Starting phenix.real_space_refine
on Tue Jan 13 16:15:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzc_41754/01_2026/8tzc_41754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzc_41754/01_2026/8tzc_41754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzc_41754/01_2026/8tzc_41754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzc_41754/01_2026/8tzc_41754.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzc_41754/01_2026/8tzc_41754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzc_41754/01_2026/8tzc_41754.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.028
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      47      5.16       5
     C    4924      2.51       5
     N    1279      2.21       5
     O    1360      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7612
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 872, 6702
          Classifications: {'peptide': 872}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 39, 'TRANS': 832}
          Chain breaks: 33
          Unresolved non-hydrogen bonds: 264
          Unresolved non-hydrogen angles: 321
          Unresolved non-hydrogen dihedrals: 221
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 6, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 15, 'HIS:plan': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 169
    Chain: "B"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 853
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 4, 'TRANS': 120}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 56
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Unusual residues: {'A1N': 1, 'GDP': 1}
          Classifications: {'undetermined': 2, 'water': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 1.77, per 1000 atoms: 0.23
  Number of scatterers: 7612
  At special positions: 0
  Unit cell: (100.98, 127.16, 90.695, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      47     16.00
     P       2     15.00
     O    1360      8.00
     N    1279      7.00
     C    4924      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A2452 " - pdb=" SG  CYS A2492 " 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: 0.75
  Conformation dependent library (CDL) restraints added in 261.1 milliseconds
  

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1872

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 15 sheets defined
      35.0% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1346 through 1347
      No H-bonds generated for 'chain 'A' and resid 1346 through 1347'
    Processing helix  chain 'A' and resid 1349 through 1349
      No H-bonds generated for 'chain 'A' and resid 1349 through 1349'
    Processing helix  chain 'A' and resid 1350 through 1355
    Processing helix  chain 'A' and resid 1398 through 1402
    Processing helix  chain 'A' and resid 1404 through 1409
    Processing helix  chain 'A' and resid 1502 through 1508
    Processing helix  chain 'A' and resid 1573 through 1580
      removed outlier: 3.740A  pdb=" N   GLU A1578 " --> pdb=" O   HIS A1574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1587 through 1591
      removed outlier: 3.596A  pdb=" N   LEU A1590 " --> pdb=" O   ASP A1587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1599 through 1610
      removed outlier: 4.033A  pdb=" N   LEU A1603 " --> pdb=" O   GLU A1599 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA A1608 " --> pdb=" O   CYS A1604 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ILE A1610 " --> pdb=" O   ILE A1606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1627 through 1633
      removed outlier: 3.712A  pdb=" N   VAL A1631 " --> pdb=" O   SER A1627 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LYS A1633 " --> pdb=" O   ARG A1629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1650 through 1656
      removed outlier: 3.788A  pdb=" N   GLU A1654 " --> pdb=" O   PHE A1650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1686 through 1688
      No H-bonds generated for 'chain 'A' and resid 1686 through 1688'
    Processing helix  chain 'A' and resid 1703 through 1716
      removed outlier: 3.669A  pdb=" N   GLU A1714 " --> pdb=" O   ASN A1710 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE A1715 " --> pdb=" O   ARG A1711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1717 through 1719
      No H-bonds generated for 'chain 'A' and resid 1717 through 1719'
    Processing helix  chain 'A' and resid 1770 through 1792
    Processing helix  chain 'A' and resid 1793 through 1797
    Processing helix  chain 'A' and resid 1827 through 1836
      removed outlier: 4.000A  pdb=" N   GLU A1836 " --> pdb=" O   LYS A1832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1853 through 1855
      No H-bonds generated for 'chain 'A' and resid 1853 through 1855'
    Processing helix  chain 'A' and resid 1871 through 1873
      No H-bonds generated for 'chain 'A' and resid 1871 through 1873'
    Processing helix  chain 'A' and resid 1880 through 1882
      No H-bonds generated for 'chain 'A' and resid 1880 through 1882'
    Processing helix  chain 'A' and resid 1913 through 1925
      removed outlier: 3.866A  pdb=" N   LEU A1917 " --> pdb=" O   SER A1913 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   VAL A1923 " --> pdb=" O   GLN A1919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1954 through 1961
    Processing helix  chain 'A' and resid 1967 through 1988
    Processing helix  chain 'A' and resid 2040 through 2046
      removed outlier: 3.689A  pdb=" N   GLY A2046 " --> pdb=" O   GLU A2042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2053 through 2069
      removed outlier: 4.021A  pdb=" N   TYR A2057 " --> pdb=" O   GLN A2053 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   SER A2058 " --> pdb=" O   ALA A2054 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2084 through 2088
      removed outlier: 3.556A  pdb=" N   ILE A2088 " --> pdb=" O   GLU A2085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2094 through 2100
      removed outlier: 3.520A  pdb=" N   GLU A2098 " --> pdb=" O   ASP A2094 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A2099 " --> pdb=" O   PRO A2095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2107 through 2115
    Processing helix  chain 'A' and resid 2124 through 2133
    Processing helix  chain 'A' and resid 2134 through 2139
      removed outlier: 3.717A  pdb=" N   VAL A2138 " --> pdb=" O   SER A2134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2346 through 2351
