Starting phenix.real_space_refine
on Wed Feb  4 20:32:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jl4_61578/02_2026/9jl4_61578.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jl4_61578/02_2026/9jl4_61578.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jl4_61578/02_2026/9jl4_61578.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jl4_61578/02_2026/9jl4_61578.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jl4_61578/02_2026/9jl4_61578.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jl4_61578/02_2026/9jl4_61578.map"
  }
  resolution = 4.0
  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 7054 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      13      5.16       5
     C    4509      2.51       5
     N    1221      2.21       5
     O    1311      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7054
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 874, 7054
          Classifications: {'peptide': 874}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 23, 'TRANS': 850}
          Chain breaks: 20
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 3, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 63
  Time building chain proxies: 1.70, per 1000 atoms: 0.24
  Number of scatterers: 7054
  At special positions: 0
  Unit cell: (71.94, 104.94, 116.82, 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      13     16.00
     O    1311      8.00
     N    1221      7.00
     C    4509      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 193.6 milliseconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1672

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      58.1% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 64
    Processing helix  chain 'A' and resid 69 through 94
      removed outlier: 3.565A  pdb=" N   ILE A  85 " --> pdb=" O   TYR A  81 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 101
      removed outlier: 3.589A  pdb=" N   LEU A 101 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 139 through 145
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.949A  pdb=" N   PHE A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 180
      removed outlier: 3.861A  pdb=" N   SER A 179 " --> pdb=" O   ASN A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 194
    Processing helix  chain 'A' and resid 217 through 228
    Processing helix  chain 'A' and resid 236 through 247
    Processing helix  chain 'A' and resid 252 through 257
    Processing helix  chain 'A' and resid 270 through 283
    Processing helix  chain 'A' and resid 286 through 307
    Processing helix  chain 'A' and resid 315 through 343
    Processing helix  chain 'A' and resid 343 through 352
      removed outlier: 4.270A  pdb=" N   LYS A 348 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLU A 349 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 376
    Processing helix  chain 'A' and resid 411 through 427
    Processing helix  chain 'A' and resid 430 through 436
    Processing helix  chain 'A' and resid 436 through 446
      removed outlier: 3.531A  pdb=" N   GLU A 441 " --> pdb=" O   ARG A 437 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A 444 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 727
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 5.570A  pdb=" N   GLY A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ILE A 737 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A 741 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS A 742 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LYS A 749 " --> pdb=" O   ASP A 745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 791
      removed outlier: 3.511A  pdb=" N   ARG A 783 " --> pdb=" O   GLU A 779 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE A 784 " --> pdb=" O   ARG A 780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 878
      removed outlier: 3.520A  pdb=" N   LYS A 878 " --> pdb=" O   GLU A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 889
      removed outlier: 3.611A  pdb=" N   GLN A 885 " --> pdb=" O   ASN A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 902
      removed outlier: 3.802A  pdb=" N   THR A 901 " --> pdb=" O   PHE A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 910 through 922
      removed outlier: 4.217A  pdb=" N   GLY A 915 " --> pdb=" O   LEU A 911 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   PHE A 916 " --> pdb=" O   ASP A 912 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE A 917 " --> pdb=" O   LYS A 913 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYS A 918 " --> pdb=" O   ALA A 914 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLN A 920 " --> pdb=" O   PHE A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 940
      removed outlier: 3.556A  pdb=" N   LYS A 929 " --> pdb=" O   ARG A 925 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 970
      removed outlier: 3.818A  pdb=" N   PHE A 966 " --> pdb=" O   LEU A 962 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   PHE A 970 " --> pdb=" O   PHE A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 1001
      removed outlier: 4.338A  pdb=" N   ALA A 991 " --> pdb=" O   ALA A 987 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL A 992 " --> pdb=" O   TYR A 988 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   VAL A 993 " --> pdb=" O   LEU A 989 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   GLY A 994 " --> pdb=" O   ASN A 990 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ALA A 996 " --> pdb=" O   VAL A 992 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LYS A 999 " --> pdb=" O   THR A 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1009
