Starting phenix.real_space_refine
on Tue Jan 13 14:26:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8txz_41709/01_2026/8txz_41709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8txz_41709/01_2026/8txz_41709.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8txz_41709/01_2026/8txz_41709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8txz_41709/01_2026/8txz_41709.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8txz_41709/01_2026/8txz_41709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8txz_41709/01_2026/8txz_41709.map"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.036
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    4321      2.51       5
     N    1116      2.21       5
     O    1168      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 6654
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6597
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 858, 6587
          Classifications: {'peptide': 858}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 42, 'TRANS': 815}
          Chain breaks: 26
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 299
          Unresolved non-hydrogen angles: 370
          Unresolved non-hydrogen dihedrals: 243
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASN:plan1': 10, 'GLN:plan1': 5, 'ARG:plan': 8, 'GLU:plan': 21, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 219
      Conformer: "B"
        Number of residues, atoms: 858, 6587
          Classifications: {'peptide': 858}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 42, 'TRANS': 815}
          Chain breaks: 26
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 299
          Unresolved non-hydrogen angles: 370
          Unresolved non-hydrogen dihedrals: 243
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASN:plan1': 10, 'GLN:plan1': 5, 'ARG:plan': 8, 'GLU:plan': 21, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 219
          bond proxies already assigned to first conformer: 6700
    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}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A1998 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A1998 " occ=0.50
  Time building chain proxies: 3.02, per 1000 atoms: 0.45
  Number of scatterers: 6654
  At special positions: 0
  Unit cell: (110.97, 82.2, 112.614, 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    1168      8.00
     N    1116      7.00
     C    4321      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 523.0 milliseconds
  

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1622

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      31.7% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1400 through 1405
      removed outlier: 4.188A  pdb=" N   SER A1403 " --> pdb=" O   GLU A1400 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   HIS A1405 " --> pdb=" O   TYR A1402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1433 through 1442
      removed outlier: 4.046A  pdb=" N   ASN A1437 " --> pdb=" O   PRO A1433 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA A1442 " --> pdb=" O   ILE A1438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1532 through 1540
      removed outlier: 4.019A  pdb=" N   SER A1536 " --> pdb=" O   LYS A1532 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASN A1540 " --> pdb=" O   SER A1536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1568 through 1579
      removed outlier: 3.971A  pdb=" N   HIS A1574 " --> pdb=" O   PRO A1570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1599 through 1606
      removed outlier: 4.011A  pdb=" N   LEU A1603 " --> pdb=" O   GLU A1599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1628 through 1633
    Processing helix  chain 'A' and resid 1646 through 1656
    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 1715
      removed outlier: 3.729A  pdb=" N   ARG A1707 " --> pdb=" O   GLY A1703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1716 through 1719
    Processing helix  chain 'A' and resid 1770 through 1776
      removed outlier: 4.310A  pdb=" N   LEU A1776 " --> pdb=" O   LYS A1772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1776 through 1791
      removed outlier: 3.512A  pdb=" N   TRP A1791 " --> pdb=" O   LEU A1787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1827 through 1835
    Processing helix  chain 'A' and resid 1851 through 1856
      removed outlier: 3.803A  pdb=" N   ILE A1855 " --> pdb=" O   PRO A1851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1865 through 1869
      removed outlier: 3.717A  pdb=" N   MET A1869 " --> pdb=" O   ARG A1866 " (cutoff:3.500A)
    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: 3.757A  pdb=" N   LEU A1917 " --> pdb=" O   SER A1913 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   VAL A1923 " --> pdb=" O   GLN A1919 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   CYS A1925 " --> pdb=" O   LEU A1921 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1954 through 1961