    Processing helix  chain 'A' and resid 2389 through 2393
      removed outlier: 3.501A  pdb=" N   LEU A2393 " --> pdb=" O   CYS A2389 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2389 through 2393'
    Processing helix  chain 'A' and resid 2499 through 2522
      removed outlier: 3.690A  pdb=" N   ARG A2522 " --> pdb=" O   ALA A2518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 26
    Processing helix  chain 'B' and resid 51 through 60
    Processing helix  chain 'B' and resid 61 through 72
      removed outlier: 3.771A  pdb=" N   VAL B  65 " --> pdb=" O   HIS B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 93
    Processing helix  chain 'B' and resid 94 through 104
    Processing helix  chain 'B' and resid 117 through 125
      removed outlier: 3.559A  pdb=" N   TYR B 125 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 135
    Processing helix  chain 'B' and resid 150 through 158
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1371 through 1373
      removed outlier: 6.544A  pdb=" N   LEU A1337 " --> pdb=" O   TRP A1393 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   PHE A1395 " --> pdb=" O   LEU A1337 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ILE A1339 " --> pdb=" O   PHE A1395 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   LEU A1416 " --> pdb=" O   LYS A1336 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   MET A1338 " --> pdb=" O   LEU A1416 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   VAL A1418 " --> pdb=" O   MET A1338 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   VAL A1340 " --> pdb=" O   VAL A1418 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   ALA A1417 " --> pdb=" O   VAL A1450 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1582 through 1583
      removed outlier: 3.789A  pdb=" N   PHE A1597 " --> pdb=" O   LEU A1583 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1730 through 1733
      removed outlier: 6.229A  pdb=" N   ALA A1746 " --> pdb=" O   TRP A1742 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   TYR A1747 " --> pdb=" O   PRO A1768 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   PHE A1762 " --> pdb=" O   GLU A1753 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   ILE A1692 " --> pdb=" O   LEU A1813 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1839 through 1840
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1875 through 1876
      removed outlier: 6.756A  pdb=" N   GLY A1891 " --> pdb=" O   ASP A1887 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   ASP A1887 " --> pdb=" O   GLY A1891 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL A1893 " --> pdb=" O   LEU A1885 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1875 through 1876
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1990 through 1991
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2000 through 2002
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2140 through 2148
      removed outlier: 6.637A  pdb=" N   LEU A2140 " --> pdb=" O   ASP A2497 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ASP A2497 " --> pdb=" O   LEU A2140 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A2146 " --> pdb=" O   SER A2491 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   SER A2491 " --> pdb=" O   LEU A2146 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   TYR A2475 " --> pdb=" O   VAL A2455 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   VAL A2455 " --> pdb=" O   TYR A2475 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2155 through 2156
      removed outlier: 3.757A  pdb=" N   SER A2180 " --> pdb=" O   LEU A2169 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2199 through 2203
      removed outlier: 6.746A  pdb=" N   GLY A2218 " --> pdb=" O   LEU A2200 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LEU A2202 " --> pdb=" O   VAL A2216 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL A2216 " --> pdb=" O   LEU A2202 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A2225 " --> pdb=" O   SER A2217 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2245 through 2249
      removed outlier: 6.349A  pdb=" N   GLY A2266 " --> pdb=" O   THR A2246 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LEU A2248 " --> pdb=" O   LEU A2264 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LEU A2264 " --> pdb=" O   LEU A2248 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2300 through 2304
      removed outlier: 3.673A  pdb=" N   CYS A2302 " --> pdb=" O   GLY A2318 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY A2318 " --> pdb=" O   CYS A2302 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLY A2317 " --> pdb=" O   PHE A2324 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2354 through 2359
      removed outlier: 6.770A  pdb=" N   ALA A2366 " --> pdb=" O   ILE A2355 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL A2357 " --> pdb=" O   TYR A2364 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   TYR A2364 " --> pdb=" O   VAL A2357 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   VAL A2359 " --> pdb=" O   ALA A2362 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ALA A2362 " --> pdb=" O   VAL A2359 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   LYS A2367 " --> pdb=" O   VAL A2372 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   VAL A2372 " --> pdb=" O   LYS A2367 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL A2373 " --> pdb=" O   LEU A2386 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   LEU A2386 " --> pdb=" O   VAL A2373 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL A2375 " --> pdb=" O   CYS A2384 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 2414 through 2419
      removed outlier: 6.565A  pdb=" N   GLY A2428 " --> pdb=" O   LYS A2415 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LEU A2417 " --> pdb=" O   TRP A2426 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   TRP A2426 " --> pdb=" O   LEU A2417 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LEU A2419 " --> pdb=" O   ALA A2424 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ALA A2424 " --> pdb=" O   LEU A2419 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   ILE A2434 " --> pdb=" O   VAL A2447 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   VAL A2447 " --> pdb=" O   ILE A2434 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU A2436 " --> pdb=" O   ILE A2445 " (cutoff:3.500A)

    282 hydrogen bonds defined for protein.