      removed outlier: 3.832A  pdb=" N   PHE A1008 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1017 through 1022
    Processing helix  chain 'A' and resid 1043 through 1047
      removed outlier: 3.502A  pdb=" N   PHE A1046 " --> pdb=" O   MET A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1088
      removed outlier: 4.097A  pdb=" N   PHE A1080 " --> pdb=" O   LYS A1076 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   ALA A1081 " --> pdb=" O   GLY A1077 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ARG A1084 " --> pdb=" O   PHE A1080 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   SER A1088 " --> pdb=" O   ARG A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1168 through 1177
      removed outlier: 4.275A  pdb=" N   SER A1172 " --> pdb=" O   ILE A1168 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER A1173 " --> pdb=" O   MET A1169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1186
      removed outlier: 3.688A  pdb=" N   LYS A1185 " --> pdb=" O   PHE A1181 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLY A1186 " --> pdb=" O   LEU A1182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1229 through 1241
      removed outlier: 4.025A  pdb=" N   LEU A1236 " --> pdb=" O   TYR A1232 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TYR A1237 " --> pdb=" O   VAL A1233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1262
    Processing helix  chain 'A' and resid 1263 through 1280
      removed outlier: 4.234A  pdb=" N   ASP A1267 " --> pdb=" O   LYS A1263 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
      removed outlier: 4.266A  pdb=" N   LYS A1289 " --> pdb=" O   ALA A1285 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TYR A1294 " --> pdb=" O   VAL A1290 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ASN A1295 " --> pdb=" O   LEU A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 3.509A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1314 through 1316
      No H-bonds generated for 'chain 'A' and resid 1314 through 1316'
    Processing helix  chain 'A' and resid 1340 through 1345
      removed outlier: 4.273A  pdb=" N   ASP A1344 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33
      removed outlier: 6.268A  pdb=" N   LEU A  47 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A  19 " --> pdb=" O   GLY A   8 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
      removed outlier: 4.047A  pdb=" N   ASN A1093 " --> pdb=" O   ASN A  46 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   ILE A  48 " --> pdb=" O   ASN A1093 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL A1095 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ALA A  50 " --> pdb=" O   VAL A1095 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 839 through 840
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1049 through 1051
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1063 through 1065
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1145
      removed outlier: 6.604A  pdb=" N   ILE A1166 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   SER A1142 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU A1164 " --> pdb=" O   SER A1142 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   LEU A1144 " --> pdb=" O   GLU A1162 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   GLU A1162 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1219 through 1222
      removed outlier: 6.530A  pdb=" N   GLU A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   HIS A1349 " --> pdb=" O   THR A1358 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   THR A1358 " --> pdb=" O   HIS A1349 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    945 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: 1.01

  Time building geometry restraints manager: 0.55 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: 2298
        1.34 -     1.46: 1276
        1.46 -     1.58: 3560
        1.58 -     1.69: 0
        1.69 -     1.81: 25
  Bond restraints: 7159
  Sorted by residual:
  bond pdb=" N   ILE A1331 "
       pdb=" CA  ILE A1331 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.42e+00
  bond pdb=" N   ARG A1333 "
       pdb=" CA  ARG A1333 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.26e-02 6.30e+03 6.56e+00
  bond pdb=" N   LYS A1334 "
       pdb=" CA  LYS A1334 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.27e-02 6.20e+03 6.50e+00
  bond pdb=" N   ILE A 927 "
       pdb=" CA  ILE A 927 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 1.19e-02 7.06e+03 6.10e+00
  bond pdb=" N   TYR A1336 "
       pdb=" CA  TYR A1336 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.031 1.29e-02 6.01e+03 5.82e+00
  ... (remaining 7154 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 9248
        1.63 -     3.26: 288
        3.26 -     4.88: 45
        4.88 -     6.51: 19
        6.51 -     8.14: 8
  Bond angle restraints: 9608
  Sorted by residual:
  angle pdb=" N   ILE A 927 "
        pdb=" CA  ILE A 927 "
        pdb=" C   ILE A 927 "
      ideal   model   delta    sigma   weight residual
     110.62  104.17    6.45 1.02e+00 9.61e-01 4.00e+01
  angle pdb=" N   THR A 928 "
        pdb=" CA  THR A 928 "
        pdb=" C   THR A 928 "
      ideal   model   delta    sigma   weight residual
     111.82  107.28    4.54 1.16e+00 7.43e-01 1.53e+01
  angle pdb=" C   ARG A 139 "
        pdb=" N   LYS A 140 "
        pdb=" CA  LYS A 140 "
      ideal   model   delta    sigma   weight residual
     122.38  115.46    6.92 1.81e+00 3.05e-01 1.46e+01
  angle pdb=" N   LYS A 929 "
        pdb=" CA  LYS A 929 "
        pdb=" C   LYS A 929 "
      ideal   model   delta    sigma   weight residual
     111.36  107.65    3.71 1.09e+00 8.42e-01 1.16e+01
