Starting phenix.real_space_refine
on Fri Sep 11 08:00:20 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6dmo_7964/09_2026/6dmo_7964.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dmo_7964/09_2026/6dmo_7964.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6dmo_7964/09_2026/6dmo_7964.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6dmo_7964/09_2026/6dmo_7964.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dmo_7964/09_2026/6dmo_7964.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dmo_7964/09_2026/6dmo_7964.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dmo_7964/09_2026/6dmo_7964.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dmo_7964/09_2026/6dmo_7964.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 764 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    5117      2.51       5
     N    1284      2.21       5
     O    1410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7853
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 982, 7755
          Classifications: {'peptide': 982}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 939}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.55, per 1000 atoms: 0.20
  Number of scatterers: 7853
  At special positions: 0
  Unit cell: (90.553, 78.552, 142.921, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1410      8.00
     N    1284      7.00
     C    5117      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 226 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 327 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 296 " - pdb=" SG  CYS A 304 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A1801 " - " ASN A 312 "
      " NAG A1802 " - " ASN A 349 "
      " NAG A1803 " - " ASN A 414 "
      " NAG A1804 " - " ASN A 875 "
      " NAG A1807 " - " ASN A 141 "
      " NAG B   1 " - " ASN A1000 "
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 452.3 milliseconds
  

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1844

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 4 sheets defined
      60.2% alpha, 4.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 97
      removed outlier: 3.595A  pdb=" N   TRP A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   PHE A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 115
      removed outlier: 3.785A  pdb=" N   PHE A 101 " --> pdb=" O   ASN A  97 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU A 102 " --> pdb=" O   CYS A  98 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   GLY A 115 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 147
    Processing helix  chain 'A' and resid 171 through 187
    Processing helix  chain 'A' and resid 216 through 223
      removed outlier: 3.598A  pdb=" N   ILE A 220 " --> pdb=" O   MET A 216 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU A 223 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 234
      removed outlier: 3.879A  pdb=" N   CYS A 234 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 241
      removed outlier: 3.734A  pdb=" N   ALA A 239 " --> pdb=" O   PHE A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 259
      removed outlier: 3.867A  pdb=" N   PHE A 259 " --> pdb=" O   TRP A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
    Processing helix  chain 'A' and resid 276 through 285
    Processing helix  chain 'A' and resid 338 through 343
      removed outlier: 3.840A  pdb=" N   ILE A 342 " --> pdb=" O   GLN A 338 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   VAL A 343 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 338 through 343'
    Processing helix  chain 'A' and resid 368 through 376
    Processing helix  chain 'A' and resid 389 through 411
      removed outlier: 4.270A  pdb=" N   VAL A 411 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 433
      removed outlier: 4.280A  pdb=" N   ASP A 428 " --> pdb=" O   THR A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 435
      No H-bonds generated for 'chain 'A' and resid 434 through 435'
    Processing helix  chain 'A' and resid 436 through 437
      No H-bonds generated for 'chain 'A' and resid 436 through 437'
    Processing helix  chain 'A' and resid 438 through 457
    Processing helix  chain 'A' and resid 466 through 491
      removed outlier: 4.131A  pdb=" N   GLY A 470 " --> pdb=" O   GLN A 466 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   LEU A 471 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 526
      removed outlier: 3.622A  pdb=" N   THR A 525 " --> pdb=" O   ALA A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 563
      removed outlier: 3.929A  pdb=" N   THR A 544 " --> pdb=" O   CYS A 540 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   ALA A 546 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   SER A 547 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA A 558 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 604
      Proline residue:  A 593  - end of helix
    Processing helix  chain 'A' and resid 732 through 744
      Proline residue:  A 742  - end of helix
    Processing helix  chain 'A' and resid 750 through 770
      removed outlier: 3.890A  pdb=" N   ILE A 754 " --> pdb=" O   LYS A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 798
    Processing helix  chain 'A' and resid 815 through 829
      removed outlier: 4.100A  pdb=" N   LEU A 819 " --> pdb=" O   ILE A 815 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   TYR A 820 " --> pdb=" O   GLN A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 843 through 863