    780 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: 1.38

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1224
        1.27 -     1.41: 1864
        1.41 -     1.55: 4584
        1.55 -     1.68: 6
        1.68 -     1.82: 71
  Bond restraints: 7749
  Sorted by residual:
  bond pdb=" C11 A1N A2601 "
       pdb=" N4  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.319  1.137  0.182 2.00e-02 2.50e+03 8.26e+01
  bond pdb=" C11 A1N A2601 "
       pdb=" C21 A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.428  1.310  0.118 2.00e-02 2.50e+03 3.49e+01
  bond pdb=" C20 A1N A2601 "
       pdb=" C21 A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.405  1.288  0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" C7  A1N A2601 "
       pdb=" C8  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.409  1.295  0.114 2.00e-02 2.50e+03 3.24e+01
  bond pdb=" C7  A1N A2601 "
       pdb=" N3  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.342  1.231  0.111 2.00e-02 2.50e+03 3.09e+01
  ... (remaining 7744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 10429
        2.85 -     5.71: 75
        5.71 -     8.56: 15
        8.56 -    11.41: 3
       11.41 -    14.27: 4
  Bond angle restraints: 10526
  Sorted by residual:
  angle pdb=" C19 A1N A2601 "
        pdb=" C16 A1N A2601 "
        pdb=" O2  A1N A2601 "
      ideal   model   delta    sigma   weight residual
     117.13  102.86   14.27 3.00e+00 1.11e-01 2.26e+01
  angle pdb=" C21 A1N A2601 "
        pdb=" C11 A1N A2601 "
        pdb=" N4  A1N A2601 "
      ideal   model   delta    sigma   weight residual
     110.25  123.83  -13.58 3.00e+00 1.11e-01 2.05e+01
  angle pdb=" CB  ILE A1868 "
        pdb=" CG1 ILE A1868 "
        pdb=" CD1 ILE A1868 "
      ideal   model   delta    sigma   weight residual
     113.80  122.08   -8.28 2.10e+00 2.27e-01 1.55e+01
  angle pdb=" CB  MET A2315 "
        pdb=" CG  MET A2315 "
        pdb=" SD  MET A2315 "
      ideal   model   delta    sigma   weight residual
     112.70  124.51  -11.81 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" C3  A1N A2601 "
        pdb=" N1  A1N A2601 "
        pdb=" C4  A1N A2601 "
      ideal   model   delta    sigma   weight residual
     111.39  122.97  -11.58 3.00e+00 1.11e-01 1.49e+01
  ... (remaining 10521 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.94: 4363
       32.94 -    65.88: 197
       65.88 -    98.82: 10
       98.82 -   131.77: 5
      131.77 -   164.71: 1
  Dihedral angle restraints: 4576
    sinusoidal: 1712
      harmonic: 2864
  Sorted by residual:
  dihedral pdb=" C19 A1N A2601 "
           pdb=" C16 A1N A2601 "
           pdb=" C18 A1N A2601 "
           pdb=" O2  A1N A2601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     251.11   86.40  164.71     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" CA  ARG A1943 "
           pdb=" C   ARG A1943 "
           pdb=" N   MET A1944 "
           pdb=" CA  MET A1944 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.69  -21.31     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" C2  A1N A2601 "
           pdb=" C5  A1N A2601 "
           pdb=" O1  A1N A2601 "
           pdb=" C4  A1N A2601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      48.12  -75.17  123.29     1      3.00e+01 1.11e-03 1.65e+01
  ... (remaining 4573 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1015
       0.051 -    0.102: 201
       0.102 -    0.152: 50
       0.152 -    0.203: 0
       0.203 -    0.254: 1
  Chirality restraints: 1267
  Sorted by residual:
  chirality pdb=" CG  LEU A1875 "
            pdb=" CB  LEU A1875 "
            pdb=" CD1 LEU A1875 "
            pdb=" CD2 LEU A1875 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" C16 A1N A2601 "
            pdb=" C18 A1N A2601 "
            pdb=" C19 A1N A2601 "
            pdb=" O2  A1N A2601 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.36    2.21    0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  PRO A2299 "
            pdb=" N   PRO A2299 "
            pdb=" C   PRO A2299 "
            pdb=" CB  PRO A2299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 1264 not shown)

  Planarity restraints: 1290
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 150 "   -0.039 5.00e-02 4.00e+02   6.00e-02 5.76e+00
        pdb=" N   PRO B 151 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 151 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 151 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1864 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO A1865 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A1865 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A1865 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1669 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.08e+00
        pdb=" C   VAL A1669 "    0.030 2.00e-02 2.50e+03
        pdb=" O   VAL A1669 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PRO A1670 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1287 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 231
        2.71 -     3.25: 6959
        3.25 -     3.80: 11698
        3.80 -     4.35: 15813
        4.35 -     4.90: 26494
  Nonbonded interactions: 61195
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A1992 "
            pdb=" O   ALA A2016 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG  SER A1688 "
            pdb=" OD2 ASP A1818 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   TYR B  81 "
            pdb=" ND1 HIS B 113 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   ASN A1871 "
            pdb=" N   GLU A1874 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   VAL A2152 "
            pdb=" OH  TYR A2475 "
     model   vdw
     2.303 3.040
  ... (remaining 61190 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.110
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.570
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
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      :  0.005   0.182   7750  Z= 0.245
  Angle     :  0.682  14.267  10528  Z= 0.307
  Chirality :  0.043   0.254   1267
