Starting phenix.real_space_refine
on Sat Aug 23 16:57:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g6i_29770/08_2025/8g6i_29770_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g6i_29770/08_2025/8g6i_29770.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g6i_29770/08_2025/8g6i_29770.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g6i_29770/08_2025/8g6i_29770.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g6i_29770/08_2025/8g6i_29770_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g6i_29770/08_2025/8g6i_29770_neut.cif"
  }
  resolution = 4.23
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    8485      2.51       5
     N    2259      2.21       5
     O    2480      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13287
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 10005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1239, 10005
          Classifications: {'peptide': 1239}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 61, 'TRANS': 1177}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 1614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1614
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199}
    Chain: "C"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1612
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.47, per 1000 atoms: 0.19
  Number of scatterers: 13287
  At special positions: 0
  Unit cell: (84.316, 116.624, 204.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    2480      8.00
     N    2259      7.00
     C    8485      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS A 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 249 " - pdb=" SG  CYS A 330 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 528 " - pdb=" SG  CYS A 554 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 630 " - pdb=" SG  CYS A 711 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1832 " - pdb=" SG  CYS A1858 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2021 " - pdb=" SG  CYS A2169 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A2174 " - pdb=" SG  CYS A2326 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 144 " - pdb=" SG  CYS C 200 " 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
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 240 "
      " NAG E   1 " - " ASN A1810 "
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 519.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3108

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 23 sheets defined
      7.6% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 172
    Processing helix  chain 'A' and resid 407 through 411
      removed outlier: 3.703A  pdb=" N   GLN A 410 " --> pdb=" O   TYR A 407 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TYR A 411 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 407 through 411'
    Processing helix  chain 'A' and resid 516 through 520
      removed outlier: 3.919A  pdb=" N   ASP A 519 " --> pdb=" O   THR A 516 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLY A 520 " --> pdb=" O   VAL A 517 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 516 through 520'
    Processing helix  chain 'A' and resid 538 through 546
      removed outlier: 3.553A  pdb=" N   LEU A 543 " --> pdb=" O   MET A 539 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   ALA A 544 " --> pdb=" O   GLU A 540 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER A 545 " --> pdb=" O   ARG A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 595
      removed outlier: 4.235A  pdb=" N   GLN A 592 " --> pdb=" O   THR A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 601
      removed outlier: 3.920A  pdb=" N   GLY A 600 " --> pdb=" O   ASN A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 613
      removed outlier: 3.740A  pdb=" N   GLN A 609 " --> pdb=" O   ASP A 605 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ILE A 613 " --> pdb=" O   GLN A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1750 through 1754
    Processing helix  chain 'A' and resid 1820 through 1824
      removed outlier: 3.666A  pdb=" N   MET A1823 " --> pdb=" O   GLN A1820 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA A1824 " --> pdb=" O   HIS A1821 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1820 through 1824'
    Processing helix  chain 'A' and resid 1913 through 1917
    Processing helix  chain 'A' and resid 1949 through 1953
      removed outlier: 3.680A  pdb=" N   ASN A1952 " --> pdb=" O   SER A1949 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE A1953 " --> pdb=" O   ASN A1950 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1949 through 1953'
    Processing helix  chain 'A' and resid 2002 through 2007
    Processing helix  chain 'A' and resid 2047 through 2051
      removed outlier: 3.950A  pdb=" N   LEU A2050 " --> pdb=" O   ALA A2047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2186 through 2190
      removed outlier: 3.667A  pdb=" N   GLN A2189 " --> pdb=" O   SER A2186 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ILE A2190 " --> pdb=" O   ASP A2187 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2186 through 2190'
    Processing helix  chain 'A' and resid 2204 through 2208
      removed outlier: 3.539A  pdb=" N   ALA A2208 " --> pdb=" O   PRO A2205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 128
      removed outlier: 4.125A  pdb=" N   LEU B 125 " --> pdb=" O   SER B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 189
      removed outlier: 3.954A  pdb=" N   HIS B 189 " --> pdb=" O   ASP B 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 91
    Processing helix  chain 'C' and resid 131 through 136
    Processing helix  chain 'C' and resid 189 through 194
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51
      removed outlier: 3.693A  pdb=" N   VAL A  51 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL A  10 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A  86 " --> pdb=" O   ARG A   3 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   TYR A   5 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   THR A  88 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS A  90 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ALA A   9 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL A  85 " --> pdb=" O   TRP A 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 80
      removed outlier: 3.799A  pdb=" N   CYS A 180 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 203
      removed outlier: 4.335A  pdb=" N   MET A 232 " --> pdb=" O   PHE A 203 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 248
      removed outlier: 3.993A  pdb=" N   GLY A 248 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 260
    Processing sheet with id=AA6, first strand: chain 'A' and resid 533 through 534
      removed outlier: 4.220A  pdb=" N   TYR A 533 " --> pdb=" O   GLY A 549 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLY A 549 " --> pdb=" O   TYR A 533 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 649 through 650
