Starting phenix.real_space_refine
on Thu Jul  2 22:28:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/12jv_76497/07_2026/12jv_76497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/12jv_76497/07_2026/12jv_76497.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/12jv_76497/07_2026/12jv_76497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/12jv_76497/07_2026/12jv_76497.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/12jv_76497/07_2026/12jv_76497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/12jv_76497/07_2026/12jv_76497.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.030
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     Cu      2      5.60       5
     S      56      5.16       5
     C    6523      2.51       5
     N    1719      2.21       5
     O    1844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10145
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1247, 10100
          Classifications: {'peptide': 1247}
          Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1184}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 42
          Ad-hoc single atom residues: {' CA': 1, ' CU': 2}
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2127  SG  CYS A 310      41.204  56.154  95.117  1.00115.72           S

  Time building chain proxies: 2.11, per 1000 atoms: 0.21
  Number of scatterers: 10145
  At special positions: 0
  Unit cell: (81.664, 94.656, 138.272, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cu      2     28.99
     Ca      1     19.99
     S      56     16.00
     O    1844      8.00
     N    1719      7.00
     C    6523      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 153 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 248 " - pdb=" SG  CYS A 329 " 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 A1899 " - pdb=" SG  CYS A1903 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2021 " - pdb=" SG  CYS A2169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2174 " - pdb=" SG  CYS A2326 " 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
    NAG-ASN
      " NAG A2401 " - " ASN A2118 "
      " NAG A2402 " - " ASN A1810 "
      " NAG A2403 " - " ASN A 239 "
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 358.2 milliseconds
  

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2338

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 20 sheets defined
      8.5% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 124
      removed outlier: 3.910A  pdb=" N   GLU A 124 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 170
      removed outlier: 3.856A  pdb=" N   ASN A 169 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'A' and resid 203 through 208
      removed outlier: 4.245A  pdb=" N   TRP A 208 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 497 through 501
    Processing helix  chain 'A' and resid 538 through 544
    Processing helix  chain 'A' and resid 586 through 594
    Processing helix  chain 'A' and resid 605 through 613
    Processing helix  chain 'A' and resid 694 through 699
      removed outlier: 3.854A  pdb=" N   ARG A 698 " --> pdb=" O   ASN A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1721 through 1725
      removed outlier: 3.736A  pdb=" N   SER A1724 " --> pdb=" O   ARG A1721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1820 through 1824
    Processing helix  chain 'A' and resid 1842 through 1849
    Processing helix  chain 'A' and resid 1890 through 1897
    Processing helix  chain 'A' and resid 1908 through 1915
      removed outlier: 3.581A  pdb=" N   PHE A1912 " --> pdb=" O   GLU A1908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2002 through 2007
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 13
    Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 78
      removed outlier: 3.728A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89
      removed outlier: 3.609A  pdb=" N   LEU A  88 " --> pdb=" O   HIS A 134 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 197
      removed outlier: 7.200A  pdb=" N   LEU A 197 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 269
    Processing sheet with id=AA7, first strand: chain 'A' and resid 381 through 384
      removed outlier: 6.319A  pdb=" N   TRP A 382 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   ILE A 464 " --> pdb=" O   TRP A 382 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   HIS A 384 " --> pdb=" O   ILE A 464 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   LYS A 466 " --> pdb=" O   HIS A 384 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 390 through 393
      removed outlier: 4.142A  pdb=" N   GLU A 391 " --> pdb=" O   LYS A 425 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS A 425 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 456
      removed outlier: 6.712A  pdb=" N   LEU A 453 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   CYS A 554 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   GLY A 455 " --> pdb=" O   CYS A 554 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLY A 549 " --> pdb=" O   TYR A 533 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   TYR A 533 " --> pdb=" O   GLY A 549 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER A 534 " --> pdb=" O   TYR A 476 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 614 through 615
      removed outlier: 3.671A  pdb=" N   LEU A 640 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE A 642 " --> pdb=" O   PHE A 576 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   TRP A 637 " --> pdb=" O   VAL A 678 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 658 through 660
    Processing sheet with id=AB3, first strand: chain 'A' and resid 689 through 690
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1733 through 1738
      removed outlier: 4.111A  pdb=" N   PHE A1699 " --> pdb=" O   PHE A1738 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   ILE A1700 " --> pdb=" O   ARG A1776 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ASP A1769 " --> pdb=" O   VAL A1819 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE A1771 " --> pdb=" O   TRP A1817 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE A1775 " --> pdb=" O   LYS A1813 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1832 through 1833
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1837 through 1838
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1919 through 1920
      removed outlier: 3.654A  pdb=" N   LEU A1944 " --> pdb=" O   GLU A1984 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLU A1984 " --> pdb=" O   LEU A1944 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR A1971 " --> pdb=" O   VAL A1965 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1933 through 1935
      removed outlier: 4.391A  pdb=" N   ARG A1997 " --> pdb=" O   SER A1959 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 2037 through 2039
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 2071 through 2085
    current: chain 'A' and resid 2113 through 2114
    Processing sheet with id=AC1, first strand: chain 'A' and resid 2089 through 2090
    Processing sheet with id=AC2, first strand: chain 'A' and resid 2190 through 2191
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 2230 through 2246
    current: chain 'A' and resid 2272 through 2273

    138 hydrogen bonds defined for protein.
    321 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.88

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3204
        1.34 -     1.46: 2395
        1.46 -     1.58: 4738
        1.58 -     1.70: 0
        1.70 -     1.82: 93
  Bond restraints: 10430
  Sorted by residual:
  bond pdb=" CA  ARG A1900 "
       pdb=" CB  ARG A1900 "
    ideal  model  delta    sigma   weight residual
    1.523  1.547 -0.024 1.94e-02 2.66e+03 1.54e+00
  bond pdb=" CG1 ILE A1925 "
       pdb=" CD1 ILE A1925 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.31e+00
  bond pdb=" C   SER A1714 "
       pdb=" N   PRO A1715 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.21e+00
  bond pdb=" CB  ARG A1900 "
       pdb=" CG  ARG A1900 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.18e+00
  bond pdb=" C   SER A2204 "
       pdb=" N   PRO A2205 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.11e+00
  ... (remaining 10425 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 13929
        2.34 -     4.68: 196
        4.68 -     7.02: 15
        7.02 -     9.36: 1
        9.36 -    11.70: 1
  Bond angle restraints: 14142
  Sorted by residual:
  angle pdb=" C   HIS A2054 "
        pdb=" CA  HIS A2054 "
        pdb=" CB  HIS A2054 "
      ideal   model   delta    sigma   weight residual
     115.89  110.71    5.18 1.32e+00 5.74e-01 1.54e+01
  angle pdb=" CA  LEU A  71 "
        pdb=" CB  LEU A  71 "
        pdb=" CG  LEU A  71 "
      ideal   model   delta    sigma   weight residual
     116.30  128.00  -11.70 3.50e+00 8.16e-02 1.12e+01
  angle pdb=" N   CYS A 248 "
        pdb=" CA  CYS A 248 "
        pdb=" C   CYS A 248 "
      ideal   model   delta    sigma   weight residual
     108.34  112.55   -4.21 1.31e+00 5.83e-01 1.03e+01
  angle pdb=" N   GLN A 190 "
        pdb=" CA  GLN A 190 "
        pdb=" CB  GLN A 190 "
      ideal   model   delta    sigma   weight residual
     113.65  109.04    4.61 1.47e+00 4.63e-01 9.81e+00
  angle pdb=" CA  ARG A1900 "
        pdb=" CB  ARG A1900 "
        pdb=" CG  ARG A1900 "
      ideal   model   delta    sigma   weight residual
     114.10  119.98   -5.88 2.00e+00 2.50e-01 8.66e+00
  ... (remaining 14137 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 5612
       17.80 -    35.60: 462
       35.60 -    53.40: 90
       53.40 -    71.20: 20
       71.20 -    89.00: 14
  Dihedral angle restraints: 6198
    sinusoidal: 2560
      harmonic: 3638
  Sorted by residual:
  dihedral pdb=" CB  CYS A2021 "
           pdb=" SG  CYS A2021 "
           pdb=" SG  CYS A2169 "
           pdb=" CB  CYS A2169 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.50  -67.50     1      1.00e+01 1.00e-02 5.93e+01
  dihedral pdb=" CB  CYS A 630 "
           pdb=" SG  CYS A 630 "
           pdb=" SG  CYS A 711 "
           pdb=" CB  CYS A 711 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   33.73   59.27     1      1.00e+01 1.00e-02 4.69e+01
  dihedral pdb=" CA  ILE A1925 "
           pdb=" C   ILE A1925 "
           pdb=" N   MET A1926 "
           pdb=" CA  MET A1926 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.24   30.76     0      5.00e+00 4.00e-02 3.78e+01
  ... (remaining 6195 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1360
       0.078 -    0.156: 155
       0.156 -    0.234: 1
       0.234 -    0.311: 0
       0.311 -    0.389: 1
  Chirality restraints: 1517
  Sorted by residual:
  chirality pdb=" C1  NAG A2401 "
            pdb=" ND2 ASN A2118 "
            pdb=" C2  NAG A2401 "
            pdb=" O5  NAG A2401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CB  ILE A2032 "
            pdb=" CA  ILE A2032 "
            pdb=" CG1 ILE A2032 "
            pdb=" CG2 ILE A2032 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CB  THR A  83 "
            pdb=" CA  THR A  83 "
            pdb=" OG1 THR A  83 "
            pdb=" CG2 THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.15 2.00e-01 2.50e+01 5.26e-01
  ... (remaining 1514 not shown)