  Planarity :  0.004   0.060   1290
  Dihedral  : 17.829 164.707   2701
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 25.77 %
    Favored  : 70.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.28), residues: 925
  helix:  0.78 (0.33), residues: 283
  sheet: -0.18 (0.37), residues: 207
  loop : -1.42 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A2339 
 TYR   0.008   0.001   TYR A1992 
 PHE   0.010   0.001   PHE A2324 
 TRP   0.008   0.001   TRP A1393 
 HIS   0.009   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 7749)
  covalent geometry    : angle       0.68196 (10526)
  SS BOND              : bond        0.00239 (    1)
  SS BOND              : angle       1.91851 (    2)
  hydrogen bonds       : bond        0.21459 (  280)
  hydrogen bonds       : angle       7.50036 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A 1400 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7029 (pm20)
REVERT: A 2178 GLN cc_start: 0.6888 (tt0) cc_final: 0.6570 (tt0)
  outliers start: 27
  outliers final: 23
  residues processed: 117
  average time/residue: 0.3762
  time to fit residues: 47.9217
Evaluate side-chains
  114 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1400 GLU
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1606 ILE
Chi-restraints excluded: chain A residue 1674 SER
Chi-restraints excluded: chain A residue 1820 GLU
Chi-restraints excluded: chain A residue 1827 LEU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 1976 LEU
Chi-restraints excluded: chain A residue 1996 LYS
Chi-restraints excluded: chain A residue 2048 VAL
Chi-restraints excluded: chain A residue 2107 VAL
Chi-restraints excluded: chain A residue 2182 LEU
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2225 LEU
Chi-restraints excluded: chain A residue 2338 THR
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2384 CYS
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2460 THR
Chi-restraints excluded: chain A residue 2494 THR
Chi-restraints excluded: chain B residue  119 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4140 r_free = 0.4140 target = 0.188235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.133755 restraints weight = 8497.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.46
r_work: 0.3388 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7750  Z= 0.181
  Angle     :  0.646   9.308  10528  Z= 0.315
  Chirality :  0.046   0.183   1267
  Planarity :  0.005   0.055   1290
  Dihedral  :  9.978 146.136   1094
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 22.56 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.28), residues: 925
  helix:  0.74 (0.32), residues: 295
  sheet: -0.24 (0.38), residues: 202
  loop : -1.41 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2122 
 TYR   0.010   0.001   TYR A2064 
 PHE   0.014   0.001   PHE A2003 
 TRP   0.011   0.001   TRP A2426 
 HIS   0.007   0.001   HIS B 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 7749)
  covalent geometry    : angle       0.64468 (10526)
  SS BOND              : bond        0.00343 (    1)
  SS BOND              : angle       2.93878 (    2)
  hydrogen bonds       : bond        0.04355 (  280)
  hydrogen bonds       : angle       5.59294 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 105
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A 1400 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7156 (pm20)
REVERT: A 1587 ASP cc_start: 0.4939 (OUTLIER) cc_final: 0.4607 (p0)
REVERT: A 1597 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.4392 (p90)
REVERT: A 1836 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6524 (pp20)
REVERT: A 2178 GLN cc_start: 0.6630 (tt0) cc_final: 0.6257 (tt0)
REVERT: B  120 HIS cc_start: 0.7217 (m90) cc_final: 0.6589 (m90)
  outliers start: 41
  outliers final: 16
  residues processed: 140
  average time/residue: 0.3660
  time to fit residues: 55.9249
Evaluate side-chains
  118 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1368 THR
Chi-restraints excluded: chain A residue 1400 GLU
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1587 ASP
Chi-restraints excluded: chain A residue 1597 PHE
Chi-restraints excluded: chain A residue 1606 ILE
Chi-restraints excluded: chain A residue 1835 GLU
Chi-restraints excluded: chain A residue 1836 GLU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 1976 LEU
Chi-restraints excluded: chain A residue 2048 VAL
Chi-restraints excluded: chain A residue 2107 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2246 THR
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2494 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 96 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0770
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4150 r_free = 0.4150 target = 0.189267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.134973 restraints weight = 8376.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.45
r_work: 0.3406 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.1086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7750  Z= 0.148
  Angle     :  0.614   9.624  10528  Z= 0.297
  Chirality :  0.044   0.192   1267
  Planarity :  0.004   0.048   1290
  Dihedral  :  9.163 145.191   1074
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 22.82 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.27), residues: 925
  helix:  0.86 (0.31), residues: 296
  sheet: -0.07 (0.36), residues: 212
  loop : -1.48 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2122 
 TYR   0.008   0.001   TYR A2064 
 PHE   0.011   0.001   PHE A2003 
 TRP   0.008   0.001   TRP A2426 
 HIS   0.006   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7749)
  covalent geometry    : angle       0.61283 (10526)
  SS BOND              : bond        0.00586 (    1)
  SS BOND              : angle       2.80644 (    2)
  hydrogen bonds       : bond        0.03844 (  280)
  hydrogen bonds       : angle       5.23128 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A 1587 ASP cc_start: 0.5134 (OUTLIER) cc_final: 0.4678 (p0)
REVERT: A 1597 PHE cc_start: 0.6190 (OUTLIER) cc_final: 0.4400 (p90)