      removed outlier: 3.665A  pdb=" N   LEU A 649 " --> pdb=" O   LEU A 670 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1701 through 1706
      removed outlier: 4.198A  pdb=" N   VAL A1703 " --> pdb=" O   VAL A1734 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A1734 " --> pdb=" O   VAL A1703 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1773 through 1774
      removed outlier: 3.855A  pdb=" N   VAL A1773 " --> pdb=" O   TYR A1815 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1836 through 1837
      removed outlier: 3.620A  pdb=" N   GLY A1853 " --> pdb=" O   TYR A1837 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1877 through 1878
      removed outlier: 4.408A  pdb=" N   LEU A1878 " --> pdb=" O   TYR A1943 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER A1964 " --> pdb=" O   GLU A1987 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1933 through 1934
      removed outlier: 4.142A  pdb=" N   MET A1934 " --> pdb=" O   LEU A2015 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2071 through 2074
      removed outlier: 3.966A  pdb=" N   ILE A2071 " --> pdb=" O   LEU A2151 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU A2151 " --> pdb=" O   ILE A2071 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A2149 " --> pdb=" O   VAL A2073 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   TYR A2148 " --> pdb=" O   SER A2106 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   SER A2106 " --> pdb=" O   TYR A2148 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   HIS A2152 " --> pdb=" O   ILE A2102 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ILE A2102 " --> pdb=" O   HIS A2152 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   THR A2154 " --> pdb=" O   GLN A2100 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   GLN A2100 " --> pdb=" O   THR A2154 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2071 through 2074
      removed outlier: 3.966A  pdb=" N   ILE A2071 " --> pdb=" O   LEU A2151 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU A2151 " --> pdb=" O   ILE A2071 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A2149 " --> pdb=" O   VAL A2073 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   TYR A2148 " --> pdb=" O   SER A2106 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   SER A2106 " --> pdb=" O   TYR A2148 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   HIS A2152 " --> pdb=" O   ILE A2102 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ILE A2102 " --> pdb=" O   HIS A2152 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   THR A2154 " --> pdb=" O   GLN A2100 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   GLN A2100 " --> pdb=" O   THR A2154 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A2101 " --> pdb=" O   PHE A2126 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE A2126 " --> pdb=" O   PHE A2101 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 2144 through 2145
      removed outlier: 3.865A  pdb=" N   HIS A2082 " --> pdb=" O   MET A2167 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   MET A2167 " --> pdb=" O   HIS A2082 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ILE A2084 " --> pdb=" O   GLU A2165 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   GLU A2165 " --> pdb=" O   ILE A2084 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 2089 through 2091
    Processing sheet with id=AB8, first strand: chain 'A' and resid 2293 through 2294
    Processing sheet with id=AB9, first strand: chain 'A' and resid 2260 through 2265
      removed outlier: 4.114A  pdb=" N   LEU A2261 " --> pdb=" O   HIS A2309 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   HIS A2309 " --> pdb=" O   LEU A2261 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   SER A2263 " --> pdb=" O   ARG A2307 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ARG A2307 " --> pdb=" O   SER A2263 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 2 through 3
      removed outlier: 6.753A  pdb=" N   ILE B   2 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'B' and resid 20 through 21
      removed outlier: 3.756A  pdb=" N   ILE B  21 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU B  73 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 33 through 34
      removed outlier: 3.876A  pdb=" N   LEU B  89 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 37
    Processing sheet with id=AC5, first strand: chain 'C' and resid 5 through 6

    94 hydrogen bonds defined for protein.
    195 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.01

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4246
        1.34 -     1.46: 3373
        1.46 -     1.58: 5919
        1.58 -     1.70: 0
        1.70 -     1.82: 100
  Bond restraints: 13638
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.546 -0.140 2.00e-02 2.50e+03 4.93e+01
  bond pdb=" CA  ASN A1915 "
       pdb=" C   ASN A1915 "
    ideal  model  delta    sigma   weight residual
    1.522  1.546 -0.023 1.38e-02 5.25e+03 2.89e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.26e+00
  bond pdb=" CA  PHE A1743 "
       pdb=" CB  PHE A1743 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 1.36e-02 5.41e+03 2.25e+00
  bond pdb=" CA  ILE A 553 "
       pdb=" CB  ILE A 553 "
    ideal  model  delta    sigma   weight residual
    1.532  1.548 -0.016 1.08e-02 8.57e+03 2.22e+00
  ... (remaining 13633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 17913
        1.72 -     3.43: 488
        3.43 -     5.15: 86
        5.15 -     6.87: 17
        6.87 -     8.59: 2
  Bond angle restraints: 18506
  Sorted by residual:
  angle pdb=" N   LYS A 124 "
        pdb=" CA  LYS A 124 "
        pdb=" C   LYS A 124 "
      ideal   model   delta    sigma   weight residual
     112.72  108.62    4.10 1.14e+00 7.69e-01 1.29e+01
  angle pdb=" C   PHE A 697 "
        pdb=" N   ARG A 698 "
        pdb=" CA  ARG A 698 "
      ideal   model   delta    sigma   weight residual
     121.54  128.02   -6.48 1.91e+00 2.74e-01 1.15e+01
  angle pdb=" N   ILE A 553 "
        pdb=" CA  ILE A 553 "
        pdb=" C   ILE A 553 "
      ideal   model   delta    sigma   weight residual
     106.42  111.47   -5.05 1.51e+00 4.39e-01 1.12e+01
  angle pdb=" C   VAL A1767 "
        pdb=" N   GLU A1768 "
        pdb=" CA  GLU A1768 "
      ideal   model   delta    sigma   weight residual
     121.54  127.68   -6.14 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" N   VAL C 167 "
        pdb=" CA  VAL C 167 "
        pdb=" C   VAL C 167 "
      ideal   model   delta    sigma   weight residual
     113.39  108.73    4.66 1.47e+00 4.63e-01 1.00e+01
  ... (remaining 18501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 7419
       17.83 -    35.67: 585
       35.67 -    53.50: 95
       53.50 -    71.33: 22
       71.33 -    89.16: 12
  Dihedral angle restraints: 8133