  Planarity restraints: 1797
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 202 "    0.018 2.00e-02 2.50e+03   1.50e-02 3.96e+00
        pdb=" CG  PHE A 202 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 202 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 202 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 202 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 202 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 202 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 684 "   -0.029 5.00e-02 4.00e+02   4.43e-02 3.13e+00
        pdb=" N   PRO A 685 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 685 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 685 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1727 "    0.025 5.00e-02 4.00e+02   3.77e-02 2.28e+00
        pdb=" N   PRO A1728 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A1728 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A1728 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1794 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 60
        2.66 -     3.22: 9677
        3.22 -     3.78: 15241
        3.78 -     4.34: 21381
        4.34 -     4.90: 33773
  Nonbonded interactions: 80132
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS A 315 "
            pdb="CU    CU A2406 "
     model   vdw
     2.101 3.060
  nonbonded pdb=" CE1 HIS A 232 "
            pdb="CU    CU A2406 "
     model   vdw
     2.233 3.200
  nonbonded pdb=" CD2 HIS A 267 "
            pdb="CU    CU A2406 "
     model   vdw
     2.275 3.200
  nonbonded pdb=" O   GLU A 122 "
            pdb="CA    CA A2404 "
     model   vdw
     2.325 3.250
  nonbonded pdb=" CD2 HIS A2005 "
            pdb="CU    CU A2405 "
     model   vdw
     2.336 3.200
  ... (remaining 80127 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             7.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.450
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6201
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   0.045  10441  Z= 0.126
  Angle     :  0.662  11.697  14167  Z= 0.337
  Chirality :  0.046   0.389   1517
  Planarity :  0.004   0.044   1794
  Dihedral  : 13.825  89.002   3836
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.24), residues: 1233
  helix: -1.98 (0.54), residues: 65
  sheet: -0.95 (0.36), residues: 256
  loop : -1.63 (0.21), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1696 
 TYR   0.019   0.001   TYR A1709 
 PHE   0.034   0.002   PHE A 202 
 TRP   0.014   0.001   TRP A 208 
 HIS   0.006   0.001   HIS A2152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.13 (10430)
  covalent geometry    : angle       0.65390 /  0.33 (14142)
  SS BOND              : bond        0.00122 /  0.09 (    8)
  SS BOND              : angle       1.08142 /  0.68 (   16)
  hydrogen bonds       : bond        0.24273 / 17.10 (  138)
  hydrogen bonds       : angle      10.99720 /  7.29 (  321)
  link_NAG-ASN         : bond        0.00743 /  0.23 (    3)
  link_NAG-ASN         : angle       3.92270 /  2.29 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.253 
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: A  572 ASN cc_start: 0.8155 (m-40) cc_final: 0.7912 (m-40)
REVERT: A  573 VAL cc_start: 0.8798 (t) cc_final: 0.8417 (m)
REVERT: A  638 TYR cc_start: 0.7384 (m-80) cc_final: 0.7055 (m-80)
REVERT: A  671 PHE cc_start: 0.6880 (m-10) cc_final: 0.6390 (m-10)
REVERT: A 1772 MET cc_start: 0.6952 (ttm) cc_final: 0.6729 (ttp)
REVERT: A 1918 PHE cc_start: 0.5644 (m-10) cc_final: 0.5416 (m-10)
REVERT: A 1927 ASP cc_start: 0.5686 (m-30) cc_final: 0.5386 (m-30)
REVERT: A 1989 LEU cc_start: 0.8288 (tt) cc_final: 0.7983 (pp)
REVERT: A 2050 LEU cc_start: 0.7769 (mt) cc_final: 0.7521 (tt)
REVERT: A 2163 ARG cc_start: 0.6301 (mtp180) cc_final: 0.4958 (mtm-85)
REVERT: A 2238 MET cc_start: 0.6631 (mmm) cc_final: 0.6315 (mmm)
REVERT: A 2240 VAL cc_start: 0.7860 (t) cc_final: 0.7649 (p)
REVERT: A 2243 VAL cc_start: 0.6412 (t) cc_final: 0.5755 (m)
REVERT: A 2249 LYS cc_start: 0.7728 (tmmt) cc_final: 0.7252 (pttt)
REVERT: A 2289 SER cc_start: 0.7647 (p) cc_final: 0.7327 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 287
  average time/residue: 0.1091
  time to fit residues: 42.6095
Evaluate side-chains
  213 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0470
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0170
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.4916

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 592 GLN
A 694 ASN
A 699 ASN
** A1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2007 HIS
A2113 GLN
A2155 HIS
A2309 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.166691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.147161 restraints weight = 21172.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.151560 restraints weight = 12122.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.154550 restraints weight = 7885.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.156644 restraints weight = 5583.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.157990 restraints weight = 4217.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.4406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6115
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  10441  Z= 0.153
  Angle     :  0.691  10.309  14167  Z= 0.350
  Chirality :  0.047   0.394   1517
  Planarity :  0.005   0.054   1794
  Dihedral  :  5.816  59.445   1420
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.81 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.25 (0.24), residues: 1233
  helix: -2.65 (0.44), residues: 72
  sheet: -0.88 (0.33), residues: 284
  loop : -1.70 (0.22), residues: 877