REVERT: A 1836 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6545 (pp20)
REVERT: A 1996 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8530 (pttt)
REVERT: A 2029 ILE cc_start: 0.7120 (tt) cc_final: 0.6905 (tt)
REVERT: A 2522 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6710 (mtp180)
REVERT: B  120 HIS cc_start: 0.7201 (m90) cc_final: 0.6600 (m90)
  outliers start: 40
  outliers final: 16
  residues processed: 141
  average time/residue: 0.3761
  time to fit residues: 57.6469
Evaluate side-chains
  120 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1587 ASP
Chi-restraints excluded: chain A residue 1597 PHE
Chi-restraints excluded: chain A residue 1827 LEU
Chi-restraints excluded: chain A residue 1835 GLU
Chi-restraints excluded: chain A residue 1836 GLU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 1976 LEU
Chi-restraints excluded: chain A residue 1996 LYS
Chi-restraints excluded: chain A residue 2048 VAL
Chi-restraints excluded: chain A residue 2107 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2246 THR
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2494 THR
Chi-restraints excluded: chain A residue 2522 ARG
Chi-restraints excluded: chain B residue  119 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 58 optimal weight:    0.1980
   chunk 24 optimal weight:    0.6980
   chunk 90 optimal weight:    4.9990
   chunk 91 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A1817 ASN
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4151 r_free = 0.4151 target = 0.189359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.135333 restraints weight = 8567.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.47
r_work: 0.3409 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7750  Z= 0.140
  Angle     :  0.619   9.647  10528  Z= 0.295
  Chirality :  0.044   0.221   1267
  Planarity :  0.004   0.047   1290
  Dihedral  :  8.711 144.995   1069
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 23.46 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.27), residues: 925
  helix:  0.91 (0.31), residues: 298
  sheet: -0.09 (0.37), residues: 200
  loop : -1.40 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2122 
 TYR   0.008   0.001   TYR A2064 
 PHE   0.014   0.001   PHE A2451 
 TRP   0.008   0.001   TRP A2426 
 HIS   0.007   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7749)
  covalent geometry    : angle       0.61753 (10526)
  SS BOND              : bond        0.00202 (    1)
  SS BOND              : angle       2.75993 (    2)
  hydrogen bonds       : bond        0.03595 (  280)
  hydrogen bonds       : angle       5.05167 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 104
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A 1587 ASP cc_start: 0.5211 (OUTLIER) cc_final: 0.4740 (p0)
REVERT: A 1597 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.4451 (p90)
REVERT: A 1733 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8928 (m-80)
REVERT: A 1836 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6581 (pp20)
REVERT: A 1866 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7161 (ptm160)
REVERT: A 1878 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6752 (tt0)
REVERT: A 2178 GLN cc_start: 0.6579 (tt0) cc_final: 0.5768 (tm-30)
REVERT: B  120 HIS cc_start: 0.7247 (m90) cc_final: 0.6661 (m90)
  outliers start: 48
  outliers final: 21
  residues processed: 145
  average time/residue: 0.3866
  time to fit residues: 60.7119
Evaluate side-chains
  126 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1368 THR
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1587 ASP
Chi-restraints excluded: chain A residue 1597 PHE
Chi-restraints excluded: chain A residue 1673 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1817 ASN
Chi-restraints excluded: chain A residue 1827 LEU
Chi-restraints excluded: chain A residue 1835 GLU
Chi-restraints excluded: chain A residue 1836 GLU
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1864 LEU
Chi-restraints excluded: chain A residue 1866 ARG
Chi-restraints excluded: chain A residue 1878 GLU
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 1976 LEU
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2246 THR
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2489 ILE
Chi-restraints excluded: chain A residue 2494 THR
Chi-restraints excluded: chain B residue  119 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0070
   chunk 54 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0670
   chunk 7 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0970
   overall best weight:    0.4134

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

Flipped N/Q/H residues before XYZ refinement:
A1817 ASN
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4163 r_free = 0.4163 target = 0.190597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.137122 restraints weight = 8454.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.45
r_work: 0.3436 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7750  Z= 0.113
  Angle     :  0.595   9.508  10528  Z= 0.283
  Chirality :  0.043   0.192   1267
  Planarity :  0.004   0.044   1290
  Dihedral  :  7.967 144.544   1067
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 25.64 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.28), residues: 925
  helix:  1.03 (0.31), residues: 304
  sheet:  0.02 (0.36), residues: 212
  loop : -1.40 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2122 
 TYR   0.008   0.001   TYR A2006 
 PHE   0.012   0.001   PHE A2451 
 TRP   0.007   0.001   TRP A2496 
 HIS   0.007   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7749)
  covalent geometry    : angle       0.59405 (10526)
  SS BOND              : bond        0.00276 (    1)
  SS BOND              : angle       2.54618 (    2)
  hydrogen bonds       : bond        0.03218 (  280)
  hydrogen bonds       : angle       4.86377 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A 1400 GLU cc_start: 0.7596 (pm20) cc_final: 0.7319 (pm20)
REVERT: A 1587 ASP cc_start: 0.5258 (OUTLIER) cc_final: 0.4791 (p0)
REVERT: A 1597 PHE cc_start: 0.6344 (OUTLIER) cc_final: 0.4549 (p90)