    Processing helix  chain 'A' and resid 1967 through 1988
      removed outlier: 3.540A  pdb=" N   HIS A1972 " --> pdb=" O   ARG A1968 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ARG A1973 " --> pdb=" O   THR A1969 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA A1975 " --> pdb=" O   GLN A1971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1996 through 1998
      No H-bonds generated for 'chain 'A' and resid 1996 through 1998'
    Processing helix  chain 'A' and resid 2040 through 2045
    Processing helix  chain 'A' and resid 2053 through 2069
      removed outlier: 3.509A  pdb=" N   TYR A2057 " --> pdb=" O   GLN A2053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2071 through 2078
    Processing helix  chain 'A' and resid 2094 through 2100
    Processing helix  chain 'A' and resid 2107 through 2115
    Processing helix  chain 'A' and resid 2124 through 2133
      removed outlier: 3.646A  pdb=" N   ASP A2130 " --> pdb=" O   ALA A2126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2134 through 2139
      removed outlier: 3.682A  pdb=" N   VAL A2138 " --> pdb=" O   SER A2134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2389 through 2396
      removed outlier: 3.584A  pdb=" N   VAL A2396 " --> pdb=" O   PHE A2392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2499 through 2522
      removed outlier: 3.755A  pdb=" N   GLN A2505 " --> pdb=" O   PRO A2501 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1391 through 1392
      removed outlier: 8.218A  pdb=" N   ILE A1448 " --> pdb=" O   ALA A1413 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   TYR A1415 " --> pdb=" O   ILE A1448 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   VAL A1450 " --> pdb=" O   TYR A1415 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   ALA A1417 " --> pdb=" O   VAL A1450 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   VAL A1447 " --> pdb=" O   ILE A1482 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   ASP A1484 " --> pdb=" O   VAL A1447 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1547 through 1548
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1626 through 1627
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1730 through 1733
      removed outlier: 6.260A  pdb=" N   ALA A1746 " --> pdb=" O   TRP A1742 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   TYR A1747 " --> pdb=" O   PRO A1768 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLU A1753 " --> pdb=" O   PHE A1762 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A1762 " --> pdb=" O   GLU A1753 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   ILE A1692 " --> pdb=" O   LEU A1813 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1875 through 1877
      removed outlier: 6.720A  pdb=" N   VAL A1893 " --> pdb=" O   LEU A1885 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1875 through 1877
      removed outlier: 6.638A  pdb=" N   MET A1944 " --> pdb=" O   ALA A1938 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   ALA A1938 " --> pdb=" O   MET A1944 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   VAL A1946 " --> pdb=" O   LEU A1936 " (cutoff:3.500A)
    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 2145
      removed outlier: 6.598A  pdb=" N   LEU A2140 " --> pdb=" O   ASP A2497 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ASP A2497 " --> pdb=" O   LEU A2140 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A2144 " --> pdb=" O   LEU A2493 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   LEU A2471 " --> pdb=" O   MET A2458 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   MET A2458 " --> pdb=" O   LEU A2471 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   LEU A2473 " --> pdb=" O   ARG A2456 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2140 through 2145
      removed outlier: 6.598A  pdb=" N   LEU A2140 " --> pdb=" O   ASP A2497 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ASP A2497 " --> pdb=" O   LEU A2140 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A2144 " --> pdb=" O   LEU A2493 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2155 through 2157
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2303 through 2305
      removed outlier: 3.606A  pdb=" N   SER A2304 " --> pdb=" O   TRP A2316 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE A2324 " --> pdb=" O   GLY A2317 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2356 through 2359
      removed outlier: 4.181A  pdb=" N   THR A2356 " --> pdb=" O   ALA A2366 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA A2366 " --> pdb=" O   THR A2356 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLY A2385 " --> pdb=" O   VAL A2375 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ASP A2377 " --> pdb=" O   LEU A2383 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU A2383 " --> pdb=" O   ASP A2377 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2416 through 2420