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 531 
 TYR   0.019   0.002   TYR A1709 
 PHE   0.025   0.002   PHE A 594 
 TRP   0.012   0.001   TRP A 208 
 HIS   0.008   0.001   HIS A1954 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 (10430)
  covalent geometry    : angle       0.68289 /  0.35 (14142)
  SS BOND              : bond        0.00305 /  0.16 (    8)
  SS BOND              : angle       1.33410 /  0.83 (   16)
  hydrogen bonds       : bond        0.04042 /  2.64 (  138)
  hydrogen bonds       : angle       7.85796 /  5.29 (  321)
  link_NAG-ASN         : bond        0.00805 /  0.24 (    3)
  link_NAG-ASN         : angle       3.97446 /  2.30 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 228
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 MET cc_start: 0.6017 (mmm) cc_final: 0.5005 (mmm)
REVERT: A  323 TYR cc_start: 0.6922 (m-10) cc_final: 0.6713 (m-80)
REVERT: A  426 VAL cc_start: 0.6949 (OUTLIER) cc_final: 0.6709 (p)
REVERT: A  612 ASN cc_start: 0.8198 (m-40) cc_final: 0.7929 (t0)
REVERT: A  613 ILE cc_start: 0.8793 (mt) cc_final: 0.8357 (mm)
REVERT: A  618 ASN cc_start: 0.7914 (m110) cc_final: 0.7418 (m-40)
REVERT: A  699 ASN cc_start: 0.7897 (t0) cc_final: 0.7268 (t0)
REVERT: A 1732 LYS cc_start: 0.8505 (mmtp) cc_final: 0.8193 (mttp)
REVERT: A 1875 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6629 (mt-10)
REVERT: A 1926 MET cc_start: 0.5274 (mmm) cc_final: 0.4819 (mmm)
REVERT: A 1927 ASP cc_start: 0.5542 (m-30) cc_final: 0.4960 (p0)
REVERT: A 1989 LEU cc_start: 0.8055 (tt) cc_final: 0.7704 (mp)
REVERT: A 2079 MET cc_start: 0.7884 (mmm) cc_final: 0.7650 (mmm)
REVERT: A 2108 ASP cc_start: 0.5617 (p0) cc_final: 0.4890 (p0)
REVERT: A 2126 PHE cc_start: 0.6647 (m-80) cc_final: 0.6377 (m-80)
REVERT: A 2129 ASN cc_start: 0.5181 (p0) cc_final: 0.4937 (p0)
REVERT: A 2139 ILE cc_start: 0.8015 (pt) cc_final: 0.7806 (tt)
REVERT: A 2148 TYR cc_start: 0.7172 (m-80) cc_final: 0.6934 (m-80)
REVERT: A 2163 ARG cc_start: 0.6088 (mtp180) cc_final: 0.5298 (mtp180)
REVERT: A 2199 MET cc_start: 0.4133 (tpp) cc_final: 0.3862 (tpp)
REVERT: A 2240 VAL cc_start: 0.7876 (t) cc_final: 0.7578 (p)
REVERT: A 2249 LYS cc_start: 0.7764 (tmmt) cc_final: 0.7259 (pttt)
REVERT: A 2289 SER cc_start: 0.7812 (p) cc_final: 0.7466 (t)
  outliers start: 18
  outliers final: 10
  residues processed: 233
  average time/residue: 0.1036
  time to fit residues: 33.0652
Evaluate side-chains
  214 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 202
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  157 SER
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  698 ARG
Chi-restraints excluded: chain A residue 1875 GLU
Chi-restraints excluded: chain A residue 2069 SER
Chi-restraints excluded: chain A residue 2131 ASP
Chi-restraints excluded: chain A residue 2145 ILE
Chi-restraints excluded: chain A residue 2198 ASN
Chi-restraints excluded: chain A residue 2232 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 113 optimal weight:    0.4980
   chunk 67 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 101 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 108 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0770
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  77 GLN
A 161 HIS
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 694 ASN
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2155 HIS
A2309 HIS
** A2316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.163841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.144601 restraints weight = 21473.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.148960 restraints weight = 12433.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.151902 restraints weight = 8059.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.153942 restraints weight = 5688.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.155388 restraints weight = 4289.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6161
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10441  Z= 0.153
  Angle     :  0.695  10.235  14167  Z= 0.350
  Chirality :  0.048   0.398   1517
  Planarity :  0.005   0.052   1794
  Dihedral  :  5.807  57.747   1420
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.60 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.24), residues: 1233
  helix: -2.35 (0.54), residues: 61
  sheet: -1.20 (0.32), residues: 291
  loop : -1.72 (0.22), residues: 881

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 531 
 TYR   0.023   0.002   TYR A 156 
 PHE   0.022   0.002   PHE A1775 
 TRP   0.014   0.001   TRP A 208 
 HIS   0.005   0.001   HIS A 615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.15 (10430)
  covalent geometry    : angle       0.68785 /  0.35 (14142)
  SS BOND              : bond        0.00137 /  0.10 (    8)
  SS BOND              : angle       1.08943 /  0.68 (   16)
  hydrogen bonds       : bond        0.03629 /  2.33 (  138)
  hydrogen bonds       : angle       6.93487 /  4.65 (  321)
  link_NAG-ASN         : bond        0.00831 /  0.25 (    3)
  link_NAG-ASN         : angle       3.95902 /  2.31 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 208
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.7428 (tttp) cc_final: 0.7149 (tttp)
REVERT: A  301 MET cc_start: 0.5913 (mmm) cc_final: 0.4896 (mmm)
REVERT: A  324 VAL cc_start: 0.8087 (m) cc_final: 0.7821 (p)
REVERT: A  426 VAL cc_start: 0.6887 (OUTLIER) cc_final: 0.6660 (p)
REVERT: A  586 TYR cc_start: 0.6308 (m-10) cc_final: 0.6044 (m-80)
REVERT: A  613 ILE cc_start: 0.8674 (mt) cc_final: 0.8284 (mm)
REVERT: A  614 MET cc_start: 0.5822 (mmt) cc_final: 0.5447 (mmt)
REVERT: A  699 ASN cc_start: 0.7798 (t0) cc_final: 0.7118 (t0)
REVERT: A 1926 MET cc_start: 0.5545 (mmm) cc_final: 0.5226 (mmm)
REVERT: A 1927 ASP cc_start: 0.5733 (m-30) cc_final: 0.5179 (p0)
REVERT: A 1989 LEU cc_start: 0.8128 (tt) cc_final: 0.7673 (mp)
REVERT: A 1992 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7433 (mtpp)
REVERT: A 2079 MET cc_start: 0.7879 (mmm) cc_final: 0.7361 (mmm)
REVERT: A 2108 ASP cc_start: 0.5743 (p0) cc_final: 0.5000 (p0)
REVERT: A 2126 PHE cc_start: 0.6523 (m-80) cc_final: 0.6302 (m-80)
REVERT: A 2163 ARG cc_start: 0.6266 (mtp180) cc_final: 0.5770 (mtt180)
REVERT: A 2199 MET cc_start: 0.3952 (tpp) cc_final: 0.3709 (tpp)
REVERT: A 2240 VAL cc_start: 0.7873 (t) cc_final: 0.7556 (p)
REVERT: A 2249 LYS cc_start: 0.7729 (tmmt) cc_final: 0.7149 (pttt)
REVERT: A 2289 SER cc_start: 0.7812 (p) cc_final: 0.7484 (t)
  outliers start: 21
  outliers final: 14
  residues processed: 220
  average time/residue: 0.1000
  time to fit residues: 30.4584
Evaluate side-chains
  203 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 188
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  698 ARG
Chi-restraints excluded: chain A residue 1774 THR
Chi-restraints excluded: chain A residue 1843 LEU
Chi-restraints excluded: chain A residue 1851 LEU
Chi-restraints excluded: chain A residue 1859 HIS
Chi-restraints excluded: chain A residue 2069 SER
Chi-restraints excluded: chain A residue 2131 ASP
Chi-restraints excluded: chain A residue 2145 ILE
Chi-restraints excluded: chain A residue 2152 HIS
Chi-restraints excluded: chain A residue 2230 LEU
Chi-restraints excluded: chain A residue 2308 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 113 optimal weight:    0.1980
   chunk 30 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 53 optimal weight:    0.7980
   chunk 118 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 315 HIS
A 590 ASN
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 694 ASN
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2155 HIS
A2309 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.161449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.142146 restraints weight = 21607.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.146447 restraints weight = 12461.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.149359 restraints weight = 8089.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.151407 restraints weight = 5733.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.152862 restraints weight = 4323.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6225
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10441  Z= 0.166
  Angle     :  0.690  10.281  14167  Z= 0.348
  Chirality :  0.048   0.398   1517
  Planarity :  0.005   0.051   1794
  Dihedral  :  5.927  58.183   1420
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.68 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.24), residues: 1233
  helix: -2.61 (0.49), residues: 69
  sheet: -1.22 (0.31), residues: 307
  loop : -1.78 (0.22), residues: 857