      removed outlier: 4.311A  pdb=" N   TYR A 847 " --> pdb=" O   MET A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 885
      removed outlier: 3.630A  pdb=" N   VAL A 881 " --> pdb=" O   SER A 877 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A 882 " --> pdb=" O   ASP A 878 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A 883 " --> pdb=" O   ASP A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 905
    Processing helix  chain 'A' and resid 919 through 930
    Processing helix  chain 'A' and resid 930 through 937
      removed outlier: 3.860A  pdb=" N   TYR A 934 " --> pdb=" O   ASP A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 1003
      removed outlier: 3.612A  pdb=" N   PHE A 987 " --> pdb=" O   ASP A 983 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   SER A1003 " --> pdb=" O   SER A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1019
    Processing helix  chain 'A' and resid 1026 through 1046
    Processing helix  chain 'A' and resid 1052 through 1075
      removed outlier: 4.015A  pdb=" N   GLY A1075 " --> pdb=" O   MET A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1106
      removed outlier: 5.137A  pdb=" N   GLU A1095 " --> pdb=" O   GLY A1091 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   PHE A1096 " --> pdb=" O   ILE A1092 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   THR A1097 " --> pdb=" O   GLY A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1138
      removed outlier: 3.716A  pdb=" N   ALA A1118 " --> pdb=" O   ARG A1114 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   MET A1122 " --> pdb=" O   ALA A1118 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   ALA A1124 " --> pdb=" O   GLU A1120 " (cutoff:3.500A)
      Proline residue:  A1125  - end of helix
    Processing helix  chain 'A' and resid 1139 through 1141
      No H-bonds generated for 'chain 'A' and resid 1139 through 1141'
    Processing helix  chain 'A' and resid 1146 through 1178
      removed outlier: 5.043A  pdb=" N   ALA A1157 " --> pdb=" O   PHE A1153 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR A1160 " --> pdb=" O   LEU A1156 " (cutoff:3.500A)
      Proline residue:  A1172  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 366
      removed outlier: 3.931A  pdb=" N   LEU A 360 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET A 158 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN A 156 " --> pdb=" O   PHE A 364 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348
      removed outlier: 7.165A  pdb=" N   VAL A 347 " --> pdb=" O   VAL A 355 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 972 through 978
      removed outlier: 3.618A  pdb=" N   ALA A 972 " --> pdb=" O   THR A 807 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   TYR A 801 " --> pdb=" O   LEU A 978 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A1007 " --> pdb=" O   GLN A 808 " (cutoff:3.500A)

    419 hydrogen bonds defined for protein.
    1245 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: 1.36

  Time building geometry restraints manager: 1.01 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: 2410
        1.34 -     1.46: 1907
        1.46 -     1.58: 3658
        1.58 -     1.70: 0
        1.70 -     1.82: 69
  Bond restraints: 8044
  Sorted by residual:
  bond pdb=" C   MET A 869 "
       pdb=" N   PRO A 870 "
    ideal  model  delta    sigma   weight residual
    1.336  1.370 -0.034 9.80e-03 1.04e+04 1.23e+01
  bond pdb=" C1  NAG A1804 "
       pdb=" O5  NAG A1804 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 6.10e+00
  bond pdb=" C   PRO A 252 "
       pdb=" N   PRO A 253 "
    ideal  model  delta    sigma   weight residual
    1.334  1.390 -0.056 2.34e-02 1.83e+03 5.83e+00
  bond pdb=" C1  NAG A1801 "
       pdb=" O5  NAG A1801 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.52e+00
  bond pdb=" CB  PRO A1082 "
       pdb=" CG  PRO A1082 "
    ideal  model  delta    sigma   weight residual
    1.492  1.382  0.110 5.00e-02 4.00e+02 4.86e+00
  ... (remaining 8039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 10374
        2.58 -     5.16: 455
        5.16 -     7.74: 82
        7.74 -    10.33: 19
       10.33 -    12.91: 7
  Bond angle restraints: 10937
  Sorted by residual:
  angle pdb=" N   TYR A 224 "
        pdb=" CA  TYR A 224 "
        pdb=" C   TYR A 224 "
      ideal   model   delta    sigma   weight residual
     109.48   96.78   12.70 1.75e+00 3.27e-01 5.26e+01
  angle pdb=" N   GLU A 534 "
        pdb=" CA  GLU A 534 "
        pdb=" C   GLU A 534 "
      ideal   model   delta    sigma   weight residual
     112.72  106.95    5.77 1.28e+00 6.10e-01 2.04e+01
  angle pdb=" C   PHE A 259 "
        pdb=" N   ASP A 260 "
        pdb=" CA  ASP A 260 "
      ideal   model   delta    sigma   weight residual
     121.80  132.76  -10.96 2.44e+00 1.68e-01 2.02e+01
  angle pdb=" N   ILE A 219 "
        pdb=" CA  ILE A 219 "
        pdb=" C   ILE A 219 "
      ideal   model   delta    sigma   weight residual
     111.05  116.54   -5.49 1.25e+00 6.40e-01 1.93e+01
  angle pdb=" CG1 ILE A 815 "
        pdb=" CB  ILE A 815 "
        pdb=" CG2 ILE A 815 "
      ideal   model   delta    sigma   weight residual
     110.70   97.79   12.91 3.00e+00 1.11e-01 1.85e+01
  ... (remaining 10932 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 4290
       17.81 -    35.62: 313
       35.62 -    53.43: 72
       53.43 -    71.23: 7
       71.23 -    89.04: 11
  Dihedral angle restraints: 4693