  angle pdb=" C   HIS A 129 "
        pdb=" N   GLU A 130 "
        pdb=" CA  GLU A 130 "
      ideal   model   delta    sigma   weight residual
     120.68  115.35    5.33 1.70e+00 3.46e-01 9.83e+00
  ... (remaining 9603 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4067
       17.83 -    35.67: 256
       35.67 -    53.50: 56
       53.50 -    71.34: 7
       71.34 -    89.17: 4
  Dihedral angle restraints: 4390
    sinusoidal: 1830
      harmonic: 2560
  Sorted by residual:
  dihedral pdb=" CA  TYR A1039 "
           pdb=" C   TYR A1039 "
           pdb=" N   SER A1040 "
           pdb=" CA  SER A1040 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.51  -22.49     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  PHE A  86 "
           pdb=" C   PHE A  86 "
           pdb=" N   SER A  87 "
           pdb=" CA  SER A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.17  -19.83     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  ASP A 288 "
           pdb=" C   ASP A 288 "
           pdb=" N   LEU A 289 "
           pdb=" CA  LEU A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.21   19.79     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 4387 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 908
       0.058 -    0.116: 158
       0.116 -    0.173: 18
       0.173 -    0.231: 1
       0.231 -    0.289: 3
  Chirality restraints: 1088
  Sorted by residual:
  chirality pdb=" CG  LEU A 153 "
            pdb=" CB  LEU A 153 "
            pdb=" CD1 LEU A 153 "
            pdb=" CD2 LEU A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  ILE A 927 "
            pdb=" N   ILE A 927 "
            pdb=" C   ILE A 927 "
            pdb=" CB  ILE A 927 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CB  ILE A 305 "
            pdb=" CA  ILE A 305 "
            pdb=" CG1 ILE A 305 "
            pdb=" CG2 ILE A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 1085 not shown)

  Planarity restraints: 1215
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 175 "   -0.061 5.00e-02 4.00e+02   9.17e-02 1.34e+01
        pdb=" N   PRO A 176 "    0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO A 176 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 176 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 842 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.53e+00
        pdb=" N   PRO A 843 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 843 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 843 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 730 "   -0.023 5.00e-02 4.00e+02   3.49e-02 1.95e+00
        pdb=" N   PRO A 731 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 731 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 731 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1212 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1278
        2.77 -     3.30: 7150
        3.30 -     3.83: 11358
        3.83 -     4.37: 14212
        4.37 -     4.90: 22336
  Nonbonded interactions: 56334
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 209 "
            pdb=" OG  SER A 213 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   TYR A1010 "
            pdb=" OH  TYR A1013 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   PRO A1061 "
            pdb=" NZ  LYS A1076 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OE1 GLU A1205 "
            pdb=" NH2 ARG A1359 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OD2 ASP A 150 "
            pdb=" NE  ARG A 152 "
     model   vdw
     2.276 3.120
  ... (remaining 56329 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.950
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.510
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4773
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      :  0.004   0.078   7159  Z= 0.193
  Angle     :  0.734   8.138   9608  Z= 0.420
  Chirality :  0.045   0.289   1088
  Planarity :  0.005   0.092   1215
  Dihedral  : 12.681  89.172   2718
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 18.53
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.45 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.26 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.28), residues: 832
  helix: -0.40 (0.25), residues: 407
  sheet: -1.03 (0.76), residues: 43
  loop : -0.63 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  63 
 TYR   0.015   0.001   TYR A1201 
 PHE   0.017   0.002   PHE A1045 
 TRP   0.010   0.002   TRP A  18 
 HIS   0.007   0.001   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7159)
  covalent geometry    : angle       0.73365 ( 9608)
  hydrogen bonds       : bond        0.25598 (  317)
  hydrogen bonds       : angle       8.01882 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 187
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1241 HIS cc_start: 0.4769 (m90) cc_final: 0.4229 (t-170)
REVERT: A 1347 LEU cc_start: 0.5132 (tp) cc_final: 0.4867 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1060
  time to fit residues: 24.8720
Evaluate side-chains
  90 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
A 224 ASN
A 328 HIS
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 940 ASN
A 980 ASN
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1317 ASN ** 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 = 0.4600 r_free = 0.4600 target = 0.139650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.125833 restraints weight = 31010.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.127820 restraints weight = 21598.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.129168 restraints weight = 16323.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.130029 restraints weight = 13172.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.130806 restraints weight = 11302.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.4430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5207