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1776 
 TYR   0.021   0.002   TYR A1709 
 PHE   0.026   0.002   PHE A 436 
 TRP   0.023   0.002   TRP A  14 
 HIS   0.004   0.001   HIS A1954 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.17 (10430)
  covalent geometry    : angle       0.68269 /  0.35 (14142)
  SS BOND              : bond        0.00261 /  0.11 (    8)
  SS BOND              : angle       0.97525 /  0.61 (   16)
  hydrogen bonds       : bond        0.03469 /  2.25 (  138)
  hydrogen bonds       : angle       6.75751 /  4.51 (  321)
  link_NAG-ASN         : bond        0.00781 /  0.24 (    3)
  link_NAG-ASN         : angle       3.97926 /  2.32 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 197
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.7508 (tttp) cc_final: 0.7258 (tttp)
REVERT: A   98 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7182 (tt)
REVERT: A  301 MET cc_start: 0.5879 (mmm) cc_final: 0.4842 (mmm)
REVERT: A  324 VAL cc_start: 0.8060 (m) cc_final: 0.7804 (p)
REVERT: A  586 TYR cc_start: 0.6500 (m-10) cc_final: 0.6254 (m-80)
REVERT: A  613 ILE cc_start: 0.8716 (mt) cc_final: 0.8333 (mm)
REVERT: A  680 MET cc_start: 0.7262 (tpp) cc_final: 0.7043 (tpp)
REVERT: A  699 ASN cc_start: 0.7826 (t0) cc_final: 0.7106 (t0)
REVERT: A 1751 GLU cc_start: 0.6261 (tt0) cc_final: 0.5996 (mt-10)
REVERT: A 1766 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6852 (mt-10)
REVERT: A 1790 ILE cc_start: 0.4864 (OUTLIER) cc_final: 0.4497 (mt)
REVERT: A 1875 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6468 (mt-10)
REVERT: A 1926 MET cc_start: 0.5717 (mmm) cc_final: 0.5499 (mmm)
REVERT: A 1927 ASP cc_start: 0.5772 (m-30) cc_final: 0.5268 (p0)
REVERT: A 1973 MET cc_start: 0.6456 (ttm) cc_final: 0.6209 (ttm)
REVERT: A 1989 LEU cc_start: 0.8178 (tt) cc_final: 0.7894 (pp)
REVERT: A 1992 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7430 (mtpp)
REVERT: A 2108 ASP cc_start: 0.5636 (p0) cc_final: 0.5005 (p0)
REVERT: A 2163 ARG cc_start: 0.6189 (mtp180) cc_final: 0.5756 (mtp180)
REVERT: A 2199 MET cc_start: 0.3623 (tpp) cc_final: 0.3340 (tpp)
REVERT: A 2238 MET cc_start: 0.6138 (mmm) cc_final: 0.5735 (mmm)
REVERT: A 2249 LYS cc_start: 0.7803 (tmmt) cc_final: 0.7177 (pttt)
REVERT: A 2289 SER cc_start: 0.7862 (p) cc_final: 0.7557 (t)
  outliers start: 35
  outliers final: 19
  residues processed: 218
  average time/residue: 0.0903
  time to fit residues: 27.8312
Evaluate side-chains
  206 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  698 ARG
Chi-restraints excluded: chain A residue 1770 ASN
Chi-restraints excluded: chain A residue 1774 THR
Chi-restraints excluded: chain A residue 1790 ILE
Chi-restraints excluded: chain A residue 1812 THR
Chi-restraints excluded: chain A residue 1859 HIS
Chi-restraints excluded: chain A residue 1962 VAL
Chi-restraints excluded: chain A residue 2069 SER
Chi-restraints excluded: chain A residue 2131 ASP
Chi-restraints excluded: chain A residue 2145 ILE
Chi-restraints excluded: chain A residue 2152 HIS
Chi-restraints excluded: chain A residue 2164 MET
Chi-restraints excluded: chain A residue 2198 ASN
Chi-restraints excluded: chain A residue 2232 VAL
Chi-restraints excluded: chain A residue 2308 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 109 optimal weight:    0.0070
   chunk 97 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 120 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0070
   chunk 62 optimal weight:    0.4980
   chunk 101 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.3816

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
A 694 ASN
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2155 HIS
A2309 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.162966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.143824 restraints weight = 21188.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.148150 restraints weight = 12148.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.151099 restraints weight = 7877.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.153028 restraints weight = 5556.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.154545 restraints weight = 4228.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6194
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10441  Z= 0.132
  Angle     :  0.682  10.086  14167  Z= 0.340
  Chirality :  0.047   0.393   1517
  Planarity :  0.004   0.040   1794
  Dihedral  :  5.839  57.684   1420
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.31 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.24), residues: 1233
  helix: -2.48 (0.51), residues: 68
  sheet: -1.21 (0.33), residues: 278
  loop : -1.84 (0.21), residues: 887