    sinusoidal: 1827
      harmonic: 2866
  Sorted by residual:
  dihedral pdb=" CA  ASN A1049 "
           pdb=" C   ASN A1049 "
           pdb=" N   PRO A1050 "
           pdb=" CA  PRO A1050 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -124.52  -55.48     0      5.00e+00 4.00e-02 1.23e+02
  dihedral pdb=" CB  CYS A 296 "
           pdb=" SG  CYS A 296 "
           pdb=" SG  CYS A 304 "
           pdb=" CB  CYS A 304 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.96  -89.04     1      1.00e+01 1.00e-02 9.44e+01
  dihedral pdb=" CA  LYS A 867 "
           pdb=" C   LYS A 867 "
           pdb=" N   ILE A 868 "
           pdb=" CA  ILE A 868 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.82  -48.18     0      5.00e+00 4.00e-02 9.28e+01
  ... (remaining 4690 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 960
       0.067 -    0.135: 255
       0.135 -    0.202: 43
       0.202 -    0.270: 6
       0.270 -    0.337: 2
  Chirality restraints: 1266
  Sorted by residual:
  chirality pdb=" CB  ILE A 531 "
            pdb=" CA  ILE A 531 "
            pdb=" CG1 ILE A 531 "
            pdb=" CG2 ILE A 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.84e+00
  chirality pdb=" CB  ILE A 815 "
            pdb=" CA  ILE A 815 "
            pdb=" CG1 ILE A 815 "
            pdb=" CG2 ILE A 815 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.94   -0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.37   -0.03 2.00e-02 2.50e+03 1.79e+00
  ... (remaining 1263 not shown)

  Planarity restraints: 1370
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1049 "    0.051 5.00e-02 4.00e+02   7.78e-02 9.68e+00
        pdb=" N   PRO A1050 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO A1050 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A1050 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 741 "    0.044 5.00e-02 4.00e+02   6.68e-02 7.14e+00
        pdb=" N   PRO A 742 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 742 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 742 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1165 "   -0.013 2.00e-02 2.50e+03   2.54e-02 6.46e+00
        pdb=" C   LEU A1165 "    0.044 2.00e-02 2.50e+03
        pdb=" O   LEU A1165 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN A1166 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1367 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 21
        2.39 -     3.02: 4207
        3.02 -     3.65: 12274
        3.65 -     4.27: 16593
        4.27 -     4.90: 26909
  Nonbonded interactions: 60004
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 120 "
            pdb=" OG  SER A 494 "
     model   vdw
     1.764 3.040
  nonbonded pdb=" O   GLU A 864 "
            pdb=" CG2 THR A 865 "
     model   vdw
     2.038 3.460
  nonbonded pdb=" O   ALA A 939 "
            pdb=" CD1 ILE A 941 "
     model   vdw
     2.276 3.460
  nonbonded pdb=" OE1 GLN A 400 "
            pdb=" OG1 THR A 425 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ASN A 154 "
            pdb=" NE2 GLN A 156 "
     model   vdw
     2.285 3.120
  ... (remaining 59999 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.700
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6420
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      :  0.008   0.110   8054  Z= 0.355
  Angle     :  1.289  12.908  10964  Z= 0.659
  Chirality :  0.063   0.337   1266
  Planarity :  0.009   0.078   1364
  Dihedral  : 13.730  82.995   2840
  Min Nonbonded Distance : 1.764

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.07 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 10.77 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.14 %
    Twisted General : 0.21 %

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: -4.11 (0.21), residues: 976
  helix: -2.12 (0.17), residues: 553
  sheet: -2.15 (0.71), residues: 47
  loop : -3.63 (0.27), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG A 786 
 TYR   0.035   0.003   TYR A 812 
 PHE   0.037   0.004   PHE A1153 
 TRP   0.027   0.003   TRP A 399 
 HIS   0.020   0.003   HIS A1099 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00777 /  0.35 ( 8044)
  covalent geometry    : angle       1.27061 /  0.66 (10937)
  SS BOND              : bond        0.00994 /  0.49 (    3)
  SS BOND              : angle       2.12103 /  1.16 (    6)
  hydrogen bonds       : bond        0.14799 / 10.38 (  419)
  hydrogen bonds       : angle       7.11781 /  5.15 ( 1245)
  link_BETA1-4         : bond        0.00563 /  0.30 (    1)
  link_BETA1-4         : angle       2.18731 /  1.08 (    3)
  link_NAG-ASN         : bond        0.00602 /  0.34 (    6)
  link_NAG-ASN         : angle       5.30445 /  3.07 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 303
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8126 (pttt) cc_final: 0.7918 (tptt)
REVERT: A   86 LEU cc_start: 0.8533 (mt) cc_final: 0.8260 (tp)
REVERT: A   94 ILE cc_start: 0.8773 (mt) cc_final: 0.8519 (tp)
REVERT: A  172 THR cc_start: 0.7547 (p) cc_final: 0.7155 (p)
REVERT: A  254 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6164 (tm)
REVERT: A  319 MET cc_start: 0.7461 (mpm) cc_final: 0.7067 (mmm)
REVERT: A  373 TYR cc_start: 0.8123 (t80) cc_final: 0.7567 (t80)
REVERT: A  430 ILE cc_start: 0.8330 (mm) cc_final: 0.8114 (pt)
REVERT: A  791 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8437 (mt)
REVERT: A 1087 ILE cc_start: 0.8254 (mm) cc_final: 0.8037 (mm)