REVERT: A 1733 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8897 (m-80)
REVERT: A 1817 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.6448 (m110)
REVERT: A 1836 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6621 (pp20)
REVERT: A 1866 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7117 (ptm160)
REVERT: A 1878 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6775 (tt0)
REVERT: A 2178 GLN cc_start: 0.6546 (tt0) cc_final: 0.5803 (tm-30)
REVERT: A 2476 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.7003 (m110)
REVERT: A 2522 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6727 (mtp180)
REVERT: B  120 HIS cc_start: 0.7275 (m90) cc_final: 0.6756 (m90)
  outliers start: 36
  outliers final: 15
  residues processed: 144
  average time/residue: 0.4010
  time to fit residues: 62.4936
Evaluate side-chains
  127 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1368 THR
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1587 ASP
Chi-restraints excluded: chain A residue 1597 PHE
Chi-restraints excluded: chain A residue 1673 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1817 ASN
Chi-restraints excluded: chain A residue 1827 LEU
Chi-restraints excluded: chain A residue 1835 GLU
Chi-restraints excluded: chain A residue 1836 GLU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1866 ARG
Chi-restraints excluded: chain A residue 1878 GLU
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 2048 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2246 THR
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2476 ASN
Chi-restraints excluded: chain A residue 2494 THR
Chi-restraints excluded: chain A residue 2522 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 95 optimal weight:    0.0870
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    0.3980
   chunk 89 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0770
   chunk 8 optimal weight:    9.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
A1817 ASN
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4164 r_free = 0.4164 target = 0.190672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.137103 restraints weight = 8555.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.48
r_work: 0.3433 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7750  Z= 0.115
  Angle     :  0.600  10.177  10528  Z= 0.284
  Chirality :  0.043   0.169   1267
  Planarity :  0.004   0.042   1290
  Dihedral  :  7.655 144.595   1065
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 26.41 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.28), residues: 925
  helix:  1.10 (0.31), residues: 304
  sheet:  0.14 (0.37), residues: 209
  loop : -1.43 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2122 
 TYR   0.009   0.001   TYR A2006 
 PHE   0.009   0.001   PHE A2059 
 TRP   0.007   0.001   TRP A2426 
 HIS   0.007   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7749)
  covalent geometry    : angle       0.59871 (10526)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       2.59285 (    2)
  hydrogen bonds       : bond        0.03193 (  280)
  hydrogen bonds       : angle       4.77739 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A 1400 GLU cc_start: 0.7534 (pm20) cc_final: 0.7291 (pm20)
REVERT: A 1587 ASP cc_start: 0.5190 (OUTLIER) cc_final: 0.4724 (p0)
REVERT: A 1597 PHE cc_start: 0.6302 (OUTLIER) cc_final: 0.4488 (p90)
REVERT: A 1733 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8854 (m-80)
REVERT: A 1836 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6560 (pp20)
REVERT: A 1866 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7067 (ptm160)
REVERT: A 1876 GLU cc_start: 0.7815 (pt0) cc_final: 0.7182 (mm-30)
REVERT: A 1878 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6759 (tt0)
REVERT: A 2178 GLN cc_start: 0.6529 (tt0) cc_final: 0.5670 (tm-30)
REVERT: A 2522 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6691 (mtp180)
REVERT: B  120 HIS cc_start: 0.7207 (m90) cc_final: 0.6721 (m90)
  outliers start: 32
  outliers final: 16
  residues processed: 136
  average time/residue: 0.3971
  time to fit residues: 58.3049
Evaluate side-chains
  128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1368 THR
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1587 ASP
Chi-restraints excluded: chain A residue 1597 PHE
Chi-restraints excluded: chain A residue 1673 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1827 LEU
Chi-restraints excluded: chain A residue 1835 GLU
Chi-restraints excluded: chain A residue 1836 GLU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1866 ARG
Chi-restraints excluded: chain A residue 1878 GLU
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2048 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2246 THR
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2494 THR
Chi-restraints excluded: chain A residue 2522 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A1817 ASN
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4150 r_free = 0.4150 target = 0.189189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.135354 restraints weight = 8485.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.47
r_work: 0.3411 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7750  Z= 0.146
  Angle     :  0.632   9.862  10528  Z= 0.301
  Chirality :  0.044   0.194   1267
  Planarity :  0.004   0.045   1290
  Dihedral  :  7.817 145.085   1065
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 26.15 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.28), residues: 925
  helix:  1.09 (0.31), residues: 302
  sheet:  0.05 (0.36), residues: 212
  loop : -1.39 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2122 
 TYR   0.008   0.001   TYR A2064 
 PHE   0.011   0.001   PHE A2003 
 TRP   0.007   0.001   TRP A2426 
 HIS   0.008   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7749)
  covalent geometry    : angle       0.63109 (10526)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       2.77526 (    2)
  hydrogen bonds       : bond        0.03510 (  280)
  hydrogen bonds       : angle       4.85809 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 107