    sinusoidal: 3293
      harmonic: 4840
  Sorted by residual:
  dihedral pdb=" CB  CYS C 144 "
           pdb=" SG  CYS C 144 "
           pdb=" SG  CYS C 200 "
           pdb=" CB  CYS C 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.01  -80.01     1      1.00e+01 1.00e-02 7.93e+01
  dihedral pdb=" CB  CYS A2021 "
           pdb=" SG  CYS A2021 "
           pdb=" SG  CYS A2169 "
           pdb=" CB  CYS A2169 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -15.81  -70.19     1      1.00e+01 1.00e-02 6.35e+01
  dihedral pdb=" CA  GLU C  46 "
           pdb=" C   GLU C  46 "
           pdb=" N   TRP C  47 "
           pdb=" CA  TRP C  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.47   28.53     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 8130 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1771
       0.070 -    0.140: 244
       0.140 -    0.210: 4
       0.210 -    0.280: 0
       0.280 -    0.350: 3
  Chirality restraints: 2022
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 240 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A1810 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CB  ILE A 553 "
            pdb=" CA  ILE A 553 "
            pdb=" CG1 ILE A 553 "
            pdb=" CG2 ILE A 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.60e+00
  ... (remaining 2019 not shown)

  Planarity restraints: 2358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A2077 "    0.036 5.00e-02 4.00e+02   5.46e-02 4.77e+00
        pdb=" N   PRO A2078 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A2078 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A2078 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 415 "   -0.032 5.00e-02 4.00e+02   4.84e-02 3.75e+00
        pdb=" N   PRO A 416 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 416 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 416 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1929 "   -0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO A1930 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A1930 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A1930 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 2355 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 400
        2.69 -     3.25: 12686
        3.25 -     3.80: 18716
        3.80 -     4.35: 23523
        4.35 -     4.90: 37592
  Nonbonded interactions: 92917
  Sorted by model distance:
  nonbonded pdb=" O   ARG A  17 "
            pdb=" NH1 ARG A  17 "
     model   vdw
     2.143 3.120
  nonbonded pdb=" O   TRP A1996 "
            pdb=" OG1 THR A2013 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OH  TYR B  87 "
            pdb=" O   ALA C  43 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   LYS A1845 "
            pdb=" OG  SER A1849 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OE2 GLU A1704 "
            pdb=" OH  TYR A1890 "
     model   vdw
     2.232 3.040
  ... (remaining 92912 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
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.760
  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:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.800
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4372
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      :  0.003   0.140  13653  Z= 0.149
  Angle     :  0.689  10.156  18540  Z= 0.365
  Chirality :  0.046   0.350   2022
  Planarity :  0.005   0.055   2356
  Dihedral  : 13.130  89.164   4992
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.30 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    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 aren not related in a simple way.
  whole: -3.49 (0.18), residues: 1645
  helix: -3.17 (0.43), residues: 76
  sheet: -1.69 (0.45), residues: 139
  loop : -2.61 (0.14), residues: 1430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1813 
 TYR   0.017   0.002   TYR A 487 
 PHE   0.009   0.001   PHE A2014 
 TRP   0.016   0.001   TRP A 139 
 HIS   0.007   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (13638)
  covalent geometry    : angle       0.67911 (18506)
  SS BOND              : bond        0.00290 (   11)
  SS BOND              : angle       0.75410 (   22)
  hydrogen bonds       : bond        0.30881 (   91)
  hydrogen bonds       : angle      12.18001 (  195)
  link_BETA1-4         : bond        0.00674 (    2)
  link_BETA1-4         : angle       1.61653 (    6)
  link_NAG-ASN         : bond        0.01161 (    2)
  link_NAG-ASN         : angle       6.27109 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 HIS cc_start: 0.6855 (t70) cc_final: 0.5919 (p-80)
REVERT: A  308 LEU cc_start: 0.8588 (tp) cc_final: 0.8372 (tp)
REVERT: A  519 ASP cc_start: 0.8436 (t70) cc_final: 0.8140 (p0)
REVERT: A  589 GLU cc_start: 0.7027 (tt0) cc_final: 0.6816 (mp0)
REVERT: A  665 GLU cc_start: 0.6052 (tm-30) cc_final: 0.5538 (pm20)
REVERT: A  682 MET cc_start: 0.5048 (tmm) cc_final: 0.4046 (tpt)
REVERT: A 1926 MET cc_start: 0.2790 (mtp) cc_final: 0.2318 (mmp)
REVERT: A 2018 SER cc_start: 0.7109 (m) cc_final: 0.6788 (t)
REVERT: A 2118 ASN cc_start: 0.8415 (t0) cc_final: 0.8205 (t0)
REVERT: A 2222 GLN cc_start: 0.9052 (pt0) cc_final: 0.8770 (pt0)
REVERT: A 2254 SER cc_start: 0.7907 (p) cc_final: 0.7552 (t)
REVERT: B   78 LEU cc_start: 0.7066 (tt) cc_final: 0.6120 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.0949
  time to fit residues: 34.2302
Evaluate side-chains
  161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    0.0270
   chunk 91 optimal weight:    0.0050
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.5656

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
A 121 GLN
A 145 ASN
A 233 HIS
A 257 HIS
A 318 HIS
A1778 GLN
A1894 ASN
A1952 ASN
A1957 HIS
A2005 HIS
A2152 HIS
A2284 GLN
A2311 GLN
B  37 GLN
B 199 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4906 r_free = 0.4906 target = 0.163415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.146147 restraints weight = 86642.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.146046 restraints weight = 90100.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.146019 restraints weight = 86462.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.146058 restraints weight = 86888.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.146274 restraints weight = 81355.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.4618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4995
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13653  Z= 0.125
  Angle     :  0.634   9.526  18540  Z= 0.319
  Chirality :  0.046   0.327   2022
  Planarity :  0.005   0.065   2356
  Dihedral  :  5.190  56.184   1892
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.79 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.46 %
    Favored  : 95.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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 aren not related in a simple way.