      removed outlier: 3.912A  pdb=" N   ALA A2424 " --> pdb=" O   GLN A2420 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG A2446 " --> pdb=" O   LEU A2436 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    684 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: 1.26

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.04 -     1.19: 31
        1.19 -     1.35: 2081
        1.35 -     1.50: 1866
        1.50 -     1.66: 2736
        1.66 -     1.81: 72
  Bond restraints: 6786
  Sorted by residual:
  bond pdb=" C   ALA A2016 "
       pdb=" O   ALA A2016 "
    ideal  model  delta    sigma   weight residual
    1.234  1.036  0.198 1.51e-02 4.39e+03 1.72e+02
  bond pdb=" C   ASP A1994 "
       pdb=" O   ASP A1994 "
    ideal  model  delta    sigma   weight residual
    1.235  1.121  0.115 1.14e-02 7.69e+03 1.01e+02
  bond pdb=" C   ILE A1991 "
       pdb=" O   ILE A1991 "
    ideal  model  delta    sigma   weight residual
    1.238  1.132  0.106 1.17e-02 7.31e+03 8.21e+01
  bond pdb=" C11 A1N A2601 "
       pdb=" N4  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.319  1.139  0.180 2.00e-02 2.50e+03 8.10e+01
  bond pdb=" C   ILE A2015 "
       pdb=" O   ILE A2015 "
    ideal  model  delta    sigma   weight residual
    1.237  1.150  0.087 1.11e-02 8.12e+03 6.19e+01
  ... (remaining 6781 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.92: 9015
        2.92 -     5.83: 159
        5.83 -     8.75: 22
        8.75 -    11.66: 6
       11.66 -    14.58: 8
  Bond angle restraints: 9210
  Sorted by residual:
  angle pdb=" C   LEU A1864 "
        pdb=" N   PRO A1865 "
        pdb=" CA  PRO A1865 "
      ideal   model   delta    sigma   weight residual
     119.90  127.92   -8.02 1.02e+00 9.61e-01 6.18e+01
  angle pdb=" N   SER A2032 "
        pdb=" CA  SER A2032 "
        pdb=" C   SER A2032 "
      ideal   model   delta    sigma   weight residual
     108.52  118.38   -9.86 1.63e+00 3.76e-01 3.66e+01
  angle pdb=" N   ASP A2017 "
        pdb=" CA  ASP A2017 "
        pdb=" C   ASP A2017 "
      ideal   model   delta    sigma   weight residual
     110.80  123.35  -12.55 2.13e+00 2.20e-01 3.47e+01
  angle pdb=" N   TYR A1992 "
        pdb=" CA  TYR A1992 "
        pdb=" C   TYR A1992 "
      ideal   model   delta    sigma   weight residual
     112.89  119.79   -6.90 1.24e+00 6.50e-01 3.09e+01
  angle pdb=" N   ARG A1993 "
        pdb=" CA  ARG A1993 "
        pdb=" C   ARG A1993 "
      ideal   model   delta    sigma   weight residual
     110.80  122.34  -11.54 2.13e+00 2.20e-01 2.94e+01
  ... (remaining 9205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.88: 3943
       32.88 -    65.76: 79
       65.76 -    98.63: 9
       98.63 -   131.51: 4
      131.51 -   164.39: 1
  Dihedral angle restraints: 4036
    sinusoidal: 1551
      harmonic: 2485
  Sorted by residual:
  dihedral pdb=" C   ARG A1993 "
           pdb=" N   ARG A1993 "
           pdb=" CA  ARG A1993 "
           pdb=" CB  ARG A1993 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -142.50   19.90     0      2.50e+00 1.60e-01 6.34e+01
  dihedral pdb=" N   ARG A1993 "
           pdb=" C   ARG A1993 "
           pdb=" CA  ARG A1993 "
           pdb=" CB  ARG A1993 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  141.86  -19.06     0      2.50e+00 1.60e-01 5.81e+01
  dihedral pdb=" CA  HIS A1405 "
           pdb=" C   HIS A1405 "
           pdb=" N   PRO A1406 "
           pdb=" CA  PRO A1406 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.29   27.71     0      5.00e+00 4.00e-02 3.07e+01
  ... (remaining 4033 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.206: 1076
       0.206 -    0.413: 9
       0.413 -    0.619: 3
       0.619 -    0.826: 0
       0.826 -    1.032: 1
  Chirality restraints: 1089
  Sorted by residual:
  chirality pdb=" CA  ARG A1993 "
            pdb=" N   ARG A1993 "
            pdb=" C   ARG A1993 "
            pdb=" CB  ARG A1993 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.48    1.03 2.00e-01 2.50e+01 2.66e+01
  chirality pdb=" CA  ASP A2017 "
            pdb=" N   ASP A2017 "
            pdb=" C   ASP A2017 "
            pdb=" CB  ASP A2017 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.34e+00
  chirality pdb=" CA  LEU A1861 "
            pdb=" N   LEU A1861 "
            pdb=" C   LEU A1861 "
            pdb=" CB  LEU A1861 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 6.93e+00
  ... (remaining 1086 not shown)

  Planarity restraints: 1125
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A1405 "   -0.087 5.00e-02 4.00e+02   1.30e-01 2.69e+01
        pdb=" N   PRO A1406 "    0.224 5.00e-02 4.00e+02