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A 1400 GLU cc_start: 0.7542 (pm20) cc_final: 0.7274 (pm20)
REVERT: A 1587 ASP cc_start: 0.5235 (OUTLIER) cc_final: 0.4705 (p0)
REVERT: A 1597 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.4434 (p90)
REVERT: A 1733 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8969 (m-80)
REVERT: A 1836 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6645 (pp20)
REVERT: A 1866 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7151 (ptm160)
REVERT: A 1878 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6738 (tt0)
REVERT: A 2029 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7127 (tt)
REVERT: A 2178 GLN cc_start: 0.6453 (tt0) cc_final: 0.5565 (tm-30)
REVERT: A 2522 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6718 (mtp180)
REVERT: B  120 HIS cc_start: 0.7222 (m90) cc_final: 0.6724 (m90)
  outliers start: 37
  outliers final: 18
  residues processed: 138
  average time/residue: 0.4013
  time to fit residues: 59.9001
Evaluate side-chains
  128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1368 THR
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1587 ASP
Chi-restraints excluded: chain A residue 1597 PHE
Chi-restraints excluded: chain A residue 1673 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1817 ASN
Chi-restraints excluded: chain A residue 1827 LEU
Chi-restraints excluded: chain A residue 1835 GLU
Chi-restraints excluded: chain A residue 1836 GLU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1866 ARG
Chi-restraints excluded: chain A residue 1878 GLU
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2029 ILE
Chi-restraints excluded: chain A residue 2048 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2246 THR
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2494 THR
Chi-restraints excluded: chain A residue 2522 ARG
Chi-restraints excluded: chain B residue  119 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0040
   chunk 30 optimal weight:    0.2980
   chunk 5 optimal weight:    0.0870
   chunk 60 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0470
   overall best weight:    0.2268

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

Flipped N/Q/H residues before XYZ refinement:
A1817 ASN
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4184 r_free = 0.4184 target = 0.192650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.139692 restraints weight = 8580.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.48
r_work: 0.3468 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7750  Z= 0.099
  Angle     :  0.592  10.278  10528  Z= 0.280
  Chirality :  0.043   0.202   1267
  Planarity :  0.004   0.041   1290
  Dihedral  :  7.383 144.237   1065
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 27.18 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.28), residues: 925
  helix:  1.32 (0.32), residues: 304
  sheet:  0.13 (0.37), residues: 204
  loop : -1.29 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2339 
 TYR   0.010   0.001   TYR A1992 
 PHE   0.008   0.001   PHE A2059 
 TRP   0.009   0.001   TRP A2496 
 HIS   0.009   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7749)
  covalent geometry    : angle       0.59109 (10526)
  SS BOND              : bond        0.00103 (    1)
  SS BOND              : angle       2.35964 (    2)
  hydrogen bonds       : bond        0.02793 (  280)
  hydrogen bonds       : angle       4.58500 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A 1400 GLU cc_start: 0.7572 (pm20) cc_final: 0.7206 (pm20)
REVERT: A 1587 ASP cc_start: 0.5168 (OUTLIER) cc_final: 0.4706 (p0)
REVERT: A 1597 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.4638 (p90)
REVERT: A 1733 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8816 (m-80)
REVERT: A 1836 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6590 (pp20)
REVERT: A 1853 SER cc_start: 0.8398 (t) cc_final: 0.8092 (p)
REVERT: A 1876 GLU cc_start: 0.7773 (pt0) cc_final: 0.7203 (mm-30)
REVERT: A 2029 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7157 (tt)
REVERT: A 2178 GLN cc_start: 0.6528 (tt0) cc_final: 0.5666 (tm-30)
REVERT: B  120 HIS cc_start: 0.7233 (m90) cc_final: 0.6714 (m90)
  outliers start: 30
  outliers final: 13
  residues processed: 140
  average time/residue: 0.4329
  time to fit residues: 65.3396
Evaluate side-chains
  122 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1504 ILE
Chi-restraints excluded: chain A residue 1587 ASP
Chi-restraints excluded: chain A residue 1597 PHE
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1817 ASN
Chi-restraints excluded: chain A residue 1835 GLU
Chi-restraints excluded: chain A residue 1836 GLU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2029 ILE
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2246 THR
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2494 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 79 optimal weight:    0.3980
   chunk 9 optimal weight:   10.0000
   chunk 25 optimal weight:    0.4980
   chunk 89 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4157 r_free = 0.4157 target = 0.190074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.136458 restraints weight = 8504.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.47
r_work: 0.3425 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7750  Z= 0.139
  Angle     :  0.646   9.991  10528  Z= 0.304
  Chirality :  0.044   0.196   1267
  Planarity :  0.004   0.044   1290
  Dihedral  :  7.647 144.975   1065
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 28.46 %
    Favored  : 68.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.28), residues: 925
  helix:  1.22 (0.31), residues: 304
  sheet:  0.11 (0.37), residues: 204
  loop : -1.28 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2122 
 TYR   0.010   0.001   TYR A2006 
 PHE   0.018   0.001   PHE A2451 
 TRP   0.007   0.001   TRP A2426 
 HIS   0.008   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7749)
  covalent geometry    : angle       0.64529 (10526)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       2.75780 (    2)
