   chunk 144 optimal weight:    0.0870
   chunk 120 optimal weight:    0.8980
   chunk 119 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 77 optimal weight:    9.9990
   overall best weight:    0.5956

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

Flipped N/Q/H residues before XYZ refinement:
A 193 ASN
A 205 GLN
A 845 HIS
A 903 ASN
A1143 ASN
A1542 ASN
** A1601 ASN ** 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 = 0.3297 r_free = 0.3297 target = 0.032981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.025641 restraints weight = 161909.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.026343 restraints weight = 105119.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.026842 restraints weight = 77549.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1973

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= 0.133
  Angle     :  0.702  10.644  18187  Z= 0.367
  Chirality :  0.042   0.170   1884
  Planarity :  0.004   0.052   2343
  Dihedral  :  6.006  40.282   1761
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.95 %
    Favored  : 85.98 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.19 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.21), residues: 1598
  helix:  0.65 (0.18), residues: 815
  sheet: -4.23 (1.06), residues: 10
  loop : -3.22 (0.20), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP A 560 
 HIS   0.004   0.001   HIS A 888 
 PHE   0.013   0.002   PHE A 276 
 TYR   0.015   0.001   TYR A 351 
 ARG   0.005   0.000   ARG A 834 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04362 (  614)
  hydrogen bonds       : angle       4.26397 ( 1800)
  SS BOND              : bond        0.00259 (   27)
  SS BOND              : angle       1.05251 (   54)
  covalent geometry    : bond        0.00279 (13457)
  covalent geometry    : angle       0.70036 (18133)

*********************** 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
  34 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 2.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  655 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8803 (m-80)
REVERT: A 1445 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8754 (p0)
  outliers start: 6
  outliers final: 2
  residues processed: 34
  average time/residue: 0.2772
  time to fit residues: 16.4866
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  : 1.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue 1105 GLU
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 79 optimal weight:    0.9990
   chunk 31 optimal weight:    9.9990
   chunk 85 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   chunk 132 optimal weight:    0.0020
   chunk 135 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
A1143 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 = 0.3306 r_free = 0.3306 target = 0.033180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.025773 restraints weight = 167216.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.026493 restraints weight = 106583.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.027010 restraints weight = 78070.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2248

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= 0.128
  Angle     :  0.692  13.004  18187  Z= 0.361
  Chirality :  0.041   0.169   1884
  Planarity :  0.004   0.052   2343
  Dihedral  :  5.812  39.539   1761
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.52 %
    Favored  : 86.42 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.40 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.21), residues: 1598
  helix:  0.75 (0.18), residues: 814
  sheet: -4.12 (1.04), residues: 10
  loop : -3.20 (0.20), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 560 
 HIS   0.004   0.001   HIS A 888 
 PHE   0.016   0.001   PHE A1695 
 TYR   0.014   0.001   TYR A 981 
 ARG   0.003   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04204 (  614)
  hydrogen bonds       : angle       4.17391 ( 1800)
  SS BOND              : bond        0.00254 (   27)
  SS BOND              : angle       1.00734 (   54)
  covalent geometry    : bond        0.00265 (13457)
  covalent geometry    : angle       0.69039 (18133)

*********************** 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  : 1.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  655 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8742 (m-80)
REVERT: A 1445 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8713 (p0)
REVERT: A 1941 ASP cc_start: 0.8912 (p0) cc_final: 0.8582 (p0)
  outliers start: 8
  outliers final: 3
  residues processed: 34
  average time/residue: 0.2313
  time to fit residues: 14.0473
Evaluate side-chains
  30 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
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 1445 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 161 optimal weight:    0.9980
   chunk 148 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 133 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 55 optimal weight:    8.9990
   chunk 110 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3305 r_free = 0.3305 target = 0.033118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.025685 restraints weight = 167470.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.026434 restraints weight = 105154.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.026955 restraints weight = 76008.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2403