        pdb=" CA  PRO A1406 "   -0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO A1406 "   -0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A1887 "   -0.018 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   ASP A1887 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ASP A1887 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLY A1888 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1894 "    0.040 2.00e-02 2.50e+03   2.06e-02 8.46e+00
        pdb=" CG  TYR A1894 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1894 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1894 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1894 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1894 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1894 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A1894 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1122 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 975
        2.76 -     3.29: 6070
        3.29 -     3.83: 10385
        3.83 -     4.36: 12894
        4.36 -     4.90: 22420
  Nonbonded interactions: 52744
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1712 "
            pdb=" OG  SER A1716 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   GLY A2037 "
            pdb=" NH2 ARG A2072 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" NH2 ARG A1693 "
            pdb=" OD2 ASP A1858 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" NZ  LYS A1996 "
            pdb=" OG1 THR A2035 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" NZ  LYS A1347 "
            pdb=" O3B GDP A2602 "
     model   vdw
     2.337 3.120
  ... (remaining 52739 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.340
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     10.190
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
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      :  0.011   0.198   6786  Z= 0.681
  Angle     :  0.958  14.580   9210  Z= 0.494
  Chirality :  0.068   1.032   1089
  Planarity :  0.007   0.130   1125
  Dihedral  : 14.885 164.391   2414
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.09 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  0.87 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.30), residues: 807
  helix: -0.48 (0.36), residues: 225
  sheet: -0.73 (0.44), residues: 173
  loop : -1.66 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1895 
 TYR   0.040   0.002   TYR A1894 
 PHE   0.033   0.002   PHE A2451 
 TRP   0.016   0.001   TRP A1602 
 HIS   0.005   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.01102 ( 6786)
  covalent geometry    : angle       0.95836 ( 9210)
  hydrogen bonds       : bond        0.27540 (  237)
  hydrogen bonds       : angle      10.32696 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A 2033 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8029 (mt-10)
REVERT: A 2315 MET cc_start: 0.5032 (ttt) cc_final: 0.4824 (ttt)
REVERT: A 2506 ASN cc_start: 0.7810 (m110) cc_final: 0.7553 (m-40)
  outliers start: 9
  outliers final: 4
  residues processed: 93
  average time/residue: 0.0693
  time to fit residues: 9.0861
Evaluate side-chains
  74 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1861 LEU
Chi-restraints excluded: chain A residue 1889 SER
Chi-restraints excluded: chain A residue 1892 SER
Chi-restraints excluded: chain A residue 1991 ILE
Chi-restraints excluded: chain A residue 2033 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0470
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0010
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.5284

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

Flipped N/Q/H residues before XYZ refinement:
A1391 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.209077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.168092 restraints weight = 18739.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 5.02
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3972 r_free = 0.3972    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3972 r_free = 0.3972    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6786  Z= 0.142
  Angle     :  0.649   7.981   9210  Z= 0.322
  Chirality :  0.046   0.173   1089
  Planarity :  0.006   0.106   1125
  Dihedral  :  8.081 144.016    932
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.09 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  5.81 %
    Favored  : 92.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.29), residues: 807
  helix: -0.21 (0.34), residues: 236
  sheet: -0.56 (0.44), residues: 165
  loop : -1.62 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1983 
 TYR   0.010   0.001   TYR A2023 
 PHE   0.034   0.001   PHE A2451 
 TRP   0.018   0.002   TRP A2426 
 HIS   0.005   0.001   HIS A1977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6786)
  covalent geometry    : angle       0.64933 ( 9210)
  hydrogen bonds       : bond        0.04750 (  237)