REVERT: A 1105 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7613 (tm)
REVERT: A 1166 ASN cc_start: 0.8414 (t0) cc_final: 0.8052 (t0)
REVERT: A 1178 PHE cc_start: 0.7848 (p90) cc_final: 0.7575 (t80)
  outliers start: 23
  outliers final: 3
  residues processed: 316
  average time/residue: 0.0910
  time to fit residues: 38.9396
Evaluate side-chains
  200 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 194
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.3980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 GLN
A 289 HIS
A 358 HIS
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 584 ASN
A 802 ASN
A 853 GLN
A 929 ASN
A 950 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.129787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.110349 restraints weight = 20445.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.113439 restraints weight = 12002.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.115662 restraints weight = 8253.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.117256 restraints weight = 6268.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.118287 restraints weight = 5111.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8054  Z= 0.164
  Angle     :  0.892  10.252  10964  Z= 0.435
  Chirality :  0.052   0.514   1266
  Planarity :  0.006   0.064   1364
  Dihedral  :  7.192  52.413   1061
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.45 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  5.21 %
    Favored  : 94.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.11 %

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: -2.11 (0.26), residues: 976
  helix: -0.18 (0.21), residues: 546
  sheet: -1.96 (0.75), residues: 52
  loop : -3.19 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 536 
 TYR   0.022   0.002   TYR A 142 
 PHE   0.033   0.002   PHE A 790 
 TRP   0.021   0.002   TRP A 129 
 HIS   0.007   0.001   HIS A 178 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 ( 8044)
  covalent geometry    : angle       0.86964 /  0.43 (10937)
  SS BOND              : bond        0.00797 /  0.42 (    3)
  SS BOND              : angle       1.98404 /  1.14 (    6)
  hydrogen bonds       : bond        0.04919 /  3.36 (  419)
  hydrogen bonds       : angle       5.34911 /  3.86 ( 1245)
  link_BETA1-4         : bond        0.00819 /  0.43 (    1)
  link_BETA1-4         : angle       0.94607 /  0.38 (    3)
  link_NAG-ASN         : bond        0.01496 /  0.90 (    6)
  link_NAG-ASN         : angle       4.81610 /  3.19 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 227
  time to evaluate  : 0.297 
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   74 LYS cc_start: 0.8442 (pttt) cc_final: 0.8150 (tptt)
REVERT: A  196 GLN cc_start: 0.7734 (tm-30) cc_final: 0.6736 (tm-30)
REVERT: A  373 TYR cc_start: 0.8006 (t80) cc_final: 0.7385 (t80)
REVERT: A  476 LEU cc_start: 0.9333 (tt) cc_final: 0.8953 (pp)
REVERT: A  791 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8422 (mt)
REVERT: A  795 PHE cc_start: 0.7438 (m-80) cc_final: 0.7214 (m-80)
REVERT: A 1015 PHE cc_start: 0.6893 (m-80) cc_final: 0.6688 (m-10)
REVERT: A 1087 ILE cc_start: 0.8170 (mm) cc_final: 0.7881 (mm)
REVERT: A 1117 LEU cc_start: 0.8715 (mp) cc_final: 0.8427 (mt)
REVERT: A 1166 ASN cc_start: 0.8707 (t0) cc_final: 0.8482 (t0)
REVERT: A 1178 PHE cc_start: 0.7894 (p90) cc_final: 0.7490 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 229
  average time/residue: 0.0802
  time to fit residues: 25.8137
Evaluate side-chains
  164 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 26 optimal weight:   20.0000
   chunk 39 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0070
   chunk 63 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.5802

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 145 GLN
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 GLN
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 HIS
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 828 ASN
A 915 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.124226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.104642 restraints weight = 20735.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.107524 restraints weight = 12417.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.109658 restraints weight = 8675.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.111199 restraints weight = 6636.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.112165 restraints weight = 5426.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.5049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8054  Z= 0.170
  Angle     :  0.821  11.445  10964  Z= 0.407
  Chirality :  0.047   0.268   1266
  Planarity :  0.006   0.068   1364
  Dihedral  :  6.579  49.577   1061
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  6.05 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.27), residues: 976
  helix:  0.49 (0.22), residues: 545
  sheet: -1.73 (0.76), residues: 51
  loop : -2.96 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 962 
 TYR   0.015   0.002   TYR A 142 
 PHE   0.029   0.002   PHE A 790 
 TRP   0.028   0.002   TRP A 926 
 HIS   0.003   0.001   HIS A 201 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.17 ( 8044)
  covalent geometry    : angle       0.80770 /  0.40 (10937)
  SS BOND              : bond        0.00845 /  0.44 (    3)
  SS BOND              : angle       1.88662 /  1.11 (    6)
  hydrogen bonds       : bond        0.04682 /  3.13 (  419)
  hydrogen bonds       : angle       4.99820 /  3.61 ( 1245)