  whole: -3.33 (0.18), residues: 1645
  helix: -2.72 (0.44), residues: 85
  sheet: -1.76 (0.41), residues: 155
  loop : -2.48 (0.15), residues: 1405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1749 
 TYR   0.018   0.001   TYR A2105 
 PHE   0.021   0.001   PHE A1743 
 TRP   0.026   0.001   TRP A 256 
 HIS   0.006   0.001   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (13638)
  covalent geometry    : angle       0.62142 (18506)
  SS BOND              : bond        0.00393 (   11)
  SS BOND              : angle       2.14844 (   22)
  hydrogen bonds       : bond        0.03916 (   91)
  hydrogen bonds       : angle       8.70615 (  195)
  link_BETA1-4         : bond        0.00913 (    2)
  link_BETA1-4         : angle       1.47934 (    6)
  link_NAG-ASN         : bond        0.01402 (    2)
  link_NAG-ASN         : angle       5.54684 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 194
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.4792 (m-10) cc_final: 0.4585 (m-80)
REVERT: A   46 LEU cc_start: 0.8174 (mt) cc_final: 0.7970 (mp)
REVERT: A  232 MET cc_start: 0.6117 (pmm) cc_final: 0.5745 (mpp)
REVERT: A  282 HIS cc_start: 0.5906 (t70) cc_final: 0.5488 (t-90)
REVERT: A  589 GLU cc_start: 0.7130 (tt0) cc_final: 0.6844 (mp0)
REVERT: A  614 MET cc_start: 0.7748 (pmm) cc_final: 0.7376 (pmm)
REVERT: A  702 MET cc_start: 0.2749 (ptp) cc_final: 0.1776 (ptp)
REVERT: A 1711 MET cc_start: -0.2129 (mmt) cc_final: -0.2495 (mmt)
REVERT: A 1926 MET cc_start: 0.2728 (mtp) cc_final: 0.2360 (mmp)
REVERT: A 2118 ASN cc_start: 0.8659 (t0) cc_final: 0.8242 (t0)
REVERT: B   70 ASP cc_start: 0.8043 (m-30) cc_final: 0.7224 (t70)
  outliers start: 2
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0896
  time to fit residues: 26.4420
Evaluate side-chains
  145 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 137 optimal weight:   20.0000
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0980
   chunk 110 optimal weight:   20.0000
   chunk 59 optimal weight:   10.0000
   chunk 119 optimal weight:   10.0000
   overall best weight:    3.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 ASN
A 609 GLN
A 693 HIS
** A1777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1778 GLN
** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1954 HIS
A2031 HIS
** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.152833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.134837 restraints weight = 83352.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.134390 restraints weight = 82414.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.134309 restraints weight = 84532.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.134612 restraints weight = 82648.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.135001 restraints weight = 76176.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.4474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5299
moved from start:          0.3683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  13653  Z= 0.225
  Angle     :  0.788  11.637  18540  Z= 0.403
  Chirality :  0.050   0.324   2022
  Planarity :  0.006   0.074   2356
  Dihedral  :  7.126  98.657   1892
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 20.34
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 12.28 %
    Favored  : 87.54 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  6.10 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    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 aren not related in a simple way.
  whole: -3.54 (0.18), residues: 1645
  helix: -2.56 (0.43), residues: 90
  sheet: -2.22 (0.37), residues: 200
  loop : -2.61 (0.15), residues: 1355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  17 
 TYR   0.030   0.002   TYR A 395 
 PHE   0.020   0.003   PHE A2014 
 TRP   0.038   0.003   TRP A 256 
 HIS   0.014   0.002   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (13638)
  covalent geometry    : angle       0.77545 (18506)
  SS BOND              : bond        0.00665 (   11)
  SS BOND              : angle       2.06879 (   22)
  hydrogen bonds       : bond        0.04327 (   91)
  hydrogen bonds       : angle       8.81919 (  195)
  link_BETA1-4         : bond        0.01127 (    2)
  link_BETA1-4         : angle       1.27579 (    6)
  link_NAG-ASN         : bond        0.04096 (    2)
  link_NAG-ASN         : angle       6.99598 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7880 (pt) cc_final: 0.7424 (tt)
REVERT: A  232 MET cc_start: 0.6180 (pmm) cc_final: 0.5646 (mpp)
REVERT: A  282 HIS cc_start: 0.6548 (t70) cc_final: 0.5991 (p-80)
REVERT: A  308 LEU cc_start: 0.8759 (tp) cc_final: 0.8436 (tp)
REVERT: A  682 MET cc_start: 0.5144 (tmm) cc_final: 0.4777 (tpt)
REVERT: A 1711 MET cc_start: -0.2787 (mmt) cc_final: -0.3056 (mmt)
REVERT: A 1926 MET cc_start: 0.3226 (mtp) cc_final: 0.2965 (mmm)
REVERT: A 1973 MET cc_start: 0.7119 (pmm) cc_final: 0.6565 (pmm)
REVERT: A 2118 ASN cc_start: 0.8780 (t0) cc_final: 0.8377 (t0)
REVERT: A 2167 MET cc_start: 0.6948 (tmm) cc_final: 0.6247 (tmm)
  outliers start: 1
  outliers final: 1
  residues processed: 186
  average time/residue: 0.0964
  time to fit residues: 26.5617
Evaluate side-chains
  132 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 69 optimal weight:    0.4980
   chunk 144 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 155 optimal weight:    8.9990
   chunk 137 optimal weight:   20.0000
   chunk 65 optimal weight:    0.6980
   chunk 104 optimal weight:    0.3980
   chunk 44 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 615 HIS
A1777 ASN
A1778 GLN
** A1922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1950 ASN
** A1954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2152 HIS
A2311 GLN
C  35 HIS
C 175 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4840 r_free = 0.4840 target = 0.157487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.140732 restraints weight = 85542.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.140295 restraints weight = 96601.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.140589 restraints weight = 89806.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.140639 restraints weight = 83266.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.140690 restraints weight = 80901.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.4548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5262
moved from start:          0.3897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13653  Z= 0.117
  Angle     :  0.647  10.074  18540  Z= 0.323
  Chirality :  0.046   0.335   2022
  Planarity :  0.005   0.054   2356
  Dihedral  :  6.457  95.645   1892
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.97 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    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 aren not related in a simple way.