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 531 
 TYR   0.022   0.001   TYR A 454 
 PHE   0.027   0.002   PHE A 594 
 TRP   0.040   0.002   TRP A  14 
 HIS   0.005   0.001   HIS A1954 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 (10430)
  covalent geometry    : angle       0.67439 /  0.34 (14142)
  SS BOND              : bond        0.00330 /  0.14 (    8)
  SS BOND              : angle       0.96939 /  0.61 (   16)
  hydrogen bonds       : bond        0.03145 /  2.06 (  138)
  hydrogen bonds       : angle       6.54645 /  4.35 (  321)
  link_NAG-ASN         : bond        0.00819 /  0.25 (    3)
  link_NAG-ASN         : angle       3.86354 /  2.25 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 197
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.7523 (tttp) cc_final: 0.7223 (tttp)
REVERT: A   98 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7106 (tt)
REVERT: A  301 MET cc_start: 0.5756 (mmm) cc_final: 0.4802 (mmm)
REVERT: A  324 VAL cc_start: 0.8128 (m) cc_final: 0.7859 (p)
REVERT: A  613 ILE cc_start: 0.8657 (mt) cc_final: 0.8269 (mm)
REVERT: A  614 MET cc_start: 0.5871 (mmt) cc_final: 0.5421 (mmt)
REVERT: A  699 ASN cc_start: 0.7834 (t0) cc_final: 0.7078 (t0)
REVERT: A 1766 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6869 (mt-10)
REVERT: A 1790 ILE cc_start: 0.4734 (OUTLIER) cc_final: 0.4391 (mt)
REVERT: A 1875 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6515 (mt-10)
REVERT: A 1926 MET cc_start: 0.5570 (mmm) cc_final: 0.5350 (mmm)
REVERT: A 1927 ASP cc_start: 0.5874 (m-30) cc_final: 0.5331 (p0)
REVERT: A 1973 MET cc_start: 0.6407 (ttm) cc_final: 0.6150 (ttm)
REVERT: A 1989 LEU cc_start: 0.8140 (tt) cc_final: 0.7838 (pp)
REVERT: A 1992 LYS cc_start: 0.7836 (mtpp) cc_final: 0.7480 (mtpp)
REVERT: A 2027 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6724 (ppp)
REVERT: A 2079 MET cc_start: 0.7971 (mmm) cc_final: 0.7750 (mmm)
REVERT: A 2108 ASP cc_start: 0.5633 (p0) cc_final: 0.4989 (p0)
REVERT: A 2163 ARG cc_start: 0.6022 (mtp180) cc_final: 0.4882 (mtp85)
REVERT: A 2199 MET cc_start: 0.3477 (tpp) cc_final: 0.3137 (tpp)
REVERT: A 2238 MET cc_start: 0.6239 (mmm) cc_final: 0.5829 (mmm)
REVERT: A 2240 VAL cc_start: 0.7869 (m) cc_final: 0.7556 (p)
REVERT: A 2249 LYS cc_start: 0.7826 (tmmt) cc_final: 0.7181 (pttt)
REVERT: A 2289 SER cc_start: 0.7893 (p) cc_final: 0.7557 (t)
  outliers start: 38
  outliers final: 19
  residues processed: 222
  average time/residue: 0.0894
  time to fit residues: 28.1365
Evaluate side-chains
  205 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 183
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue 1770 ASN
Chi-restraints excluded: chain A residue 1774 THR
Chi-restraints excluded: chain A residue 1790 ILE
Chi-restraints excluded: chain A residue 1812 THR
Chi-restraints excluded: chain A residue 1859 HIS
Chi-restraints excluded: chain A residue 1872 THR
Chi-restraints excluded: chain A residue 1912 PHE
Chi-restraints excluded: chain A residue 1962 VAL
Chi-restraints excluded: chain A residue 2027 MET
Chi-restraints excluded: chain A residue 2069 SER
Chi-restraints excluded: chain A residue 2131 ASP
Chi-restraints excluded: chain A residue 2145 ILE
Chi-restraints excluded: chain A residue 2152 HIS
Chi-restraints excluded: chain A residue 2164 MET
Chi-restraints excluded: chain A residue 2232 VAL
Chi-restraints excluded: chain A residue 2308 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0980
   chunk 104 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 88 optimal weight:    0.4980
   chunk 102 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 43 optimal weight:    0.1980
   chunk 54 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.5582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 169 ASN
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 590 ASN
A 609 GLN
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 645 GLN
A 660 HIS
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2155 HIS
A2309 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.160901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.142094 restraints weight = 20989.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.146287 restraints weight = 12060.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.149207 restraints weight = 7796.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.151246 restraints weight = 5480.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.152672 restraints weight = 4100.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6233
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10441  Z= 0.159
  Angle     :  0.763  20.845  14167  Z= 0.378
  Chirality :  0.050   0.398   1517
  Planarity :  0.004   0.040   1794
  Dihedral  :  5.984  57.897   1420
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.81 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.12 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.57 (0.24), residues: 1233
  helix: -2.55 (0.49), residues: 71
  sheet: -1.42 (0.31), residues: 309
  loop : -1.84 (0.22), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A   3 
 TYR   0.022   0.002   TYR A 454 
 PHE   0.026   0.002   PHE A 436 
 TRP   0.053   0.002   TRP A  14 
 HIS   0.007   0.001   HIS A 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 (10430)
  covalent geometry    : angle       0.74501 /  0.37 (14142)
  SS BOND              : bond        0.00644 /  0.21 (    8)
  SS BOND              : angle       3.98577 /  2.23 (   16)
  hydrogen bonds       : bond        0.03375 /  2.18 (  138)
  hydrogen bonds       : angle       6.53764 /  4.37 (  321)
  link_NAG-ASN         : bond        0.00809 /  0.26 (    3)
  link_NAG-ASN         : angle       3.93533 /  2.30 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 195
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7109 (tt)
REVERT: A  301 MET cc_start: 0.5719 (mmm) cc_final: 0.4761 (mmm)
REVERT: A  324 VAL cc_start: 0.8108 (m) cc_final: 0.7855 (p)
REVERT: A  459 ASP cc_start: 0.6084 (m-30) cc_final: 0.4913 (t0)
REVERT: A  528 CYS cc_start: 0.3898 (p) cc_final: 0.3638 (p)
REVERT: A  613 ILE cc_start: 0.8720 (mt) cc_final: 0.8315 (mm)
REVERT: A  614 MET cc_start: 0.6023 (mmt) cc_final: 0.5486 (mmt)
REVERT: A  680 MET cc_start: 0.6980 (tpp) cc_final: 0.6566 (mmm)
REVERT: A  699 ASN cc_start: 0.7784 (t0) cc_final: 0.7028 (t0)
REVERT: A 1766 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6752 (mt-10)
REVERT: A 1790 ILE cc_start: 0.4887 (OUTLIER) cc_final: 0.4536 (mt)
REVERT: A 1875 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6436 (mt-10)
REVERT: A 1927 ASP cc_start: 0.5881 (m-30) cc_final: 0.5359 (p0)
REVERT: A 1973 MET cc_start: 0.6567 (ttm) cc_final: 0.6315 (ttm)
REVERT: A 1989 LEU cc_start: 0.8140 (tt) cc_final: 0.7860 (pp)
REVERT: A 1992 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7441 (mtpp)
REVERT: A 2079 MET cc_start: 0.7926 (mmm) cc_final: 0.7701 (mmm)
REVERT: A 2104 MET cc_start: 0.1769 (ptm) cc_final: 0.1318 (ptm)
REVERT: A 2108 ASP cc_start: 0.5615 (p0) cc_final: 0.4952 (p0)
REVERT: A 2163 ARG cc_start: 0.6198 (mtp180) cc_final: 0.5649 (mtp85)
REVERT: A 2199 MET cc_start: 0.3420 (tpp) cc_final: 0.3073 (tpp)
REVERT: A 2235 GLN cc_start: 0.7641 (pp30) cc_final: 0.7440 (pp30)
REVERT: A 2238 MET cc_start: 0.6127 (mmm) cc_final: 0.5787 (mmm)
REVERT: A 2240 VAL cc_start: 0.7876 (m) cc_final: 0.7561 (p)
REVERT: A 2249 LYS cc_start: 0.7779 (tmmt) cc_final: 0.7172 (pttt)
REVERT: A 2289 SER cc_start: 0.7879 (p) cc_final: 0.7544 (t)
  outliers start: 37
  outliers final: 25
  residues processed: 216
  average time/residue: 0.0977
  time to fit residues: 29.7297
Evaluate side-chains
  216 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 189
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   16 TYR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  698 ARG
Chi-restraints excluded: chain A residue 1770 ASN
Chi-restraints excluded: chain A residue 1790 ILE
Chi-restraints excluded: chain A residue 1812 THR
Chi-restraints excluded: chain A residue 1859 HIS
Chi-restraints excluded: chain A residue 1872 THR
Chi-restraints excluded: chain A residue 1912 PHE
Chi-restraints excluded: chain A residue 1962 VAL
Chi-restraints excluded: chain A residue 2069 SER
Chi-restraints excluded: chain A residue 2131 ASP
Chi-restraints excluded: chain A residue 2145 ILE
Chi-restraints excluded: chain A residue 2152 HIS
Chi-restraints excluded: chain A residue 2164 MET
Chi-restraints excluded: chain A residue 2232 VAL
Chi-restraints excluded: chain A residue 2308 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 108 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 112 optimal weight:    0.0970
   chunk 84 optimal weight:    0.0670
   chunk 7 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0020
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.3324