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= 0.133
  Angle     :  0.686  11.406  18187  Z= 0.358
  Chirality :  0.041   0.275   1884
  Planarity :  0.004   0.051   2343
  Dihedral  :  5.700  39.765   1761
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.27 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.54 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.21), residues: 1598
  helix:  0.79 (0.18), residues: 814
  sheet: -4.10 (0.99), residues: 10
  loop : -3.17 (0.20), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 283 
 HIS   0.004   0.001   HIS A 888 
 PHE   0.011   0.001   PHE A1031 
 TYR   0.012   0.001   TYR A 351 
 ARG   0.003   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  614)
  hydrogen bonds       : angle       4.15645 ( 1800)
  SS BOND              : bond        0.00261 (   27)
  SS BOND              : angle       0.96536 (   54)
  covalent geometry    : bond        0.00278 (13457)
  covalent geometry    : angle       0.68501 (18133)

*********************** 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
  34 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 1.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LYS cc_start: 0.9497 (OUTLIER) cc_final: 0.9204 (tptp)
REVERT: A  655 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8801 (m-80)
REVERT: A 1445 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8645 (p0)
REVERT: A 1941 ASP cc_start: 0.8851 (p0) cc_final: 0.8538 (p0)
  outliers start: 8
  outliers final: 5
  residues processed: 33
  average time/residue: 0.2705
  time to fit residues: 16.3912
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  : 1.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LYS
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 1445 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 89 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 135 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 955 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.032363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.024989 restraints weight = 170854.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.025721 restraints weight = 106601.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.026247 restraints weight = 77131.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2990
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13484  Z= 0.194
  Angle     :  0.705  10.535  18187  Z= 0.373
  Chirality :  0.042   0.265   1884
  Planarity :  0.004   0.050   2343
  Dihedral  :  5.782  39.174   1761
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.58 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.75 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.21), residues: 1598
  helix:  0.75 (0.18), residues: 827
  sheet: -4.15 (1.05), residues: 10
  loop : -3.17 (0.21), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 283 
 HIS   0.006   0.001   HIS A1709 
 PHE   0.015   0.002   PHE A1031 
 TYR   0.012   0.001   TYR A1715 
 ARG   0.003   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04254 (  614)
  hydrogen bonds       : angle       4.24324 ( 1800)
  SS BOND              : bond        0.00334 (   27)
  SS BOND              : angle       1.03126 (   54)
  covalent geometry    : bond        0.00404 (13457)
  covalent geometry    : angle       0.70398 (18133)

*********************** 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
  36 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 1.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9280 (tptp)
REVERT: A 1357 MET cc_start: 0.9662 (tmm) cc_final: 0.9395 (tmm)
REVERT: A 1445 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8683 (p0)
  outliers start: 12
  outliers final: 5
  residues processed: 35
  average time/residue: 0.2305
  time to fit residues: 14.4234
Evaluate side-chains
  29 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 1.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   98 VAL
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 1445 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 121 optimal weight:    0.7980
   chunk 76 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 113 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 111 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    1.6182

-------------------------------------------------------------------------------
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 = 0.3286 r_free = 0.3286 target = 0.032662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.025300 restraints weight = 167987.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.026031 restraints weight = 105177.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.026558 restraints weight = 76224.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3009
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  13484  Z= 0.148
  Angle     :  0.701  10.783  18187  Z= 0.367
  Chirality :  0.042   0.250   1884
  Planarity :  0.004   0.050   2343
  Dihedral  :  5.763  39.861   1761
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.70 %
    Favored  : 86.23 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 10.04 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.21), residues: 1598
  helix:  0.73 (0.18), residues: 821
  sheet: -4.19 (0.96), residues: 10
  loop : -3.17 (0.20), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 283 
 HIS   0.004   0.001   HIS A1709 
 PHE   0.013   0.001   PHE A1031 
 TYR   0.012   0.001   TYR A 351 
 ARG   0.004   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04257 (  614)
  hydrogen bonds       : angle       4.24653 ( 1800)
  SS BOND              : bond        0.00294 (   27)
  SS BOND              : angle       1.66870 (   54)
  covalent geometry    : bond        0.00314 (13457)
  covalent geometry    : angle       0.69644 (18133)