  link_BETA1-4         : bond        0.00360 /  0.19 (    1)
  link_BETA1-4         : angle       0.75367 /  0.35 (    3)
  link_NAG-ASN         : bond        0.00482 /  0.27 (    6)
  link_NAG-ASN         : angle       3.52814 /  2.00 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 216
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8502 (pttt) cc_final: 0.8090 (tptt)
REVERT: A  103 VAL cc_start: 0.7665 (t) cc_final: 0.7361 (p)
REVERT: A  228 ILE cc_start: 0.8776 (mt) cc_final: 0.8571 (mp)
REVERT: A  475 LEU cc_start: 0.9026 (tt) cc_final: 0.8811 (pp)
REVERT: A  833 MET cc_start: 0.6349 (tpp) cc_final: 0.6143 (tpp)
REVERT: A 1056 ILE cc_start: 0.8564 (mm) cc_final: 0.8237 (mm)
REVERT: A 1066 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7549 (tm-30)
REVERT: A 1087 ILE cc_start: 0.8382 (mm) cc_final: 0.8083 (mm)
REVERT: A 1097 THR cc_start: 0.8505 (p) cc_final: 0.8214 (p)
REVERT: A 1178 PHE cc_start: 0.8072 (p90) cc_final: 0.7551 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 218
  average time/residue: 0.0720
  time to fit residues: 22.4680
Evaluate side-chains
  155 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 92 optimal weight:    0.6980
   chunk 88 optimal weight:    0.4980
   chunk 35 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0030
   chunk 66 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0000
   overall best weight:    0.4394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 HIS
A 365 GLN
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.125930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.106372 restraints weight = 20497.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.109511 restraints weight = 11862.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.111717 restraints weight = 8060.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.113318 restraints weight = 6110.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.114479 restraints weight = 4965.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.5683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8054  Z= 0.143
  Angle     :  0.829  15.425  10964  Z= 0.396
  Chirality :  0.048   0.275   1266
  Planarity :  0.005   0.069   1364
  Dihedral  :  6.238  48.549   1061
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.87 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.27), residues: 976
  helix:  0.69 (0.22), residues: 543
  sheet: -1.45 (0.74), residues: 51
  loop : -2.98 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 960 
 TYR   0.015   0.001   TYR A 191 
 PHE   0.024   0.002   PHE A 790 
 TRP   0.022   0.002   TRP A 129 
 HIS   0.004   0.001   HIS A 201 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.14 ( 8044)
  covalent geometry    : angle       0.80435 /  0.39 (10937)
  SS BOND              : bond        0.00800 /  0.42 (    3)
  SS BOND              : angle       1.71239 /  1.00 (    6)
  hydrogen bonds       : bond        0.04247 /  2.82 (  419)
  hydrogen bonds       : angle       4.82407 /  3.48 ( 1245)
  link_BETA1-4         : bond        0.00599 /  0.32 (    1)
  link_BETA1-4         : angle       0.80216 /  0.41 (    3)
  link_NAG-ASN         : bond        0.01080 /  0.69 (    6)
  link_NAG-ASN         : angle       4.90516 /  3.83 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 204
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8390 (pttt) cc_final: 0.8090 (tptt)
REVERT: A  103 VAL cc_start: 0.7642 (t) cc_final: 0.7345 (p)
REVERT: A  158 MET cc_start: 0.7957 (tmm) cc_final: 0.7705 (tmm)
REVERT: A  228 ILE cc_start: 0.8538 (mt) cc_final: 0.8296 (pt)
REVERT: A  432 LYS cc_start: 0.8329 (tppt) cc_final: 0.7908 (tppt)
REVERT: A  475 LEU cc_start: 0.9029 (tt) cc_final: 0.8775 (pp)
REVERT: A  522 PHE cc_start: 0.8289 (t80) cc_final: 0.8064 (t80)
REVERT: A  791 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8521 (mp)
REVERT: A  795 PHE cc_start: 0.7530 (m-80) cc_final: 0.7295 (m-80)
REVERT: A  833 MET cc_start: 0.6350 (tpp) cc_final: 0.6106 (tpp)
REVERT: A 1087 ILE cc_start: 0.8245 (mm) cc_final: 0.8039 (mm)
REVERT: A 1162 LEU cc_start: 0.8601 (tp) cc_final: 0.8307 (tp)
REVERT: A 1178 PHE cc_start: 0.7960 (p90) cc_final: 0.7415 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0737
  time to fit residues: 21.8226
Evaluate side-chains
  154 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 62 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 45 optimal weight:    8.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 GLN
A 258 ASN
A 358 HIS
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 GLN
A 520 HIS
A 828 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.121491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.102537 restraints weight = 20747.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.105638 restraints weight = 11996.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.107807 restraints weight = 8129.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.109350 restraints weight = 6158.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.110346 restraints weight = 4978.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.6403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8054  Z= 0.156
  Angle     :  0.812  12.093  10964  Z= 0.395
  Chirality :  0.048   0.249   1266
  Planarity :  0.005   0.068   1364
  Dihedral  :  6.031  45.602   1061
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.45 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.63 %