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7159  Z= 0.174
  Angle     :  0.724  11.034   9608  Z= 0.371
  Chirality :  0.044   0.182   1088
  Planarity :  0.005   0.064   1215
  Dihedral  :  5.233  21.783    935
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 17.97
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.93 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 12.17 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.28), residues: 832
  helix: -0.06 (0.23), residues: 441
  sheet: -0.89 (0.71), residues: 43
  loop : -0.34 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 753 
 TYR   0.018   0.002   TYR A 325 
 PHE   0.020   0.002   PHE A  97 
 TRP   0.006   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7159)
  covalent geometry    : angle       0.72354 ( 9608)
  hydrogen bonds       : bond        0.04937 (  317)
  hydrogen bonds       : angle       5.96545 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6234 (mm)
REVERT: A  970 PHE cc_start: 0.6753 (m-10) cc_final: 0.6503 (m-10)
REVERT: A 1080 PHE cc_start: 0.1644 (OUTLIER) cc_final: 0.0211 (m-80)
REVERT: A 1347 LEU cc_start: 0.4941 (tp) cc_final: 0.4595 (tp)
  outliers start: 23
  outliers final: 14
  residues processed: 116
  average time/residue: 0.0878
  time to fit residues: 13.4567
Evaluate side-chains
  95 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue 1080 PHE
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1173 SER
Chi-restraints excluded: chain A residue 1317 ASN
Chi-restraints excluded: chain A residue 1340 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1091 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.127058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.111865 restraints weight = 30438.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.113669 restraints weight = 21305.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.115046 restraints weight = 16521.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.115992 restraints weight = 13572.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.116535 restraints weight = 11749.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5732
moved from start:          0.5844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.082   7159  Z= 0.302
  Angle     :  0.885  10.238   9608  Z= 0.459
  Chirality :  0.050   0.193   1088
  Planarity :  0.006   0.059   1215
  Dihedral  :  6.281  23.748    935
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 27.06
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.25 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 14.92 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.27), residues: 832
  helix: -0.52 (0.22), residues: 444
  sheet: -1.38 (0.63), residues: 59
  loop : -0.79 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  71 
 TYR   0.025   0.003   TYR A 325 
 PHE   0.021   0.003   PHE A1276 
 TRP   0.015   0.003   TRP A1074 
 HIS   0.006   0.002   HIS A1349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 7159)
  covalent geometry    : angle       0.88483 ( 9608)
  hydrogen bonds       : bond        0.05973 (  317)
  hydrogen bonds       : angle       6.32845 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 ARG cc_start: 0.8423 (tpt-90) cc_final: 0.8162 (tpt-90)
REVERT: A  890 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7944 (tppt)
REVERT: A  895 ARG cc_start: 0.4265 (OUTLIER) cc_final: 0.3831 (ttt180)
REVERT: A 1080 PHE cc_start: 0.2008 (OUTLIER) cc_final: 0.0434 (m-80)
  outliers start: 34
  outliers final: 22
  residues processed: 106
  average time/residue: 0.0737
  time to fit residues: 10.2317
Evaluate side-chains
  95 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 PHE
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  895 ARG
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1057 ILE
Chi-restraints excluded: chain A residue 1080 PHE
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1173 SER
Chi-restraints excluded: chain A residue 1174 PHE
Chi-restraints excluded: chain A residue 1317 ASN
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1340 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 79 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 HIS
** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.131516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.117278 restraints weight = 28902.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.119241 restraints weight = 20455.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.120708 restraints weight = 15063.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.120845 restraints weight = 11572.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.121482 restraints weight = 11935.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5507
moved from start:          0.6059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7159  Z= 0.139
  Angle     :  0.661  11.154   9608  Z= 0.339
  Chirality :  0.043   0.175   1088
  Planarity :  0.004   0.057   1215
  Dihedral  :  5.365  24.646    935
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.85 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 15.58 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.28), residues: 832
  helix: -0.18 (0.22), residues: 449
  sheet: -1.49 (0.64), residues: 52
  loop : -0.73 (0.36), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  69 
 TYR   0.015   0.001   TYR A1010 
 PHE   0.014   0.001   PHE A 446 