*********************** 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
  33 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 24
  time to evaluate  : 1.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9284 (tptp)
REVERT: A 1445 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8673 (p0)
REVERT: A 1941 ASP cc_start: 0.8874 (p0) cc_final: 0.8622 (p0)
REVERT: A 1943 MET cc_start: 0.7851 (ptp) cc_final: 0.7552 (ptp)
  outliers start: 9
  outliers final: 7
  residues processed: 32
  average time/residue: 0.2239
  time to fit residues: 13.1287
Evaluate side-chains
  33 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 24
  time to evaluate  : 1.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   98 VAL
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 1445 ASN
Chi-restraints excluded: chain A residue 1574 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 23 optimal weight:    0.2980
   chunk 16 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 117 optimal weight:    8.9990
   chunk 121 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 160 optimal weight:   10.0000
   chunk 120 optimal weight:    5.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3317 r_free = 0.3317 target = 0.033393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.025960 restraints weight = 166240.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.026713 restraints weight = 104530.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.027241 restraints weight = 75956.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3041
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3041
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13484  Z= 0.125
  Angle     :  0.688  11.205  18187  Z= 0.359
  Chirality :  0.042   0.252   1884
  Planarity :  0.004   0.051   2343
  Dihedral  :  5.596  39.120   1761
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 13.45 %
    Favored  : 86.48 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 10.18 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.21), residues: 1598
  helix:  0.81 (0.18), residues: 821
  sheet: -4.02 (1.00), residues: 10
  loop : -3.15 (0.20), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 283 
 HIS   0.003   0.001   HIS A 888 
 PHE   0.010   0.001   PHE A 159 
 TYR   0.015   0.001   TYR A 981 
 ARG   0.003   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04120 (  614)
  hydrogen bonds       : angle       4.17222 ( 1800)
  SS BOND              : bond        0.00232 (   27)
  SS BOND              : angle       1.34151 (   54)
  covalent geometry    : bond        0.00262 (13457)
  covalent geometry    : angle       0.68533 (18133)

********************** 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
  32 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 1.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LYS cc_start: 0.9513 (OUTLIER) cc_final: 0.9235 (tptp)
REVERT: A 1272 LEU cc_start: 0.8934 (tp) cc_final: 0.8546 (tt)
REVERT: A 1445 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8566 (p0)
REVERT: A 1941 ASP cc_start: 0.8697 (p0) cc_final: 0.8467 (p0)
REVERT: A 1943 MET cc_start: 0.7741 (ptp) cc_final: 0.7463 (ptp)
  outliers start: 7
  outliers final: 5
  residues processed: 31
  average time/residue: 0.2390
  time to fit residues: 13.4313
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  : 1.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   98 VAL
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 1445 ASN
Chi-restraints excluded: chain A residue 1574 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   chunk 114 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 3 optimal weight:   20.0000
   chunk 77 optimal weight:    0.0770
   chunk 161 optimal weight:    5.9990
   chunk 37 optimal weight:    0.3980
   chunk 39 optimal weight:    6.9990
   chunk 96 optimal weight:    0.7980
   chunk 115 optimal weight:    0.9990
   overall best weight:    1.0542

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.033148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.025848 restraints weight = 165915.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.026583 restraints weight = 104302.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.027106 restraints weight = 75443.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    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 = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2867

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= 0.129
  Angle     :  0.683  11.928  18187  Z= 0.357
  Chirality :  0.041   0.241   1884
  Planarity :  0.004   0.051   2343
  Dihedral  :  5.512  39.491   1761
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.11
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.21), residues: 1598
  helix:  0.84 (0.18), residues: 822
  sheet: -4.06 (1.00), residues: 10
  loop : -3.17 (0.20), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 283 
 HIS   0.004   0.001   HIS A1709 
 PHE   0.010   0.001   PHE A1031 
 TYR   0.011   0.001   TYR A 351 
 ARG   0.003   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04070 (  614)
  hydrogen bonds       : angle       4.19795 ( 1800)
  SS BOND              : bond        0.00254 (   27)
  SS BOND              : angle       1.22653 (   54)
  covalent geometry    : bond        0.00272 (13457)
  covalent geometry    : angle       0.68120 (18133)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4767.98 seconds
wall clock time: 87 minutes 42.54 seconds (5262.54 seconds total)