    Favored  : 96.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.28), residues: 976
  helix:  0.87 (0.22), residues: 544
  sheet: -1.33 (0.76), residues: 51
  loop : -2.91 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 960 
 TYR   0.020   0.002   TYR A 873 
 PHE   0.020   0.002   PHE A 790 
 TRP   0.038   0.002   TRP A 278 
 HIS   0.006   0.001   HIS A 178 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.16 ( 8044)
  covalent geometry    : angle       0.79439 /  0.39 (10937)
  SS BOND              : bond        0.00325 /  0.17 (    3)
  SS BOND              : angle       1.12321 /  0.66 (    6)
  hydrogen bonds       : bond        0.04290 /  2.87 (  419)
  hydrogen bonds       : angle       4.80894 /  3.46 ( 1245)
  link_BETA1-4         : bond        0.00239 /  0.13 (    1)
  link_BETA1-4         : angle       0.91781 /  0.46 (    3)
  link_NAG-ASN         : bond        0.00814 /  0.51 (    6)
  link_NAG-ASN         : angle       4.22927 /  3.29 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8425 (pttt) cc_final: 0.8147 (tptt)
REVERT: A  103 VAL cc_start: 0.7744 (t) cc_final: 0.7485 (p)
REVERT: A  216 MET cc_start: 0.5422 (tpp) cc_final: 0.4263 (tpt)
REVERT: A  292 MET cc_start: 0.5146 (mmp) cc_final: 0.4242 (mmp)
REVERT: A  432 LYS cc_start: 0.8306 (tppt) cc_final: 0.7950 (tppt)
REVERT: A  475 LEU cc_start: 0.9043 (tt) cc_final: 0.8815 (pp)
REVERT: A  791 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.9014 (mp)
REVERT: A  920 TYR cc_start: 0.7692 (m-10) cc_final: 0.7437 (m-10)
REVERT: A 1087 ILE cc_start: 0.8378 (mm) cc_final: 0.8161 (mm)
REVERT: A 1146 ASP cc_start: 0.7077 (t0) cc_final: 0.6764 (t0)
REVERT: A 1162 LEU cc_start: 0.8598 (tp) cc_final: 0.8348 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0685
  time to fit residues: 20.5202
Evaluate side-chains
  152 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 13 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    1.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 HIS
A 375 HIS
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 871 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.118600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.099735 restraints weight = 20852.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.102684 restraints weight = 12028.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.104768 restraints weight = 8175.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.106123 restraints weight = 6205.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.107199 restraints weight = 5113.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.7165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8054  Z= 0.157
  Angle     :  0.800  12.286  10964  Z= 0.389
  Chirality :  0.047   0.240   1266
  Planarity :  0.005   0.070   1364
  Dihedral  :  5.928  45.702   1061
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.27), residues: 976
  helix:  0.87 (0.22), residues: 545
  sheet: -1.21 (0.78), residues: 51
  loop : -2.74 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 772 
 TYR   0.011   0.001   TYR A 873 
 PHE   0.026   0.002   PHE A 790 
 TRP   0.027   0.002   TRP A 129 
 HIS   0.007   0.001   HIS A 178 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.16 ( 8044)
  covalent geometry    : angle       0.78104 /  0.38 (10937)
  SS BOND              : bond        0.00326 /  0.17 (    3)
  SS BOND              : angle       1.08856 /  0.64 (    6)
  hydrogen bonds       : bond        0.04238 /  2.86 (  419)
  hydrogen bonds       : angle       4.77109 /  3.46 ( 1245)
  link_BETA1-4         : bond        0.00088 /  0.05 (    1)
  link_BETA1-4         : angle       1.05708 /  0.56 (    3)
  link_NAG-ASN         : bond        0.00673 /  0.43 (    6)
  link_NAG-ASN         : angle       4.30106 /  3.39 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.7701 (t) cc_final: 0.7494 (p)
REVERT: A  154 ASN cc_start: 0.8884 (t0) cc_final: 0.8470 (m110)
REVERT: A  475 LEU cc_start: 0.9072 (tt) cc_final: 0.8773 (pp)
REVERT: A  993 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8680 (mmtm)
REVERT: A 1139 MET cc_start: 0.8528 (pmm) cc_final: 0.7576 (ptm)
REVERT: A 1146 ASP cc_start: 0.7219 (t0) cc_final: 0.6934 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0731
  time to fit residues: 20.8443
Evaluate side-chains
  147 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 76 optimal weight:    0.4980
   overall best weight:    1.4186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 GLN
A 358 HIS
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 823 HIS
A 871 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.117446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.098257 restraints weight = 21288.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.101257 restraints weight = 12270.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.103371 restraints weight = 8326.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.104864 restraints weight = 6298.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.105959 restraints weight = 5140.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.7730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8054  Z= 0.154
  Angle     :  0.797  12.126  10964  Z= 0.388
  Chirality :  0.047   0.267   1266
  Planarity :  0.005   0.073   1364
  Dihedral  :  5.802  43.871   1061
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.28), residues: 976
  helix:  0.93 (0.22), residues: 545
  sheet: -1.18 (0.78), residues: 51