  hydrogen bonds       : bond        0.03356 (  280)
  hydrogen bonds       : angle       4.72478 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A 1353 GLN cc_start: 0.5377 (mt0) cc_final: 0.5126 (mp10)
REVERT: A 1400 GLU cc_start: 0.7449 (pm20) cc_final: 0.7083 (pm20)
REVERT: A 1587 ASP cc_start: 0.5110 (OUTLIER) cc_final: 0.4598 (p0)
REVERT: A 1597 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.4423 (p90)
REVERT: A 1677 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7389 (tpt-90)
REVERT: A 1733 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8936 (m-80)
REVERT: A 1836 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6571 (pp20)
REVERT: A 1962 ASP cc_start: 0.7628 (t0) cc_final: 0.7205 (t0)
REVERT: A 2029 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.7098 (tt)
REVERT: A 2178 GLN cc_start: 0.6444 (tt0) cc_final: 0.5545 (tm-30)
REVERT: B  120 HIS cc_start: 0.7204 (m90) cc_final: 0.6695 (m90)
  outliers start: 21
  outliers final: 13
  residues processed: 127
  average time/residue: 0.4343
  time to fit residues: 59.3834
Evaluate side-chains
  122 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1587 ASP
Chi-restraints excluded: chain A residue 1597 PHE
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1817 ASN
Chi-restraints excluded: chain A residue 1835 GLU
Chi-restraints excluded: chain A residue 1836 GLU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2029 ILE
Chi-restraints excluded: chain A residue 2107 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2246 THR
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2494 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 87 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0020
   chunk 59 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A1817 ASN
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4157 r_free = 0.4157 target = 0.190030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.136641 restraints weight = 8509.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.44
r_work: 0.3427 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7750  Z= 0.136
  Angle     :  0.642  10.490  10528  Z= 0.302
  Chirality :  0.044   0.203   1267
  Planarity :  0.004   0.043   1290
  Dihedral  :  7.677 144.901   1065
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 29.10 %
    Favored  : 68.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.28), residues: 925
  helix:  1.18 (0.31), residues: 304
  sheet:  0.10 (0.37), residues: 204
  loop : -1.28 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2122 
 TYR   0.010   0.001   TYR A2006 
 PHE   0.017   0.001   PHE A2451 
 TRP   0.007   0.001   TRP A2426 
 HIS   0.009   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7749)
  covalent geometry    : angle       0.64038 (10526)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       2.83280 (    2)
  hydrogen bonds       : bond        0.03327 (  280)
  hydrogen bonds       : angle       4.75894 (  780)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A 1353 GLN cc_start: 0.5350 (mt0) cc_final: 0.5067 (mp10)
REVERT: A 1400 GLU cc_start: 0.7473 (pm20) cc_final: 0.7164 (pm20)
REVERT: A 1587 ASP cc_start: 0.5236 (OUTLIER) cc_final: 0.4725 (p0)
REVERT: A 1597 PHE cc_start: 0.6185 (OUTLIER) cc_final: 0.4437 (p90)
REVERT: A 1677 ARG cc_start: 0.7725 (ttt-90) cc_final: 0.7398 (tpt-90)
REVERT: A 1733 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.8905 (m-80)
REVERT: A 1836 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6588 (pp20)
REVERT: A 1962 ASP cc_start: 0.7642 (t0) cc_final: 0.7247 (t0)
REVERT: A 2029 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7120 (tt)
REVERT: A 2178 GLN cc_start: 0.6407 (tt0) cc_final: 0.5517 (tm-30)
REVERT: B  120 HIS cc_start: 0.7220 (m90) cc_final: 0.6709 (m90)
  outliers start: 18
  outliers final: 11
  residues processed: 123
  average time/residue: 0.4217
  time to fit residues: 56.0277
Evaluate side-chains
  123 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1448 ILE
Chi-restraints excluded: chain A residue 1503 THR
Chi-restraints excluded: chain A residue 1587 ASP
Chi-restraints excluded: chain A residue 1597 PHE
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1835 GLU
Chi-restraints excluded: chain A residue 1836 GLU
Chi-restraints excluded: chain A residue 1849 THR
Chi-restraints excluded: chain A residue 1936 LEU
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2029 ILE
Chi-restraints excluded: chain A residue 2107 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2246 THR
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2494 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0170
   chunk 60 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 97 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A1817 ASN
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2391 HIS
** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.189977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.136694 restraints weight = 8494.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.45
r_work: 0.3427 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7750  Z= 0.134
  Angle     :  0.658  16.258  10528  Z= 0.304
  Chirality :  0.044   0.196   1267
  Planarity :  0.004   0.044   1290
  Dihedral  :  7.605 144.895   1064
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 28.72 %
    Favored  : 68.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.28), residues: 925
  helix:  1.19 (0.31), residues: 304
  sheet:  0.20 (0.37), residues: 209
  loop : -1.32 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2339 
 TYR   0.011   0.001   TYR A2006 
 PHE   0.017   0.001   PHE A2451 
 TRP   0.007   0.001   TRP A2426 
 HIS   0.009   0.001   HIS A2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7749)
  covalent geometry    : angle       0.65672 (10526)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       2.81494 (    2)
  hydrogen bonds       : bond        0.03313 (  280)
  hydrogen bonds       : angle       4.74290 (  780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3675.30 seconds
wall clock time: 63 minutes 12.15 seconds (3792.15 seconds total)