  whole: -3.42 (0.18), residues: 1645
  helix: -2.47 (0.47), residues: 84
  sheet: -1.97 (0.38), residues: 183
  loop : -2.55 (0.15), residues: 1378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  27 
 TYR   0.020   0.001   TYR A1783 
 PHE   0.025   0.002   PHE A2274 
 TRP   0.014   0.001   TRP A1942 
 HIS   0.018   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (13638)
  covalent geometry    : angle       0.63269 (18506)
  SS BOND              : bond        0.00745 (   11)
  SS BOND              : angle       1.96231 (   22)
  hydrogen bonds       : bond        0.02893 (   91)
  hydrogen bonds       : angle       7.86631 (  195)
  link_BETA1-4         : bond        0.00906 (    2)
  link_BETA1-4         : angle       1.43049 (    6)
  link_NAG-ASN         : bond        0.01316 (    2)
  link_NAG-ASN         : angle       6.56764 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.2593 (mpp) cc_final: 0.2224 (mpp)
REVERT: A  162 HIS cc_start: 0.6993 (m90) cc_final: 0.5905 (m-70)
REVERT: A  232 MET cc_start: 0.6342 (pmm) cc_final: 0.5664 (mpp)
REVERT: A  282 HIS cc_start: 0.6288 (t70) cc_final: 0.5736 (p-80)
REVERT: A  665 GLU cc_start: 0.8008 (pp20) cc_final: 0.6381 (pm20)
REVERT: A  696 ASP cc_start: 0.8056 (p0) cc_final: 0.7571 (p0)
REVERT: A 1711 MET cc_start: -0.1919 (mmt) cc_final: -0.2292 (mmt)
REVERT: A 1851 LEU cc_start: 0.7038 (mt) cc_final: 0.6809 (mt)
REVERT: A 1973 MET cc_start: 0.7643 (pmm) cc_final: 0.6972 (pmm)
REVERT: A 2007 GLN cc_start: 0.7635 (pt0) cc_final: 0.7236 (pt0)
REVERT: A 2118 ASN cc_start: 0.8569 (t0) cc_final: 0.8185 (t0)
REVERT: A 2167 MET cc_start: 0.6216 (tmm) cc_final: 0.5773 (tmm)
REVERT: A 2180 MET cc_start: 0.6226 (mmp) cc_final: 0.5994 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0933
  time to fit residues: 24.2566
Evaluate side-chains
  131 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 129 optimal weight:   10.0000
   chunk 131 optimal weight:   10.0000
   chunk 92 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 99 optimal weight:    8.9990
   chunk 77 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 136 optimal weight:   50.0000
   chunk 122 optimal weight:    0.0020
   overall best weight:    3.9794

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
A1770 ASN
A1778 GLN
A1870 GLN
** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2031 HIS
** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2138 ASN
** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2286 ASN
A2311 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.148594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.128373 restraints weight = 82449.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.129101 restraints weight = 73021.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.129482 restraints weight = 66746.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.130112 restraints weight = 63015.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.130112 restraints weight = 59767.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5496
moved from start:          0.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  13653  Z= 0.225
  Angle     :  0.809  10.564  18540  Z= 0.417
  Chirality :  0.051   0.345   2022
  Planarity :  0.006   0.068   2356
  Dihedral  :  7.678 109.626   1892
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 25.18
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 13.68 %
    Favored  : 86.02 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  5.35 %
    Favored  : 94.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    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 aren not related in a simple way.
  whole: -3.72 (0.18), residues: 1645
  helix: -2.77 (0.45), residues: 85
  sheet: -2.37 (0.34), residues: 220
  loop : -2.73 (0.15), residues: 1340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1749 
 TYR   0.029   0.003   TYR A 395 
 PHE   0.027   0.003   PHE A 671 
 TRP   0.024   0.003   TRP A 139 
 HIS   0.009   0.002   HIS A1755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (13638)
  covalent geometry    : angle       0.80064 (18506)
  SS BOND              : bond        0.00749 (   11)
  SS BOND              : angle       1.81245 (   22)
  hydrogen bonds       : bond        0.04040 (   91)
  hydrogen bonds       : angle       8.64719 (  195)
  link_BETA1-4         : bond        0.01339 (    2)
  link_BETA1-4         : angle       1.39576 (    6)
  link_NAG-ASN         : bond        0.01409 (    2)
  link_NAG-ASN         : angle       5.41407 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.2315 (mpp) cc_final: 0.1937 (mpp)
REVERT: A  232 MET cc_start: 0.6059 (pmm) cc_final: 0.5692 (pmm)
REVERT: A  273 GLU cc_start: 0.8698 (pp20) cc_final: 0.7906 (mp0)
REVERT: A  282 HIS cc_start: 0.6633 (t70) cc_final: 0.6131 (t-90)
REVERT: A  308 LEU cc_start: 0.8907 (tp) cc_final: 0.8196 (tp)
REVERT: A  658 PHE cc_start: 0.5051 (p90) cc_final: 0.4829 (p90)
REVERT: A  682 MET cc_start: 0.5388 (tmm) cc_final: 0.4733 (tpt)
REVERT: A  696 ASP cc_start: 0.7287 (p0) cc_final: 0.7041 (p0)
REVERT: A 1711 MET cc_start: -0.2093 (mmt) cc_final: -0.2307 (mmt)
REVERT: A 1852 ILE cc_start: 0.8028 (mt) cc_final: 0.7691 (mt)
REVERT: A 1926 MET cc_start: 0.1875 (mtt) cc_final: 0.1144 (mtt)
REVERT: A 1973 MET cc_start: 0.7378 (pmm) cc_final: 0.6420 (pmm)
REVERT: A 2007 GLN cc_start: 0.8075 (pt0) cc_final: 0.7605 (pt0)
REVERT: A 2104 MET cc_start: 0.4796 (tmm) cc_final: 0.4558 (tmm)
REVERT: A 2118 ASN cc_start: 0.8529 (t0) cc_final: 0.8204 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0927
  time to fit residues: 21.8718
Evaluate side-chains
  124 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 107 optimal weight:    0.6980
   chunk 56 optimal weight:    8.9990
   chunk 119 optimal weight:    8.9990
   chunk 147 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 170 ASN
A 316 HIS
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1778 GLN
A1822 HIS
** A1922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2031 HIS
A2129 ASN
** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2311 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.150062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.132192 restraints weight = 88970.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.133111 restraints weight = 76366.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.133883 restraints weight = 67621.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.134416 restraints weight = 61291.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.134915 restraints weight = 56770.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.4468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5335
moved from start:          0.5534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13653  Z= 0.159
  Angle     :  0.693  10.580  18540  Z= 0.355
  Chirality :  0.048   0.347   2022
  Planarity :  0.005   0.056   2356
  Dihedral  :  7.551 111.100   1892
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 11.85 %
    Favored  : 87.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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 aren not related in a simple way.