  loop : -2.66 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 962 
 TYR   0.018   0.001   TYR A 922 
 PHE   0.019   0.002   PHE A1031 
 TRP   0.041   0.002   TRP A 844 
 HIS   0.005   0.001   HIS A 178 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 ( 8044)
  covalent geometry    : angle       0.77968 /  0.38 (10937)
  SS BOND              : bond        0.00281 /  0.14 (    3)
  SS BOND              : angle       1.70477 /  1.00 (    6)
  hydrogen bonds       : bond        0.04218 /  2.79 (  419)
  hydrogen bonds       : angle       4.77754 /  3.46 ( 1245)
  link_BETA1-4         : bond        0.00322 /  0.17 (    1)
  link_BETA1-4         : angle       1.01640 /  0.55 (    3)
  link_NAG-ASN         : bond        0.00778 /  0.50 (    6)
  link_NAG-ASN         : angle       4.07783 /  3.26 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 PHE cc_start: 0.7526 (m-80) cc_final: 0.7320 (m-10)
REVERT: A  154 ASN cc_start: 0.8962 (t0) cc_final: 0.8457 (m110)
REVERT: A  475 LEU cc_start: 0.9031 (tt) cc_final: 0.8752 (pp)
REVERT: A  843 MET cc_start: 0.6909 (mtt) cc_final: 0.6607 (mtt)
REVERT: A 1041 LEU cc_start: 0.8851 (tp) cc_final: 0.8534 (tt)
REVERT: A 1146 ASP cc_start: 0.7291 (t0) cc_final: 0.7082 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0695
  time to fit residues: 19.8490
Evaluate side-chains
  142 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 35 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 6 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 196 GLN
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 HIS
A 584 ASN
A 828 ASN
A 871 ASN
A 950 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.113343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.094717 restraints weight = 21755.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.097650 restraints weight = 12232.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.099713 restraints weight = 8200.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.101161 restraints weight = 6161.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.102178 restraints weight = 5015.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.8446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8054  Z= 0.179
  Angle     :  0.832  12.071  10964  Z= 0.407
  Chirality :  0.048   0.318   1266
  Planarity :  0.005   0.073   1364
  Dihedral  :  5.958  43.327   1061
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.82 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.28), residues: 976
  helix:  1.00 (0.23), residues: 534
  sheet: -1.23 (0.78), residues: 51
  loop : -2.55 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 962 
 TYR   0.013   0.002   TYR A 922 
 PHE   0.020   0.002   PHE A1153 
 TRP   0.034   0.002   TRP A 844 
 HIS   0.005   0.001   HIS A 178 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 ( 8044)
  covalent geometry    : angle       0.81475 /  0.40 (10937)
  SS BOND              : bond        0.00324 /  0.16 (    3)
  SS BOND              : angle       1.78791 /  1.05 (    6)
  hydrogen bonds       : bond        0.04378 /  2.90 (  419)
  hydrogen bonds       : angle       4.78662 /  3.48 ( 1245)
  link_BETA1-4         : bond        0.00113 /  0.06 (    1)
  link_BETA1-4         : angle       0.93673 /  0.52 (    3)
  link_NAG-ASN         : bond        0.00728 /  0.46 (    6)
  link_NAG-ASN         : angle       4.12220 /  3.29 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 PHE cc_start: 0.7421 (m-80) cc_final: 0.7183 (m-10)
REVERT: A  154 ASN cc_start: 0.8912 (t0) cc_final: 0.8540 (m110)
REVERT: A  220 ILE cc_start: 0.6419 (mm) cc_final: 0.6151 (mm)
REVERT: A  372 MET cc_start: 0.7769 (ttm) cc_final: 0.7530 (ttm)
REVERT: A  513 ASP cc_start: 0.7980 (t0) cc_final: 0.7762 (m-30)
REVERT: A  561 MET cc_start: 0.7796 (tpt) cc_final: 0.7574 (tpt)
REVERT: A 1097 THR cc_start: 0.8879 (p) cc_final: 0.8670 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 191
  average time/residue: 0.0665
  time to fit residues: 19.1204
Evaluate side-chains
  133 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0270
   chunk 46 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.7640

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 HIS
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 584 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.117032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.098202 restraints weight = 21428.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.101199 restraints weight = 12199.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.103333 restraints weight = 8215.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.104851 restraints weight = 6181.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.105797 restraints weight = 5015.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.8790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8054  Z= 0.144
  Angle     :  0.805  11.992  10964  Z= 0.385
  Chirality :  0.047   0.221   1266
  Planarity :  0.005   0.075   1364
  Dihedral  :  5.697  43.262   1061
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.28), residues: 976
  helix:  1.05 (0.22), residues: 525
  sheet: -1.10 (0.79), residues: 51
  loop : -2.44 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 960 
 TYR   0.018   0.001   TYR A 922 
 PHE   0.037   0.002   PHE A1031 
 TRP   0.021   0.002   TRP A 129 
 HIS   0.004   0.001   HIS A 178 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 8044)
  covalent geometry    : angle       0.78909 /  0.38 (10937)
