Starting phenix.real_space_refine
on Sat Aug 23 03:50:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8woo_37694/08_2025/8woo_37694_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8woo_37694/08_2025/8woo_37694.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8woo_37694/08_2025/8woo_37694_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8woo_37694/08_2025/8woo_37694_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8woo_37694/08_2025/8woo_37694.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8woo_37694/08_2025/8woo_37694.map"
  }
  resolution = 3.9
  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=   0.005 sd=   0.083
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      38      5.16       5
     C    6007      2.51       5
     N    1595      2.21       5
     O    1764      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9412
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1217, 9314
          Classifications: {'peptide': 1217}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 30, 'TRANS': 1186}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 98
          Unusual residues: {' MG': 2, 'ANP': 2, 'BLD': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 1.99, per 1000 atoms: 0.21
  Number of scatterers: 9412
  At special positions: 0
  Unit cell: (73.7, 108.9, 141.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      38     16.00
     P       6     15.00
     Mg      2     11.99
     O    1764      8.00
     N    1595      7.00
     C    6007      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 343.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2228

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 6 sheets defined
      45.9% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 51
      removed outlier: 4.398A  pdb=" N   ALA A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 66
      removed outlier: 3.511A  pdb=" N   PHE A  59 " --> pdb=" O   MET A  55 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU A  60 " --> pdb=" O   PRO A  56 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLY A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLN A  64 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL A  66 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 82
      removed outlier: 4.044A  pdb=" N   VAL A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   HIS A  81 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 93
    Processing helix  chain 'A' and resid 93 through 98
    Processing helix  chain 'A' and resid 115 through 129
      removed outlier: 3.862A  pdb=" N   LYS A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 3.709A  pdb=" N   PHE A 135 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 150
    Processing helix  chain 'A' and resid 155 through 160
    Processing helix  chain 'A' and resid 161 through 177
      removed outlier: 3.687A  pdb=" N   HIS A 168 " --> pdb=" O   GLY A 164 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A 170 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   PHE A 173 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 184
    Processing helix  chain 'A' and resid 189 through 194
      removed outlier: 3.545A  pdb=" N   VAL A 194 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 221
      removed outlier: 4.213A  pdb=" N   ALA A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ALA A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR A 210 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LYS A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ALA A 221 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 247 through 252
      removed outlier: 3.779A  pdb=" N   ASP A 252 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 274
      removed outlier: 3.764A  pdb=" N   LYS A 259 " --> pdb=" O   GLN A 255 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   LEU A 260 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LYS A 263 " --> pdb=" O   LYS A 259 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY A 265 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLY A 269 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLY A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 282 through 289
      removed outlier: 3.729A  pdb=" N   TYR A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 294
      removed outlier: 3.526A  pdb=" N   ILE A 294 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 316
      removed outlier: 3.661A  pdb=" N   THR A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ALA A 311 " --> pdb=" O   ALA A 307 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL A 313 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 3.927A  pdb=" N   LYS A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY A 331 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA A 333 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   TYR A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LYS A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU A 338 " --> pdb=" O   ALA A 334 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE A 341 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 414
      removed outlier: 3.617A  pdb=" N   ILE A 413 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLU A 414 " --> pdb=" O   VAL A 410 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 409 through 414'
    Processing helix  chain 'A' and resid 432 through 434
      No H-bonds generated for 'chain 'A' and resid 432 through 434'
    Processing helix  chain 'A' and resid 439 through 441
      No H-bonds generated for 'chain 'A' and resid 439 through 441'
    Processing helix  chain 'A' and resid 460 through 464
    Processing helix  chain 'A' and resid 470 through 479
      removed outlier: 3.596A  pdb=" N   GLU A 474 " --> pdb=" O   MET A 470 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA A 479 " --> pdb=" O   ALA A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 520
      removed outlier: 4.012A  pdb=" N   ARG A 516 " --> pdb=" O   ILE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 548
      removed outlier: 3.564A  pdb=" N   ILE A 541 " --> pdb=" O   SER A 537 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   VAL A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 545 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 604
    Processing helix  chain 'A' and resid 622 through 632
      removed outlier: 3.668A  pdb=" N   SER A 628 " --> pdb=" O   SER A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 680
      removed outlier: 3.916A  pdb=" N   LEU A 677 " --> pdb=" O   PHE A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 683
      No H-bonds generated for 'chain 'A' and resid 681 through 683'
    Processing helix  chain 'A' and resid 684 through 696
      removed outlier: 3.868A  pdb=" N   GLY A 690 " --> pdb=" O   TYR A 686 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLY A 693 " --> pdb=" O   MET A 689 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU A 696 " --> pdb=" O   VAL A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 709
      removed outlier: 3.939A  pdb=" N   VAL A 707 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 715
    Processing helix  chain 'A' and resid 741 through 751