  hydrogen bonds       : angle       6.58212 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A 1646 MET cc_start: 0.8087 (tpt) cc_final: 0.7550 (tpt)
REVERT: A 1902 GLU cc_start: 0.6695 (tp30) cc_final: 0.6356 (tt0)
REVERT: A 1958 LEU cc_start: 0.8517 (tp) cc_final: 0.8300 (tp)
REVERT: A 2516 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7271 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 84
  average time/residue: 0.0775
  time to fit residues: 9.2116
Evaluate side-chains
  69 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1594 ASP
Chi-restraints excluded: chain A residue 1660 LEU
Chi-restraints excluded: chain A residue 1671 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2136 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 36 optimal weight:    0.0870
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A1391 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.208673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.161266 restraints weight = 13491.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 5.32
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6786  Z= 0.138
  Angle     :  0.626   8.043   9210  Z= 0.309
  Chirality :  0.046   0.175   1089
  Planarity :  0.005   0.094   1125
  Dihedral  :  7.360 143.982    923
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.34 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  8.13 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.29), residues: 807
  helix:  0.05 (0.34), residues: 238
  sheet: -0.56 (0.43), residues: 162
  loop : -1.55 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1983 
 TYR   0.011   0.001   TYR A2023 
 PHE   0.044   0.002   PHE A2451 
 TRP   0.013   0.001   TRP A2426 
 HIS   0.004   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6786)
  covalent geometry    : angle       0.62573 ( 9210)
  hydrogen bonds       : bond        0.03988 (  237)
  hydrogen bonds       : angle       5.81264 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A 1371 ILE cc_start: 0.7757 (mt) cc_final: 0.7556 (mt)
REVERT: A 2315 MET cc_start: 0.5160 (ttt) cc_final: 0.4860 (ttt)
REVERT: A 2506 ASN cc_start: 0.7991 (m-40) cc_final: 0.7685 (m110)
REVERT: A 2516 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7208 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 81
  average time/residue: 0.0798
  time to fit residues: 8.9444
Evaluate side-chains
  74 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1594 ASP
Chi-restraints excluded: chain A residue 1660 LEU
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2136 GLU
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 64 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0970
   overall best weight:    0.5578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.208199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.158832 restraints weight = 10163.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 4.69
r_work: 0.3378 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2976
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2976
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6786  Z= 0.134
  Angle     :  0.609   6.567   9210  Z= 0.301
  Chirality :  0.046   0.200   1089
  Planarity :  0.005   0.089   1125
  Dihedral  :  7.318 143.876    923
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.85 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 10.16 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.29), residues: 807
  helix:  0.19 (0.34), residues: 238
  sheet: -0.62 (0.42), residues: 162
  loop : -1.51 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2514 
 TYR   0.011   0.001   TYR A2023 
 PHE   0.009   0.001   PHE A1585 
 TRP   0.011   0.001   TRP A1602 
 HIS   0.004   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6786)
  covalent geometry    : angle       0.60888 ( 9210)
  hydrogen bonds       : bond        0.03607 (  237)
  hydrogen bonds       : angle       5.44936 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A 1371 ILE cc_start: 0.7378 (mt) cc_final: 0.7110 (mt)
REVERT: A 2136 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8101 (mt-10)
REVERT: A 2506 ASN cc_start: 0.8398 (m-40) cc_final: 0.8083 (m-40)
REVERT: A 2516 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7178 (mt-10)
  outliers start: 9
  outliers final: 5
  residues processed: 79
  average time/residue: 0.0800
  time to fit residues: 8.6788
Evaluate side-chains
  76 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1660 LEU
Chi-restraints excluded: chain A residue 1671 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2136 GLU
Chi-restraints excluded: chain A residue 2472 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 77 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0670
   overall best weight:    0.6320

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

Flipped N/Q/H residues before XYZ refinement:
A2490 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.208873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.168168 restraints weight = 17894.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 4.90
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6786  Z= 0.139
  Angle     :  0.603   5.742   9210  Z= 0.296
  Chirality :  0.046   0.174   1089
  Planarity :  0.005   0.085   1125
  Dihedral  :  7.298 143.887    923
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.09 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 10.01 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.29), residues: 807
  helix:  0.25 (0.35), residues: 238
  sheet: -0.63 (0.41), residues: 162
  loop : -1.48 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2514 
 TYR   0.011   0.001   TYR A2023 
 PHE   0.044   0.002   PHE A2451 
 TRP   0.011   0.001   TRP A1602 
 HIS   0.004   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6786)
  covalent geometry    : angle       0.60320 ( 9210)
  hydrogen bonds       : bond        0.03513 (  237)
  hydrogen bonds       : angle       5.27230 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A 2506 ASN cc_start: 0.7956 (m-40) cc_final: 0.7735 (m-40)
REVERT: A 2516 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7322 (mt-10)
  outliers start: 10
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0783
  time to fit residues: 8.7585
Evaluate side-chains
  76 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1660 LEU
Chi-restraints excluded: chain A residue 1671 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 39 optimal weight:    0.0870
   chunk 13 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 69 optimal weight:    9.9990
   chunk 82 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 68 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   overall best weight:    0.5558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.209353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.168931 restraints weight = 17830.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 4.90
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3963 r_free = 0.3963    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3963 r_free = 0.3963    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6786  Z= 0.132
  Angle     :  0.613   9.669   9210  Z= 0.300
  Chirality :  0.046   0.231   1089
  Planarity :  0.005   0.084   1125
  Dihedral  :  7.282 143.912    923
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.72 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 10.45 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.29), residues: 807
  helix:  0.37 (0.35), residues: 233
  sheet: -0.59 (0.41), residues: 162
  loop : -1.42 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2514 
 TYR   0.010   0.001   TYR A2023 
 PHE   0.010   0.001   PHE A1585 
 TRP   0.010   0.001   TRP A1811 
 HIS   0.004   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6786)
  covalent geometry    : angle       0.61279 ( 9210)
  hydrogen bonds       : bond        0.03373 (  237)
  hydrogen bonds       : angle       5.15943 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A 2506 ASN cc_start: 0.7994 (m-40) cc_final: 0.7739 (m-40)
REVERT: A 2516 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7309 (mt-10)
  outliers start: 8
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0713
  time to fit residues: 7.7648
Evaluate side-chains
  80 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1660 LEU
Chi-restraints excluded: chain A residue 1671 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1922 VAL
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2472 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0270
   chunk 81 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 63 optimal weight:    0.3980
   chunk 80 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0970
   chunk 28 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
** A1783 HIS ** 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 = 0.4350 r_free = 0.4350 target = 0.207972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.159465 restraints weight = 12428.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 5.27
r_work: 0.3313 rms_B_bonded: 5.19 restraints_weight: 2.0000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6786  Z= 0.122
  Angle     :  0.600  10.269   9210  Z= 0.293
  Chirality :  0.046   0.228   1089
  Planarity :  0.005   0.083   1125
  Dihedral  :  7.204 143.886    923
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.09 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.45 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.29), residues: 807
  helix:  0.33 (0.34), residues: 242
  sheet: -0.53 (0.41), residues: 162
  loop : -1.41 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2514 
 TYR   0.011   0.001   TYR A1992 