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2155 HIS
A2309 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.162969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.144083 restraints weight = 20828.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.148328 restraints weight = 11940.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.151248 restraints weight = 7725.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.153305 restraints weight = 5429.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.154758 restraints weight = 4076.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.4369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6194
moved from start:          0.4476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10441  Z= 0.130
  Angle     :  0.732  17.050  14167  Z= 0.361
  Chirality :  0.048   0.392   1517
  Planarity :  0.004   0.041   1794
  Dihedral  :  5.801  57.346   1420
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.94 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.24), residues: 1233
  helix: -2.38 (0.52), residues: 70
  sheet: -1.41 (0.33), residues: 278
  loop : -1.83 (0.22), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.028   0.002   TYR A1890 
 PHE   0.026   0.002   PHE A1775 
 TRP   0.029   0.002   TRP A  14 
 HIS   0.015   0.001   HIS A 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 (10430)
  covalent geometry    : angle       0.71641 /  0.36 (14142)
  SS BOND              : bond        0.00464 /  0.16 (    8)
  SS BOND              : angle       3.57360 /  2.04 (   16)
  hydrogen bonds       : bond        0.03035 /  1.97 (  138)
  hydrogen bonds       : angle       6.38236 /  4.23 (  321)
  link_NAG-ASN         : bond        0.00838 /  0.26 (    3)
  link_NAG-ASN         : angle       3.82135 /  2.23 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 195
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7078 (tt)
REVERT: A  231 MET cc_start: 0.4085 (ttt) cc_final: 0.3540 (ttt)
REVERT: A  301 MET cc_start: 0.5750 (mmm) cc_final: 0.4819 (mmm)
REVERT: A  324 VAL cc_start: 0.8108 (m) cc_final: 0.7848 (p)
REVERT: A  459 ASP cc_start: 0.6045 (m-30) cc_final: 0.4831 (t0)
REVERT: A  612 ASN cc_start: 0.8026 (m-40) cc_final: 0.7708 (t0)
REVERT: A  613 ILE cc_start: 0.8673 (mt) cc_final: 0.8251 (mm)
REVERT: A  614 MET cc_start: 0.5905 (mmt) cc_final: 0.5248 (mmt)
REVERT: A  680 MET cc_start: 0.6839 (tpp) cc_final: 0.6506 (mmm)
REVERT: A  699 ASN cc_start: 0.7667 (t0) cc_final: 0.6895 (t0)
REVERT: A 1766 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6792 (mt-10)
REVERT: A 1790 ILE cc_start: 0.4731 (OUTLIER) cc_final: 0.4397 (mt)
REVERT: A 1872 THR cc_start: 0.5958 (OUTLIER) cc_final: 0.5665 (m)
REVERT: A 1875 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6470 (mt-10)
REVERT: A 1927 ASP cc_start: 0.5828 (m-30) cc_final: 0.5251 (p0)
REVERT: A 1973 MET cc_start: 0.6538 (ttm) cc_final: 0.6279 (ttm)
REVERT: A 1989 LEU cc_start: 0.8056 (tt) cc_final: 0.7700 (pp)
REVERT: A 2079 MET cc_start: 0.7944 (mmm) cc_final: 0.7741 (mmm)
REVERT: A 2104 MET cc_start: 0.2070 (ptm) cc_final: 0.1861 (ptm)
REVERT: A 2108 ASP cc_start: 0.5475 (p0) cc_final: 0.4871 (p0)
REVERT: A 2163 ARG cc_start: 0.5977 (mtp180) cc_final: 0.5296 (mtp180)
REVERT: A 2199 MET cc_start: 0.3435 (tpp) cc_final: 0.3084 (tpp)
REVERT: A 2235 GLN cc_start: 0.7682 (pp30) cc_final: 0.7434 (pp30)
REVERT: A 2238 MET cc_start: 0.6155 (mmm) cc_final: 0.5823 (mmm)
REVERT: A 2240 VAL cc_start: 0.7873 (m) cc_final: 0.7559 (p)
REVERT: A 2249 LYS cc_start: 0.7750 (tmmt) cc_final: 0.7179 (pttt)
REVERT: A 2289 SER cc_start: 0.7885 (p) cc_final: 0.7506 (t)
  outliers start: 31
  outliers final: 20
  residues processed: 213
  average time/residue: 0.0933
  time to fit residues: 27.9651
Evaluate side-chains
  212 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 189
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 TYR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  698 ARG
Chi-restraints excluded: chain A residue 1770 ASN
Chi-restraints excluded: chain A residue 1790 ILE
Chi-restraints excluded: chain A residue 1859 HIS
Chi-restraints excluded: chain A residue 1872 THR
Chi-restraints excluded: chain A residue 1912 PHE
Chi-restraints excluded: chain A residue 1962 VAL
Chi-restraints excluded: chain A residue 2053 LEU
Chi-restraints excluded: chain A residue 2131 ASP
Chi-restraints excluded: chain A residue 2145 ILE
Chi-restraints excluded: chain A residue 2152 HIS
Chi-restraints excluded: chain A residue 2164 MET
Chi-restraints excluded: chain A residue 2232 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 70 optimal weight:    0.0040
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0970
   chunk 96 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 11 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.4190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2155 HIS
A2309 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.163293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.144039 restraints weight = 21730.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.148151 restraints weight = 12857.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.150988 restraints weight = 8559.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.153009 restraints weight = 6205.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.154450 restraints weight = 4764.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6218
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10441  Z= 0.140
  Angle     :  0.736  15.040  14167  Z= 0.366
  Chirality :  0.049   0.392   1517
  Planarity :  0.004   0.041   1794
  Dihedral  :  5.867  57.443   1420
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.81 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.94 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.65 (0.24), residues: 1233
  helix: -2.32 (0.50), residues: 81
  sheet: -1.51 (0.32), residues: 293
  loop : -1.89 (0.22), residues: 859