 TRP   0.015   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7159)
  covalent geometry    : angle       0.66138 ( 9608)
  hydrogen bonds       : bond        0.04391 (  317)
  hydrogen bonds       : angle       5.59851 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.286 
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  939 MET cc_start: 0.6335 (tpt) cc_final: 0.6113 (tmm)
REVERT: A 1010 TYR cc_start: 0.4416 (OUTLIER) cc_final: 0.3998 (m-80)
REVERT: A 1080 PHE cc_start: 0.1866 (OUTLIER) cc_final: 0.1598 (m-80)
REVERT: A 1296 LYS cc_start: 0.7713 (mttt) cc_final: 0.6940 (tttm)
  outliers start: 25
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0751
  time to fit residues: 10.4461
Evaluate side-chains
  91 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1010 TYR
Chi-restraints excluded: chain A residue 1080 PHE
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1174 PHE
Chi-restraints excluded: chain A residue 1317 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 83 optimal weight:    0.3980
   chunk 31 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 36 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1221 GLN
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.129296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.113964 restraints weight = 29239.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.115881 restraints weight = 20714.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.117269 restraints weight = 15981.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.117764 restraints weight = 13181.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.118707 restraints weight = 11840.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5608
moved from start:          0.6537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7159  Z= 0.162
  Angle     :  0.681  12.163   9608  Z= 0.345
  Chirality :  0.044   0.192   1088
  Planarity :  0.004   0.058   1215
  Dihedral  :  5.303  23.738    935
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 20.79
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.05 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.49 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.28), residues: 832
  helix: -0.18 (0.23), residues: 452
  sheet: -1.40 (0.65), residues: 52
  loop : -0.96 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 424 
 TYR   0.015   0.002   TYR A 359 
 PHE   0.012   0.002   PHE A 446 
 TRP   0.011   0.002   TRP A1074 
 HIS   0.004   0.001   HIS A1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 7159)
  covalent geometry    : angle       0.68093 ( 9608)
  hydrogen bonds       : bond        0.04459 (  317)
  hydrogen bonds       : angle       5.56457 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.279 
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 1010 TYR cc_start: 0.4721 (OUTLIER) cc_final: 0.4206 (m-80)
REVERT: A 1286 ASN cc_start: 0.5399 (OUTLIER) cc_final: 0.5170 (m110)
  outliers start: 26
  outliers final: 18
  residues processed: 99
  average time/residue: 0.0773
  time to fit residues: 10.4060
Evaluate side-chains
  97 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1010 TYR
Chi-restraints excluded: chain A residue 1057 ILE
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1173 SER
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1317 ASN
Chi-restraints excluded: chain A residue 1346 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 75 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 5 optimal weight:    0.2980
   chunk 79 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1295 ASN
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.126503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.112268 restraints weight = 30634.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.113294 restraints weight = 24193.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.114704 restraints weight = 18772.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.115223 restraints weight = 14280.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.115625 restraints weight = 13911.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5750
moved from start:          0.7285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7159  Z= 0.197
  Angle     :  0.736  10.530   9608  Z= 0.374
  Chirality :  0.046   0.178   1088
  Planarity :  0.005   0.059   1215
  Dihedral  :  5.611  23.601    935
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 22.69
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.53 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 17.15 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.28), residues: 832
  helix: -0.32 (0.23), residues: 456
  sheet: -1.07 (0.60), residues: 60
  loop : -1.28 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 895 
 TYR   0.023   0.002   TYR A 271 
 PHE   0.012   0.002   PHE A1080 
 TRP   0.010   0.002   TRP A1074 
 HIS   0.004   0.001   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 7159)
  covalent geometry    : angle       0.73634 ( 9608)
  hydrogen bonds       : bond        0.04807 (  317)
  hydrogen bonds       : angle       5.84964 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 87
  time to evaluate  : 0.283 
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 1010 TYR cc_start: 0.5151 (OUTLIER) cc_final: 0.4674 (m-80)
  outliers start: 32
  outliers final: 24
  residues processed: 110
  average time/residue: 0.0755
  time to fit residues: 11.4864
Evaluate side-chains
  101 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1010 TYR
Chi-restraints excluded: chain A residue 1057 ILE
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1173 SER
Chi-restraints excluded: chain A residue 1174 PHE