  whole: -3.72 (0.18), residues: 1645
  helix: -2.50 (0.48), residues: 78
  sheet: -2.51 (0.35), residues: 203
  loop : -2.72 (0.15), residues: 1364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1749 
 TYR   0.019   0.002   TYR A1976 
 PHE   0.022   0.002   PHE A  52 
 TRP   0.026   0.002   TRP A2229 
 HIS   0.007   0.001   HIS A1755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (13638)
  covalent geometry    : angle       0.68259 (18506)
  SS BOND              : bond        0.00467 (   11)
  SS BOND              : angle       2.16822 (   22)
  hydrogen bonds       : bond        0.03073 (   91)
  hydrogen bonds       : angle       8.13734 (  195)
  link_BETA1-4         : bond        0.00992 (    2)
  link_BETA1-4         : angle       1.21899 (    6)
  link_NAG-ASN         : bond        0.01420 (    2)
  link_NAG-ASN         : angle       5.37883 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7498 (pp) cc_final: 0.7298 (tp)
REVERT: A   92 MET cc_start: 0.1923 (mpp) cc_final: 0.1391 (mpp)
REVERT: A  232 MET cc_start: 0.5991 (pmm) cc_final: 0.5652 (pmm)
REVERT: A  273 GLU cc_start: 0.8655 (pp20) cc_final: 0.7809 (mp0)
REVERT: A  282 HIS cc_start: 0.6727 (t70) cc_final: 0.6249 (t-90)
REVERT: A  308 LEU cc_start: 0.8939 (tp) cc_final: 0.8077 (tp)
REVERT: A  428 PHE cc_start: 0.7617 (t80) cc_final: 0.7075 (t80)
REVERT: A  665 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6296 (pm20)
REVERT: A  696 ASP cc_start: 0.7573 (p0) cc_final: 0.7341 (p0)
REVERT: A 1711 MET cc_start: -0.1755 (mmt) cc_final: -0.2010 (mmt)
REVERT: A 1921 ILE cc_start: 0.4788 (mp) cc_final: 0.4526 (mm)
REVERT: A 1926 MET cc_start: 0.1860 (mtt) cc_final: 0.1410 (mtt)
REVERT: A 1947 MET cc_start: 0.6376 (mmm) cc_final: 0.6156 (mmm)
REVERT: A 2007 GLN cc_start: 0.8008 (pt0) cc_final: 0.7621 (pt0)
REVERT: A 2104 MET cc_start: 0.4758 (tmm) cc_final: 0.4491 (tmm)
REVERT: A 2118 ASN cc_start: 0.8298 (t0) cc_final: 0.8045 (t0)
REVERT: A 2167 MET cc_start: 0.6516 (tmm) cc_final: 0.6124 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1078
  time to fit residues: 27.3990
Evaluate side-chains
  126 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 150 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 135 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 110 optimal weight:   20.0000
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 HIS
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 632 HIS
A 660 HIS
A1755 HIS
A1778 GLN
A1977 ASN
A2031 HIS
** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2311 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.147179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.128181 restraints weight = 84473.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.128741 restraints weight = 77243.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.129245 restraints weight = 71723.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.129729 restraints weight = 67806.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.129898 restraints weight = 64404.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.4410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5424
moved from start:          0.6264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  13653  Z= 0.186
  Angle     :  0.761  11.198  18540  Z= 0.388
  Chirality :  0.050   0.391   2022
  Planarity :  0.006   0.055   2356
  Dihedral  :  7.778 110.823   1892
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 21.37
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 14.53 %
    Favored  : 85.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    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 aren not related in a simple way.