 PHE   0.046   0.002   PHE A2451 
 TRP   0.010   0.001   TRP A1811 
 HIS   0.004   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6786)
  covalent geometry    : angle       0.59982 ( 9210)
  hydrogen bonds       : bond        0.03279 (  237)
  hydrogen bonds       : angle       5.02496 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A 1735 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7329 (ttt180)
REVERT: A 2506 ASN cc_start: 0.8431 (m-40) cc_final: 0.8081 (m-40)
REVERT: A 2516 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7020 (mt-10)
  outliers start: 11
  outliers final: 8
  residues processed: 79
  average time/residue: 0.0821
  time to fit residues: 8.8944
Evaluate side-chains
  79 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1660 LEU
Chi-restraints excluded: chain A residue 1671 SER
Chi-restraints excluded: chain A residue 1735 ARG
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1922 VAL
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2472 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 74 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 7 optimal weight:    9.9990
   chunk 11 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0570
   overall best weight:    0.7498

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

Flipped N/Q/H residues before XYZ refinement:
** A1783 HIS ** 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 = 0.4353 r_free = 0.4353 target = 0.207865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.158154 restraints weight = 13013.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 5.38
r_work: 0.3287 rms_B_bonded: 5.14 restraints_weight: 2.0000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6786  Z= 0.154
  Angle     :  0.631   7.921   9210  Z= 0.310
  Chirality :  0.047   0.235   1089
  Planarity :  0.005   0.084   1125
  Dihedral  :  7.321 143.940    923
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.85 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.03 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.29), residues: 807
  helix:  0.33 (0.34), residues: 240
  sheet: -0.53 (0.41), residues: 162
  loop : -1.44 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1983 
 TYR   0.013   0.001   TYR A1992 
 PHE   0.011   0.001   PHE A1585 
 TRP   0.011   0.001   TRP A1811 
 HIS   0.006   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6786)
  covalent geometry    : angle       0.63100 ( 9210)
  hydrogen bonds       : bond        0.03397 (  237)
  hydrogen bonds       : angle       5.07466 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A 1735 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7289 (ttt180)
REVERT: A 2086 LEU cc_start: 0.7506 (pp) cc_final: 0.7151 (mp)
REVERT: A 2516 GLU cc_start: 0.7728 (mm-30) cc_final: 0.6992 (mt-10)
  outliers start: 10
  outliers final: 8
  residues processed: 79
  average time/residue: 0.0818
  time to fit residues: 8.8320
Evaluate side-chains
  81 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1660 LEU
Chi-restraints excluded: chain A residue 1671 SER
Chi-restraints excluded: chain A residue 1735 ARG
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1922 VAL
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2472 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 13 optimal weight:    6.9990
   chunk 61 optimal weight:    0.4980
   chunk 65 optimal weight:    0.8980
   chunk 69 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 70 optimal weight:   20.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A1783 HIS ** 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 = 0.4356 r_free = 0.4356 target = 0.208048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.157730 restraints weight = 14450.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 5.95
r_work: 0.3209 rms_B_bonded: 5.01 restraints_weight: 2.0000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6786  Z= 0.145
  Angle     :  0.620   7.875   9210  Z= 0.304
  Chirality :  0.047   0.234   1089
  Planarity :  0.005   0.083   1125
  Dihedral  :  7.316 143.980    923
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.85 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.18 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.29), residues: 807
  helix:  0.23 (0.34), residues: 246
  sheet: -0.49 (0.41), residues: 162
  loop : -1.46 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1983 
 TYR   0.014   0.001   TYR A1992 
 PHE   0.046   0.002   PHE A2451 
 TRP   0.011   0.001   TRP A1811 
 HIS   0.005   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6786)
  covalent geometry    : angle       0.62023 ( 9210)
  hydrogen bonds       : bond        0.03329 (  237)
  hydrogen bonds       : angle       5.02622 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A 1654 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: A 1735 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7234 (ttt180)