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 490 
 TYR   0.034   0.002   TYR A1890 
 PHE   0.025   0.002   PHE A1775 
 TRP   0.030   0.002   TRP A  14 
 HIS   0.009   0.001   HIS A 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 (10430)
  covalent geometry    : angle       0.72103 /  0.36 (14142)
  SS BOND              : bond        0.00417 /  0.14 (    8)
  SS BOND              : angle       3.42232 /  1.96 (   16)
  hydrogen bonds       : bond        0.03157 /  2.03 (  138)
  hydrogen bonds       : angle       6.36318 /  4.24 (  321)
  link_NAG-ASN         : bond        0.00817 /  0.25 (    3)
  link_NAG-ASN         : angle       3.86284 /  2.25 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 192
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6985 (tt)
REVERT: A  301 MET cc_start: 0.5820 (mmm) cc_final: 0.4887 (mmm)
REVERT: A  324 VAL cc_start: 0.8038 (m) cc_final: 0.7809 (p)
REVERT: A  459 ASP cc_start: 0.5946 (m-30) cc_final: 0.4757 (t0)
REVERT: A  612 ASN cc_start: 0.8026 (m-40) cc_final: 0.7719 (t0)
REVERT: A  613 ILE cc_start: 0.8651 (mt) cc_final: 0.8275 (mm)
REVERT: A  614 MET cc_start: 0.5991 (mmt) cc_final: 0.5563 (mmt)
REVERT: A  680 MET cc_start: 0.6967 (tpp) cc_final: 0.6679 (mmm)
REVERT: A  699 ASN cc_start: 0.7574 (t0) cc_final: 0.6822 (t0)
REVERT: A 1766 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6750 (mt-10)
REVERT: A 1790 ILE cc_start: 0.4774 (OUTLIER) cc_final: 0.4445 (mt)
REVERT: A 1806 PHE cc_start: 0.6971 (t80) cc_final: 0.6602 (t80)
REVERT: A 1872 THR cc_start: 0.5951 (OUTLIER) cc_final: 0.5688 (m)
REVERT: A 1875 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6313 (mt-10)
REVERT: A 1927 ASP cc_start: 0.5697 (m-30) cc_final: 0.5254 (p0)
REVERT: A 1973 MET cc_start: 0.6561 (ttm) cc_final: 0.6348 (ttm)
REVERT: A 1989 LEU cc_start: 0.8045 (tt) cc_final: 0.7828 (pp)
REVERT: A 2108 ASP cc_start: 0.5415 (p0) cc_final: 0.4847 (p0)
REVERT: A 2163 ARG cc_start: 0.6209 (mtp180) cc_final: 0.5649 (mtp85)
REVERT: A 2199 MET cc_start: 0.3589 (tpp) cc_final: 0.3161 (tpp)
REVERT: A 2235 GLN cc_start: 0.7669 (pp30) cc_final: 0.7402 (pp30)
REVERT: A 2238 MET cc_start: 0.6049 (mmm) cc_final: 0.5792 (mmm)
REVERT: A 2240 VAL cc_start: 0.7843 (m) cc_final: 0.7545 (p)
REVERT: A 2249 LYS cc_start: 0.7688 (tmmt) cc_final: 0.7242 (pttt)
REVERT: A 2289 SER cc_start: 0.7895 (p) cc_final: 0.7536 (t)
  outliers start: 38
  outliers final: 24
  residues processed: 213
  average time/residue: 0.0911
  time to fit residues: 27.3679
Evaluate side-chains
  216 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 189
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TRP
Chi-restraints excluded: chain A residue   16 TYR
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue 1770 ASN
Chi-restraints excluded: chain A residue 1790 ILE
Chi-restraints excluded: chain A residue 1812 THR
Chi-restraints excluded: chain A residue 1859 HIS
Chi-restraints excluded: chain A residue 1872 THR
Chi-restraints excluded: chain A residue 1912 PHE
Chi-restraints excluded: chain A residue 1962 VAL
Chi-restraints excluded: chain A residue 1995 ILE
Chi-restraints excluded: chain A residue 2053 LEU
Chi-restraints excluded: chain A residue 2069 SER
Chi-restraints excluded: chain A residue 2131 ASP
Chi-restraints excluded: chain A residue 2145 ILE
Chi-restraints excluded: chain A residue 2152 HIS
Chi-restraints excluded: chain A residue 2164 MET
Chi-restraints excluded: chain A residue 2232 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 106 optimal weight:    0.0170
   chunk 39 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0370
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.4096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 618 ASN
A 660 HIS
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2155 HIS
A2309 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.162804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.143887 restraints weight = 20751.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.148157 restraints weight = 11913.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.151076 restraints weight = 7709.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.153132 restraints weight = 5434.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.154480 restraints weight = 4077.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6213
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10441  Z= 0.140
  Angle     :  0.764  16.728  14167  Z= 0.374
  Chirality :  0.049   0.396   1517
  Planarity :  0.004   0.053   1794
  Dihedral  :  5.904  57.632   1420
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.66 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.65 (0.24), residues: 1233
  helix: -2.24 (0.53), residues: 76
  sheet: -1.53 (0.31), residues: 298
  loop : -1.90 (0.22), residues: 859

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 698 
 TYR   0.034   0.002   TYR A1890 
 PHE   0.024   0.002   PHE A1775 
 TRP   0.028   0.002   TRP A  14 
 HIS   0.016   0.001   HIS A 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 (10430)
  covalent geometry    : angle       0.74861 /  0.37 (14142)
  SS BOND              : bond        0.00285 /  0.13 (    8)
  SS BOND              : angle       3.61725 /  2.08 (   16)
  hydrogen bonds       : bond        0.03109 /  2.02 (  138)
  hydrogen bonds       : angle       6.44687 /  4.33 (  321)
  link_NAG-ASN         : bond        0.00852 /  0.26 (    3)
  link_NAG-ASN         : angle       3.83868 /  2.24 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 197
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6746 (tt)
REVERT: A  301 MET cc_start: 0.5768 (mmm) cc_final: 0.4854 (mmm)
REVERT: A  324 VAL cc_start: 0.8100 (m) cc_final: 0.7851 (p)
REVERT: A  459 ASP cc_start: 0.6003 (m-30) cc_final: 0.4851 (t0)
REVERT: A  612 ASN cc_start: 0.8068 (m-40) cc_final: 0.7782 (t0)
REVERT: A  613 ILE cc_start: 0.8711 (mt) cc_final: 0.8317 (mm)
REVERT: A  614 MET cc_start: 0.5944 (mmt) cc_final: 0.5561 (mmt)
REVERT: A  680 MET cc_start: 0.6946 (tpp) cc_final: 0.6626 (mmm)
REVERT: A  699 ASN cc_start: 0.7601 (t0) cc_final: 0.6856 (t0)
REVERT: A 1762 TYR cc_start: 0.7274 (m-10) cc_final: 0.6880 (m-10)
REVERT: A 1790 ILE cc_start: 0.4727 (OUTLIER) cc_final: 0.4392 (mt)
REVERT: A 1806 PHE cc_start: 0.7080 (t80) cc_final: 0.6707 (t80)
REVERT: A 1813 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7518 (tptm)
REVERT: A 1872 THR cc_start: 0.5973 (OUTLIER) cc_final: 0.5740 (m)
REVERT: A 1875 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6358 (mt-10)
REVERT: A 1927 ASP cc_start: 0.5773 (m-30) cc_final: 0.5257 (p0)
REVERT: A 1973 MET cc_start: 0.6614 (ttm) cc_final: 0.6357 (ttm)
REVERT: A 1989 LEU cc_start: 0.8092 (tt) cc_final: 0.7868 (pp)
REVERT: A 1992 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7475 (mttp)
REVERT: A 2079 MET cc_start: 0.7791 (mmm) cc_final: 0.7534 (mmm)
REVERT: A 2108 ASP cc_start: 0.5509 (p0) cc_final: 0.4990 (p0)
REVERT: A 2171 LEU cc_start: 0.7299 (tp) cc_final: 0.7068 (tp)
REVERT: A 2199 MET cc_start: 0.3393 (tpp) cc_final: 0.3022 (tpp)
REVERT: A 2235 GLN cc_start: 0.7711 (pp30) cc_final: 0.7434 (pp30)
REVERT: A 2238 MET cc_start: 0.6108 (mmm) cc_final: 0.5811 (mmm)
REVERT: A 2240 VAL cc_start: 0.7860 (m) cc_final: 0.7543 (p)
REVERT: A 2249 LYS cc_start: 0.7726 (tmmt) cc_final: 0.7251 (pttt)
REVERT: A 2289 SER cc_start: 0.7952 (p) cc_final: 0.7564 (t)
  outliers start: 33
  outliers final: 24
  residues processed: 217
  average time/residue: 0.1040
  time to fit residues: 31.6474
Evaluate side-chains
  218 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 TYR
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue   90 ASN
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue 1770 ASN
Chi-restraints excluded: chain A residue 1790 ILE
Chi-restraints excluded: chain A residue 1812 THR
Chi-restraints excluded: chain A residue 1859 HIS
Chi-restraints excluded: chain A residue 1872 THR
Chi-restraints excluded: chain A residue 1912 PHE
Chi-restraints excluded: chain A residue 1962 VAL
Chi-restraints excluded: chain A residue 1995 ILE
Chi-restraints excluded: chain A residue 2032 ILE
Chi-restraints excluded: chain A residue 2053 LEU
Chi-restraints excluded: chain A residue 2069 SER
Chi-restraints excluded: chain A residue 2131 ASP
Chi-restraints excluded: chain A residue 2145 ILE
Chi-restraints excluded: chain A residue 2152 HIS
Chi-restraints excluded: chain A residue 2164 MET
Chi-restraints excluded: chain A residue 2232 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0470
   chunk 12 optimal weight:    0.0670
   chunk 116 optimal weight:    0.0770
   chunk 105 optimal weight:    0.0020
   chunk 81 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0870
   chunk 47 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.0560