Chi-restraints excluded: chain A residue 1273 ILE
Chi-restraints excluded: chain A residue 1317 ASN
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1346 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.121412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.107459 restraints weight = 31102.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.108777 restraints weight = 22034.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.110499 restraints weight = 16566.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.110610 restraints weight = 14860.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.110860 restraints weight = 12368.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5943
moved from start:          0.8282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067   7159  Z= 0.293
  Angle     :  0.886  13.540   9608  Z= 0.457
  Chirality :  0.051   0.226   1088
  Planarity :  0.006   0.062   1215
  Dihedral  :  6.305  24.648    935
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 29.46
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.45 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 19.63 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.27), residues: 832
  helix: -0.87 (0.22), residues: 446
  sheet: -1.07 (0.61), residues: 55
  loop : -1.60 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 139 
 TYR   0.047   0.003   TYR A 271 
 PHE   0.017   0.003   PHE A  86 
 TRP   0.007   0.002   TRP A1074 
 HIS   0.008   0.002   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 ( 7159)
  covalent geometry    : angle       0.88649 ( 9608)
  hydrogen bonds       : bond        0.05827 (  317)
  hydrogen bonds       : angle       6.58331 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 82
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1010 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.5047 (m-80)
REVERT: A 1068 GLU cc_start: 0.2078 (OUTLIER) cc_final: -0.0139 (pp20)
  outliers start: 36
  outliers final: 26
  residues processed: 107
  average time/residue: 0.0805
  time to fit residues: 11.5782
Evaluate side-chains
  98 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 70
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1010 TYR
Chi-restraints excluded: chain A residue 1057 ILE
Chi-restraints excluded: chain A residue 1068 GLU
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1173 SER
Chi-restraints excluded: chain A residue 1174 PHE
Chi-restraints excluded: chain A residue 1273 ILE
Chi-restraints excluded: chain A residue 1276 PHE
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1317 ASN
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1346 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 67 optimal weight:    0.2980
   chunk 35 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1091 GLN
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.126097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.112085 restraints weight = 31014.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.113986 restraints weight = 21543.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.115358 restraints weight = 16366.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.116357 restraints weight = 13257.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.117088 restraints weight = 11287.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5679
moved from start:          0.8293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   7159  Z= 0.157
  Angle     :  0.749  13.272   9608  Z= 0.380
  Chirality :  0.046   0.187   1088
  Planarity :  0.004   0.058   1215
  Dihedral  :  5.567  22.421    935
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 22.76
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.29 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.51 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.28), residues: 832
  helix: -0.57 (0.22), residues: 451
  sheet: -1.23 (0.65), residues: 50
  loop : -1.39 (0.36), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 424 
 TYR   0.023   0.002   TYR A 271 
 PHE   0.011   0.001   PHE A  86 
 TRP   0.014   0.002   TRP A  18 
 HIS   0.008   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7159)
  covalent geometry    : angle       0.74947 ( 9608)
  hydrogen bonds       : bond        0.04674 (  317)
  hydrogen bonds       : angle       5.94794 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5274 (pp20)
REVERT: A  890 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7562 (mmmt)
REVERT: A 1010 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.4845 (m-80)
  outliers start: 22
  outliers final: 19
  residues processed: 92
  average time/residue: 0.0925
  time to fit residues: 11.4646
Evaluate side-chains
  92 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1010 TYR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1173 SER
Chi-restraints excluded: chain A residue 1273 ILE
Chi-restraints excluded: chain A residue 1317 ASN
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1346 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 GLN
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1091 GLN
A1093 ASN
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.127325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.113139 restraints weight = 30712.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.115083 restraints weight = 21450.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.116506 restraints weight = 16362.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.117367 restraints weight = 13192.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.118181 restraints weight = 11334.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.4264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5624