  whole: -3.88 (0.18), residues: 1645
  helix: -2.64 (0.46), residues: 84
  sheet: -2.70 (0.33), residues: 223
  loop : -2.81 (0.15), residues: 1338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  17 
 TYR   0.024   0.002   TYR A1976 
 PHE   0.017   0.002   PHE B  98 
 TRP   0.026   0.002   TRP C 110 
 HIS   0.005   0.001   HIS A1755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (13638)
  covalent geometry    : angle       0.75297 (18506)
  SS BOND              : bond        0.00553 (   11)
  SS BOND              : angle       1.68911 (   22)
  hydrogen bonds       : bond        0.03539 (   91)
  hydrogen bonds       : angle       8.29418 (  195)
  link_BETA1-4         : bond        0.00949 (    2)
  link_BETA1-4         : angle       1.25645 (    6)
  link_NAG-ASN         : bond        0.01258 (    2)
  link_NAG-ASN         : angle       5.21041 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 MET cc_start: 0.5920 (pmm) cc_final: 0.5537 (pmm)
REVERT: A  273 GLU cc_start: 0.8600 (pp20) cc_final: 0.7824 (mp0)
REVERT: A  282 HIS cc_start: 0.6787 (t70) cc_final: 0.6306 (p-80)
REVERT: A  308 LEU cc_start: 0.8782 (tp) cc_final: 0.8025 (tp)
REVERT: A  428 PHE cc_start: 0.7631 (t80) cc_final: 0.6977 (t80)
REVERT: A  696 ASP cc_start: 0.7324 (p0) cc_final: 0.7116 (p0)
REVERT: A 1926 MET cc_start: 0.1792 (mtt) cc_final: 0.0904 (mtm)
REVERT: A 1988 MET cc_start: 0.0341 (ptt) cc_final: 0.0133 (ptt)
REVERT: A 2007 GLN cc_start: 0.8147 (pt0) cc_final: 0.7741 (pt0)
REVERT: A 2118 ASN cc_start: 0.8401 (t0) cc_final: 0.8145 (t0)
REVERT: A 2124 MET cc_start: 0.4086 (pmm) cc_final: 0.3880 (pmm)
REVERT: A 2281 LYS cc_start: 0.7930 (ptmm) cc_final: 0.7582 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1029
  time to fit residues: 24.9330
Evaluate side-chains
  126 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0030
   chunk 132 optimal weight:    7.9990
   chunk 128 optimal weight:    0.1980
   chunk 85 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 117 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9990
   chunk 161 optimal weight:    0.0370
   overall best weight:    1.2472

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

Flipped N/Q/H residues before XYZ refinement:
A 384 HIS
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
A1778 GLN
** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2284 GLN
A2311 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.149979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.131991 restraints weight = 86396.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.132650 restraints weight = 72878.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.133748 restraints weight = 65172.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.134360 restraints weight = 58237.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.134938 restraints weight = 53229.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.4483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5208
moved from start:          0.6248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13653  Z= 0.125
  Angle     :  0.692  10.624  18540  Z= 0.347
  Chirality :  0.049   0.355   2022
  Planarity :  0.005   0.068   2356
  Dihedral  :  7.429 111.477   1892
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 11.73 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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 aren not related in a simple way.
  whole: -3.75 (0.18), residues: 1645
  helix: -2.48 (0.46), residues: 90
  sheet: -2.57 (0.35), residues: 198
  loop : -2.74 (0.15), residues: 1357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2052 
 TYR   0.016   0.001   TYR A1762 
 PHE   0.024   0.002   PHE A2283 
 TRP   0.018   0.002   TRP A1835 
 HIS   0.008   0.001   HIS A 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (13638)
  covalent geometry    : angle       0.68247 (18506)
  SS BOND              : bond        0.00352 (   11)
  SS BOND              : angle       1.67586 (   22)
  hydrogen bonds       : bond        0.02817 (   91)
  hydrogen bonds       : angle       7.62378 (  195)
  link_BETA1-4         : bond        0.00813 (    2)
  link_BETA1-4         : angle       1.48691 (    6)
  link_NAG-ASN         : bond        0.01267 (    2)
  link_NAG-ASN         : angle       5.39706 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7776 (pp) cc_final: 0.7445 (tp)
REVERT: A  232 MET cc_start: 0.5978 (pmm) cc_final: 0.5624 (pmm)
REVERT: A  273 GLU cc_start: 0.8575 (pp20) cc_final: 0.7774 (mp0)
REVERT: A  282 HIS cc_start: 0.6754 (t70) cc_final: 0.6354 (p-80)
REVERT: A  308 LEU cc_start: 0.8885 (tp) cc_final: 0.7903 (tp)
REVERT: A  428 PHE cc_start: 0.7451 (t80) cc_final: 0.7021 (t80)
REVERT: A 1921 ILE cc_start: 0.4413 (mp) cc_final: 0.4139 (mm)
REVERT: A 1956 ILE cc_start: 0.6713 (mm) cc_final: 0.6502 (mm)
REVERT: A 2007 GLN cc_start: 0.7949 (pt0) cc_final: 0.7630 (pt0)
REVERT: A 2167 MET cc_start: 0.6669 (tmm) cc_final: 0.6011 (tmm)
REVERT: B    4 MET cc_start: 0.6811 (ptt) cc_final: 0.6552 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0982
  time to fit residues: 24.9379
Evaluate side-chains
  129 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 143 optimal weight:    1.9990
   chunk 99 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9980
   chunk 112 optimal weight:   10.0000
   chunk 126 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 139 optimal weight:    8.9990
   chunk 100 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   chunk 104 optimal weight:    8.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 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 = 0.4761 r_free = 0.4761 target = 0.149894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.132446 restraints weight = 89771.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.133446 restraints weight = 76256.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.134179 restraints weight = 67042.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.134808 restraints weight = 60445.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.135311 restraints weight = 55515.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5240
moved from start:          0.6296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  13653  Z= 0.121
  Angle     :  0.690  12.606  18540  Z= 0.340
  Chirality :  0.049   0.349   2022
  Planarity :  0.005   0.061   2356
  Dihedral  :  7.237 110.176   1892
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 11.61 %
    Favored  : 88.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    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 aren not related in a simple way.