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 161 HIS
A 660 HIS
A 693 HIS
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2155 HIS
A2309 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.167791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.148676 restraints weight = 21237.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.153023 restraints weight = 12208.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.155928 restraints weight = 7948.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.157959 restraints weight = 5650.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.159278 restraints weight = 4287.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.4420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6089
moved from start:          0.5005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10441  Z= 0.119
  Angle     :  0.758  13.853  14167  Z= 0.371
  Chirality :  0.048   0.385   1517
  Planarity :  0.004   0.060   1794
  Dihedral  :  5.698  56.445   1420
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.65 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.24), residues: 1233
  helix: -2.22 (0.51), residues: 74
  sheet: -1.52 (0.31), residues: 284
  loop : -1.90 (0.21), residues: 875

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A   3 
 TYR   0.034   0.001   TYR A1890 
 PHE   0.022   0.001   PHE A1775 
 TRP   0.025   0.002   TRP A2229 
 HIS   0.015   0.001   HIS A 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 (10430)
  covalent geometry    : angle       0.74425 /  0.37 (14142)
  SS BOND              : bond        0.00572 /  0.20 (    8)
  SS BOND              : angle       3.39732 /  1.94 (   16)
  hydrogen bonds       : bond        0.03056 /  1.92 (  138)
  hydrogen bonds       : angle       6.24760 /  4.10 (  321)
  link_NAG-ASN         : bond        0.00919 /  0.29 (    3)
  link_NAG-ASN         : angle       3.70780 /  2.15 (    9)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 199
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 MET cc_start: 0.5874 (mmm) cc_final: 0.5022 (mmm)
REVERT: A  324 VAL cc_start: 0.8072 (m) cc_final: 0.7828 (p)
REVERT: A  459 ASP cc_start: 0.5658 (m-30) cc_final: 0.4784 (t0)
REVERT: A  612 ASN cc_start: 0.7771 (m-40) cc_final: 0.7510 (t0)
REVERT: A  613 ILE cc_start: 0.8607 (mt) cc_final: 0.8209 (mm)
REVERT: A  614 MET cc_start: 0.5700 (mmt) cc_final: 0.5053 (mmt)
REVERT: A  699 ASN cc_start: 0.7370 (t0) cc_final: 0.6671 (t0)
REVERT: A 1762 TYR cc_start: 0.7061 (m-10) cc_final: 0.6133 (m-10)
REVERT: A 1813 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7756 (tptp)
REVERT: A 1872 THR cc_start: 0.5795 (OUTLIER) cc_final: 0.5547 (m)
REVERT: A 1875 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6518 (mt-10)
REVERT: A 1927 ASP cc_start: 0.5601 (m-30) cc_final: 0.4991 (p0)
REVERT: A 1973 MET cc_start: 0.6347 (ttm) cc_final: 0.6079 (ttm)
REVERT: A 2108 ASP cc_start: 0.5365 (p0) cc_final: 0.4856 (p0)
REVERT: A 2176 MET cc_start: 0.3981 (mmp) cc_final: 0.3030 (mtp)
REVERT: A 2199 MET cc_start: 0.3347 (tpp) cc_final: 0.3066 (tpp)
REVERT: A 2235 GLN cc_start: 0.7618 (pp30) cc_final: 0.7384 (pp30)
REVERT: A 2238 MET cc_start: 0.6081 (mmm) cc_final: 0.5811 (mmm)
REVERT: A 2240 VAL cc_start: 0.7841 (m) cc_final: 0.7543 (p)
REVERT: A 2249 LYS cc_start: 0.7566 (tmmt) cc_final: 0.7126 (pttt)
REVERT: A 2289 SER cc_start: 0.7897 (p) cc_final: 0.7487 (t)
  outliers start: 24
  outliers final: 15
  residues processed: 212
  average time/residue: 0.0963
  time to fit residues: 28.9742
Evaluate side-chains
  200 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 184
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue 1770 ASN
Chi-restraints excluded: chain A residue 1872 THR
Chi-restraints excluded: chain A residue 1912 PHE
Chi-restraints excluded: chain A residue 1962 VAL
Chi-restraints excluded: chain A residue 1995 ILE
Chi-restraints excluded: chain A residue 2032 ILE
Chi-restraints excluded: chain A residue 2131 ASP
Chi-restraints excluded: chain A residue 2145 ILE
Chi-restraints excluded: chain A residue 2232 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 16 optimal weight:    0.1980
   chunk 106 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0970
   chunk 21 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2007 HIS
A2155 HIS
A2309 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.162969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.143692 restraints weight = 21297.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.147927 restraints weight = 12397.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.150807 restraints weight = 8147.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.152871 restraints weight = 5844.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.154351 restraints weight = 4458.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6227
moved from start:          0.5180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10441  Z= 0.159
  Angle     :  0.788  14.041  14167  Z= 0.384
  Chirality :  0.049   0.392   1517
  Planarity :  0.004   0.041   1794
  Dihedral  :  5.915  57.979   1420
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.01 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.24), residues: 1233
  helix: -1.93 (0.55), residues: 74
  sheet: -1.52 (0.31), residues: 295
  loop : -1.92 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 489 
 TYR   0.032   0.002   TYR A1890 
 PHE   0.021   0.002   PHE A 436 
 TRP   0.060   0.002   TRP A  14 
 HIS   0.017   0.001   HIS A 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.16 (10430)
  covalent geometry    : angle       0.77373 /  0.38 (14142)
  SS BOND              : bond        0.00251 /  0.14 (    8)
  SS BOND              : angle       3.40293 /  1.97 (   16)
  hydrogen bonds       : bond        0.03241 /  2.04 (  138)
  hydrogen bonds       : angle       6.30592 /  4.16 (  321)
  link_NAG-ASN         : bond        0.00816 /  0.26 (    3)
  link_NAG-ASN         : angle       3.87450 /  2.26 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1853.67 seconds
wall clock time: 32 minutes 55.42 seconds (1975.42 seconds total)