REVERT: A 2086 LEU cc_start: 0.7456 (pp) cc_final: 0.7128 (mp)
REVERT: A 2155 MET cc_start: 0.7325 (ptt) cc_final: 0.6775 (tmm)
REVERT: A 2516 GLU cc_start: 0.7670 (mm-30) cc_final: 0.6929 (mt-10)
  outliers start: 11
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0802
  time to fit residues: 8.9804
Evaluate side-chains
  84 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1660 LEU
Chi-restraints excluded: chain A residue 1671 SER
Chi-restraints excluded: chain A residue 1735 ARG
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1922 VAL
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2472 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0470
   chunk 52 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0170
   chunk 53 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0970
   chunk 29 optimal weight:    0.5980
   chunk 44 optimal weight:    0.3980
   chunk 70 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.2314

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

Flipped N/Q/H residues before XYZ refinement:
A1783 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.211608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.156874 restraints weight = 10096.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 6.30
r_work: 0.3168 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6786  Z= 0.102
  Angle     :  0.586  11.340   9210  Z= 0.289
  Chirality :  0.045   0.234   1089
  Planarity :  0.005   0.083   1125
  Dihedral  :  7.111 143.875    923
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.60 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.32 %
    Favored  : 87.23 %
  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: -0.94 (0.30), residues: 807
  helix:  0.38 (0.34), residues: 247
  sheet: -0.38 (0.42), residues: 169
  loop : -1.37 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1983 
 TYR   0.019   0.001   TYR A1992 
 PHE   0.010   0.001   PHE A2451 
 TRP   0.012   0.001   TRP A1705 
 HIS   0.003   0.001   HIS A1972 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 6786)
  covalent geometry    : angle       0.58607 ( 9210)
  hydrogen bonds       : bond        0.02937 (  237)
  hydrogen bonds       : angle       4.77849 (  684)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A 1735 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7039 (ttt180)
REVERT: A 2086 LEU cc_start: 0.7282 (pp) cc_final: 0.7050 (mp)
REVERT: A 2155 MET cc_start: 0.6893 (ptt) cc_final: 0.6411 (tmm)
REVERT: A 2506 ASN cc_start: 0.8184 (m-40) cc_final: 0.7775 (m-40)
REVERT: A 2516 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6818 (mt-10)
  outliers start: 9
  outliers final: 8
  residues processed: 85
  average time/residue: 0.0758
  time to fit residues: 9.1646
Evaluate side-chains
  85 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1660 LEU
Chi-restraints excluded: chain A residue 1671 SER
Chi-restraints excluded: chain A residue 1735 ARG
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1922 VAL
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2472 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 27 optimal weight:    0.0570
   chunk 68 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 1 optimal weight:    7.9990
   chunk 59 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0050
   chunk 79 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0010
   overall best weight:    0.2518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.209893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.171865 restraints weight = 18680.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 4.86
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4001 r_free = 0.4001    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4001 r_free = 0.4001    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6786  Z= 0.105
  Angle     :  0.589  10.607   9210  Z= 0.289
  Chirality :  0.045   0.243   1089
  Planarity :  0.005   0.082   1125
  Dihedral  :  7.072 143.768    923
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.85 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.76 %
    Favored  : 86.79 %
  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: -0.72 (0.30), residues: 807
  helix:  0.69 (0.34), residues: 239
  sheet: -0.30 (0.42), residues: 169
  loop : -1.27 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2514 
 TYR   0.018   0.001   TYR A1992 
 PHE   0.045   0.001   PHE A2451 
 TRP   0.012   0.001   TRP A1705 
 HIS   0.004   0.001   HIS A1972 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6786)
  covalent geometry    : angle       0.58897 ( 9210)
  hydrogen bonds       : bond        0.02956 (  237)
  hydrogen bonds       : angle       4.63375 (  684)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1926.89 seconds
wall clock time: 33 minutes 40.41 seconds (2020.41 seconds total)