moved from start:          0.8398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   7159  Z= 0.144
  Angle     :  0.732  12.886   9608  Z= 0.370
  Chirality :  0.045   0.198   1088
  Planarity :  0.005   0.107   1215
  Dihedral  :  5.196  21.618    935
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 21.00
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.69 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.47 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.28), residues: 832
  helix: -0.40 (0.23), residues: 458
  sheet: -1.14 (0.67), residues: 50
  loop : -1.37 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 951 
 TYR   0.023   0.002   TYR A 271 
 PHE   0.010   0.001   PHE A 446 
 TRP   0.013   0.002   TRP A1074 
 HIS   0.005   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7159)
  covalent geometry    : angle       0.73249 ( 9608)
  hydrogen bonds       : bond        0.04281 (  317)
  hydrogen bonds       : angle       5.74767 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5217 (pp20)
REVERT: A 1296 LYS cc_start: 0.6946 (pttm) cc_final: 0.6124 (tttm)
REVERT: A 1347 LEU cc_start: 0.6706 (tp) cc_final: 0.6470 (tp)
  outliers start: 23
  outliers final: 17
  residues processed: 90
  average time/residue: 0.0804
  time to fit residues: 10.0735
Evaluate side-chains
  89 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1057 ILE
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1173 SER
Chi-restraints excluded: chain A residue 1317 ASN
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1346 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 75 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:   20.0000
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.126583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.112397 restraints weight = 31006.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.114341 restraints weight = 21559.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.115796 restraints weight = 16332.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.116826 restraints weight = 13167.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.117401 restraints weight = 11163.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5663
moved from start:          0.8552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   7159  Z= 0.155
  Angle     :  0.749  12.712   9608  Z= 0.374
  Chirality :  0.045   0.226   1088
  Planarity :  0.005   0.062   1215
  Dihedral  :  5.169  21.583    935
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.05 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.47 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.28), residues: 832
  helix: -0.39 (0.23), residues: 452
  sheet: -0.96 (0.54), residues: 70
  loop : -1.30 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 951 
 TYR   0.020   0.001   TYR A 271 
 PHE   0.011   0.001   PHE A  86 
 TRP   0.011   0.002   TRP A1074 
 HIS   0.005   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7159)
  covalent geometry    : angle       0.74899 ( 9608)
  hydrogen bonds       : bond        0.04433 (  317)
  hydrogen bonds       : angle       5.74831 (  945)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5053 (pp20)
REVERT: A  271 TYR cc_start: 0.5198 (t80) cc_final: 0.4852 (t80)
REVERT: A 1296 LYS cc_start: 0.6975 (pttm) cc_final: 0.6146 (tttm)
  outliers start: 19
  outliers final: 18
  residues processed: 90
  average time/residue: 0.0762
  time to fit residues: 9.6056
Evaluate side-chains
  90 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  882 TYR
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1057 ILE
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1173 SER
Chi-restraints excluded: chain A residue 1317 ASN
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1346 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0770
   chunk 84 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    1.0144

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1093 ASN
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.127510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.113332 restraints weight = 30840.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.115302 restraints weight = 21600.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.116745 restraints weight = 16184.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.117769 restraints weight = 13110.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.118497 restraints weight = 11116.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5611
moved from start:          0.8677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   7159  Z= 0.142
  Angle     :  0.733  12.463   9608  Z= 0.366
  Chirality :  0.044   0.220   1088
  Planarity :  0.004   0.061   1215
  Dihedral  :  4.992  20.853    935
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 19.87
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.69 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.12 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.28), residues: 832
  helix: -0.34 (0.23), residues: 457
  sheet: -0.90 (0.60), residues: 60
  loop : -1.32 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 951 
 TYR   0.020   0.001   TYR A 271 
 PHE   0.011   0.001   PHE A  86 
 TRP   0.012   0.002   TRP A1074 
 HIS   0.005   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7159)
  covalent geometry    : angle       0.73342 ( 9608)
  hydrogen bonds       : bond        0.04200 (  317)
  hydrogen bonds       : angle       5.59848 (  945)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1298.35 seconds
wall clock time: 23 minutes 14.53 seconds (1394.53 seconds total)