  SS BOND              : bond        0.00171 /  0.08 (    3)
  SS BOND              : angle       1.28866 /  0.75 (    6)
  hydrogen bonds       : bond        0.04082 /  2.73 (  419)
  hydrogen bonds       : angle       4.71297 /  3.41 ( 1245)
  link_BETA1-4         : bond        0.00346 /  0.18 (    1)
  link_BETA1-4         : angle       1.01188 /  0.57 (    3)
  link_NAG-ASN         : bond        0.00714 /  0.46 (    6)
  link_NAG-ASN         : angle       3.98558 /  3.22 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 MET cc_start: 0.6240 (tmm) cc_final: 0.5959 (tmm)
REVERT: A  372 MET cc_start: 0.7621 (ttm) cc_final: 0.7415 (ttm)
REVERT: A  561 MET cc_start: 0.7869 (tpt) cc_final: 0.7647 (tpt)
REVERT: A  825 SER cc_start: 0.8959 (m) cc_final: 0.8742 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0685
  time to fit residues: 19.2761
Evaluate side-chains
  140 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 45 optimal weight:    0.1980
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 289 HIS
A 358 HIS
A 520 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.116059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.097131 restraints weight = 21435.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.099941 restraints weight = 12531.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.102012 restraints weight = 8664.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.103338 restraints weight = 6612.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.104434 restraints weight = 5490.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.9104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8054  Z= 0.148
  Angle     :  0.819  12.059  10964  Z= 0.391
  Chirality :  0.047   0.285   1266
  Planarity :  0.005   0.075   1364
  Dihedral  :  5.716  42.921   1061
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.85 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.28), residues: 976
  helix:  1.09 (0.23), residues: 526
  sheet: -1.08 (0.78), residues: 51
  loop : -2.43 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 960 
 TYR   0.017   0.001   TYR A 873 
 PHE   0.025   0.002   PHE A 859 
 TRP   0.026   0.002   TRP A 844 
 HIS   0.003   0.001   HIS A 817 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.15 ( 8044)
  covalent geometry    : angle       0.80348 /  0.39 (10937)
  SS BOND              : bond        0.00226 /  0.11 (    3)
  SS BOND              : angle       1.24021 /  0.72 (    6)
  hydrogen bonds       : bond        0.04148 /  2.73 (  419)
  hydrogen bonds       : angle       4.69068 /  3.40 ( 1245)
  link_BETA1-4         : bond        0.00252 /  0.13 (    1)
  link_BETA1-4         : angle       0.99746 /  0.56 (    3)
  link_NAG-ASN         : bond        0.00725 /  0.47 (    6)
  link_NAG-ASN         : angle       3.96933 /  3.22 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LEU cc_start: 0.8936 (tt) cc_final: 0.8486 (tt)
REVERT: A  372 MET cc_start: 0.7716 (ttm) cc_final: 0.7502 (ttm)
REVERT: A  825 SER cc_start: 0.9120 (m) cc_final: 0.8885 (p)
REVERT: A  984 THR cc_start: 0.7298 (m) cc_final: 0.7013 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 185
  average time/residue: 0.0657
  time to fit residues: 18.2824
Evaluate side-chains
  137 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 73 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 77 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 154 ASN
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 GLN
A 289 HIS
A 358 HIS
A 584 ASN
** A 823 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.115103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.096494 restraints weight = 21563.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.099349 restraints weight = 12510.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.101376 restraints weight = 8570.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.102826 restraints weight = 6537.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.103874 restraints weight = 5358.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.9371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8054  Z= 0.150
  Angle     :  0.818  12.197  10964  Z= 0.393
  Chirality :  0.048   0.347   1266
  Planarity :  0.005   0.074   1364
  Dihedral  :  5.694  42.993   1061
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.35 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.36 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.28), residues: 976
  helix:  1.05 (0.23), residues: 527
  sheet: -1.13 (0.78), residues: 51
  loop : -2.51 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 962 
 TYR   0.016   0.001   TYR A 452 
 PHE   0.027   0.002   PHE A1096 
 TRP   0.021   0.002   TRP A 844 
 HIS   0.004   0.001   HIS A 817 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.15 ( 8044)
  covalent geometry    : angle       0.80253 /  0.39 (10937)
  SS BOND              : bond        0.00272 /  0.13 (    3)
  SS BOND              : angle       1.31391 /  0.77 (    6)
  hydrogen bonds       : bond        0.04171 /  2.75 (  419)
  hydrogen bonds       : angle       4.67981 /  3.40 ( 1245)
  link_BETA1-4         : bond        0.00170 /  0.09 (    1)
  link_BETA1-4         : angle       1.03903 /  0.58 (    3)
  link_NAG-ASN         : bond        0.00745 /  0.48 (    6)
  link_NAG-ASN         : angle       3.95926 /  3.21 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1407.02 seconds
wall clock time: 25 minutes 0.75 seconds (1500.75 seconds total)