  whole: -3.63 (0.18), residues: 1645
  helix: -2.36 (0.49), residues: 84
  sheet: -2.52 (0.36), residues: 185
  loop : -2.66 (0.15), residues: 1376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2052 
 TYR   0.011   0.001   TYR A1976 
 PHE   0.018   0.002   PHE A  60 
 TRP   0.013   0.001   TRP A  14 
 HIS   0.014   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13638)
  covalent geometry    : angle       0.68205 (18506)
  SS BOND              : bond        0.00297 (   11)
  SS BOND              : angle       1.50669 (   22)
  hydrogen bonds       : bond        0.02738 (   91)
  hydrogen bonds       : angle       7.44484 (  195)
  link_BETA1-4         : bond        0.00986 (    2)
  link_BETA1-4         : angle       1.14015 (    6)
  link_NAG-ASN         : bond        0.01234 (    2)
  link_NAG-ASN         : angle       5.30697 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7967 (pp) cc_final: 0.7598 (tp)
REVERT: A   92 MET cc_start: 0.3033 (mpp) cc_final: 0.2830 (mpp)
REVERT: A  232 MET cc_start: 0.5922 (pmm) cc_final: 0.5519 (pmm)
REVERT: A  273 GLU cc_start: 0.8552 (pp20) cc_final: 0.7771 (mp0)
REVERT: A  282 HIS cc_start: 0.6719 (t70) cc_final: 0.6284 (p-80)
REVERT: A  308 LEU cc_start: 0.8904 (tp) cc_final: 0.7929 (tp)
REVERT: A  428 PHE cc_start: 0.7478 (t80) cc_final: 0.6996 (t80)
REVERT: A 1956 ILE cc_start: 0.6707 (mm) cc_final: 0.6464 (mm)
REVERT: A 2007 GLN cc_start: 0.7934 (pt0) cc_final: 0.7620 (pt0)
REVERT: A 2167 MET cc_start: 0.6657 (tmm) cc_final: 0.5965 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1117
  time to fit residues: 28.2853
Evaluate side-chains
  128 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 76 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 115 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 111 optimal weight:   20.0000
   chunk 43 optimal weight:    3.9990
   chunk 131 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2031 HIS
** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 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 = 0.4729 r_free = 0.4729 target = 0.147244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.129308 restraints weight = 87333.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.130282 restraints weight = 73748.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.131067 restraints weight = 64838.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.131705 restraints weight = 58277.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.131933 restraints weight = 53462.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5406
moved from start:          0.6774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13653  Z= 0.163
  Angle     :  0.746  13.535  18540  Z= 0.373
  Chirality :  0.050   0.361   2022
  Planarity :  0.006   0.059   2356
  Dihedral  :  7.207 104.355   1892
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 13.50 %
    Favored  : 86.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    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 aren not related in a simple way.
  whole: -3.76 (0.18), residues: 1645
  helix: -2.55 (0.44), residues: 96
  sheet: -2.49 (0.36), residues: 196
  loop : -2.76 (0.15), residues: 1353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1749 
 TYR   0.018   0.002   TYR A1976 
 PHE   0.024   0.002   PHE A  52 
 TRP   0.023   0.002   TRP C  47 
 HIS   0.006   0.001   HIS A1755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (13638)
  covalent geometry    : angle       0.73618 (18506)
  SS BOND              : bond        0.00443 (   11)
  SS BOND              : angle       1.58216 (   22)
  hydrogen bonds       : bond        0.03277 (   91)
  hydrogen bonds       : angle       7.72878 (  195)
  link_BETA1-4         : bond        0.01262 (    2)
  link_BETA1-4         : angle       0.99730 (    6)
  link_NAG-ASN         : bond        0.01679 (    2)
  link_NAG-ASN         : angle       6.00737 (    6)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.3268 (mpp) cc_final: 0.2836 (mpp)
REVERT: A  232 MET cc_start: 0.5898 (pmm) cc_final: 0.5471 (pmm)
REVERT: A  273 GLU cc_start: 0.8614 (pp20) cc_final: 0.7796 (mp0)
REVERT: A  282 HIS cc_start: 0.6733 (t70) cc_final: 0.6356 (p-80)
REVERT: A  308 LEU cc_start: 0.8971 (tp) cc_final: 0.8137 (tp)
REVERT: A  428 PHE cc_start: 0.7364 (t80) cc_final: 0.7151 (t80)
REVERT: A 2007 GLN cc_start: 0.8111 (pt0) cc_final: 0.7734 (pt0)
REVERT: A 2167 MET cc_start: 0.6923 (tmm) cc_final: 0.6196 (tmm)
REVERT: A 2255 MET cc_start: 0.3060 (ptm) cc_final: 0.2740 (ptp)
REVERT: B    4 MET cc_start: 0.7127 (ptt) cc_final: 0.6906 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1079
  time to fit residues: 25.7186
Evaluate side-chains
  128 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 136 optimal weight:   30.0000
   chunk 87 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 145 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 112 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0370
   chunk 45 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.5662

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

Flipped N/Q/H residues before XYZ refinement:
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 684 ASN
** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2031 HIS
** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 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 = 0.4748 r_free = 0.4748 target = 0.148710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.131370 restraints weight = 87362.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.132211 restraints weight = 80257.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.132422 restraints weight = 73538.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.133130 restraints weight = 67315.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.133462 restraints weight = 60972.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.4451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5374
moved from start:          0.6823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13653  Z= 0.125
  Angle     :  0.703  12.509  18540  Z= 0.347
  Chirality :  0.048   0.360   2022
  Planarity :  0.005   0.061   2356
  Dihedral  :  6.967 101.677   1892
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.64 %
    Favored  : 87.05 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.34 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.66 %
    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 aren not related in a simple way.
  whole: -3.71 (0.18), residues: 1645
  helix: -2.50 (0.45), residues: 96
  sheet: -2.39 (0.37), residues: 195
  loop : -2.74 (0.15), residues: 1354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 531 
 TYR   0.017   0.001   TYR C  53 
 PHE   0.017   0.002   PHE A  60 
 TRP   0.015   0.002   TRP A 139 
 HIS   0.004   0.001   HIS A 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (13638)
  covalent geometry    : angle       0.69327 (18506)
  SS BOND              : bond        0.00331 (   11)
  SS BOND              : angle       1.53353 (   22)
  hydrogen bonds       : bond        0.02892 (   91)
  hydrogen bonds       : angle       7.38649 (  195)
  link_BETA1-4         : bond        0.01014 (    2)
  link_BETA1-4         : angle       1.19290 (    6)
  link_NAG-ASN         : bond        0.01567 (    2)
  link_NAG-ASN         : angle       5.94281 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2203.20 seconds
wall clock time: 38 minutes 57.64 seconds (2337.64 seconds total)