      removed outlier: 4.761A  pdb=" N   ILE A 747 " --> pdb=" O   GLY A 743 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLN A 748 " --> pdb=" O   ALA A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 772
      removed outlier: 4.033A  pdb=" N   LEU A 768 " --> pdb=" O   ARG A 764 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER A 769 " --> pdb=" O   ARG A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 779
    Processing helix  chain 'A' and resid 781 through 785
      removed outlier: 3.792A  pdb=" N   ASN A 785 " --> pdb=" O   ASP A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 824 through 829
      removed outlier: 3.812A  pdb=" N   GLU A 829 " --> pdb=" O   ALA A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 850
      Proline residue:  A 841  - end of helix
      removed outlier: 4.070A  pdb=" N   LEU A 845 " --> pdb=" O   PRO A 841 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASN A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN A 850 " --> pdb=" O   ALA A 846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 865
      removed outlier: 4.180A  pdb=" N   ALA A 864 " --> pdb=" O   ASP A 860 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   HIS A 865 " --> pdb=" O   THR A 861 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 860 through 865'
    Processing helix  chain 'A' and resid 866 through 872
      removed outlier: 3.863A  pdb=" N   MET A 870 " --> pdb=" O   ALA A 866 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE A 871 " --> pdb=" O   LYS A 867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 884
      removed outlier: 3.683A  pdb=" N   VAL A 882 " --> pdb=" O   ASN A 878 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA A 884 " --> pdb=" O   ARG A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 895
      removed outlier: 3.660A  pdb=" N   PHE A 895 " --> pdb=" O   LEU A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 905
      removed outlier: 3.674A  pdb=" N   LYS A 904 " --> pdb=" O   ARG A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 907 through 919
      removed outlier: 4.451A  pdb=" N   PHE A 917 " --> pdb=" O   SER A 913 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLY A 918 " --> pdb=" O   GLY A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 921 through 926
      removed outlier: 3.515A  pdb=" N   TYR A 925 " --> pdb=" O   GLN A 921 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 939
      removed outlier: 3.661A  pdb=" N   LEU A 938 " --> pdb=" O   TYR A 934 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 939 " --> pdb=" O   GLY A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 940 through 942
      No H-bonds generated for 'chain 'A' and resid 940 through 942'
    Processing helix  chain 'A' and resid 949 through 954
    Processing helix  chain 'A' and resid 954 through 964
      removed outlier: 3.587A  pdb=" N   ILE A 958 " --> pdb=" O   VAL A 954 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   ALA A 960 " --> pdb=" O   LEU A 956 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER A 962 " --> pdb=" O   ILE A 958 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA A 964 " --> pdb=" O   ALA A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 968
      removed outlier: 4.191A  pdb=" N   SER A 968 " --> pdb=" O   GLU A 965 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 965 through 968'
    Processing helix  chain 'A' and resid 969 through 975
      removed outlier: 3.507A  pdb=" N   ILE A 973 " --> pdb=" O   LEU A 969 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ILE A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1050 through 1058
      removed outlier: 4.088A  pdb=" N   VAL A1054 " --> pdb=" O   LYS A1051 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   ILE A1055 " --> pdb=" O   SER A1052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1079
      No H-bonds generated for 'chain 'A' and resid 1077 through 1079'
    Processing helix  chain 'A' and resid 1080 through 1085
    Processing helix  chain 'A' and resid 1086 through 1088
      No H-bonds generated for 'chain 'A' and resid 1086 through 1088'
    Processing helix  chain 'A' and resid 1115 through 1123
      removed outlier: 3.979A  pdb=" N   ILE A1119 " --> pdb=" O   GLU A1115 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ASP A1120 " --> pdb=" O   SER A1116 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA A1122 " --> pdb=" O   VAL A1118 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ARG A1123 " --> pdb=" O   ILE A1119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1133
    Processing helix  chain 'A' and resid 1150 through 1166
      removed outlier: 3.912A  pdb=" N   ARG A1156 " --> pdb=" O   GLY A1152 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A1157 " --> pdb=" O   GLN A1153 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE A1159 " --> pdb=" O   GLN A1155 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA A1160 " --> pdb=" O   ARG A1156 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ARG A1161 " --> pdb=" O   ILE A1157 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ALA A1162 " --> pdb=" O   ALA A1158 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL A1163 " --> pdb=" O   ILE A1159 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU A1164 " --> pdb=" O   ALA A1160 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN A1166 " --> pdb=" O   ALA A1162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1241 through 1247
      removed outlier: 3.888A  pdb=" N   GLN A1246 " --> pdb=" O   SER A1242 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A1247 " --> pdb=" O   ARG A1243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1250
      No H-bonds generated for 'chain 'A' and resid 1248 through 1250'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 367
      removed outlier: 3.673A  pdb=" N   GLU A 366 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A 425 " --> pdb=" O   GLU A 366 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 443 through 445
      removed outlier: 6.177A  pdb=" N   GLY A 444 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ALA A 559 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   ALA A 572 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   ALA A 397 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ILE A 574 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   VAL A 399 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL A 573 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 645 through 647
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1011 through 1012
      removed outlier: 3.553A  pdb=" N   MET A1070 " --> pdb=" O   GLU A1011 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1042 through 1043
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1217 through 1220
      removed outlier: 7.464A  pdb=" N   VAL A1218 " --> pdb=" O   VAL A1225 " (cutoff:3.500A)

    226 hydrogen bonds defined for protein.
    627 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: 1.32

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1529
        1.31 -     1.44: 2558
        1.44 -     1.56: 5424
        1.56 -     1.68: 8
        1.68 -     1.81: 71
  Bond restraints: 9590
  Sorted by residual:
  bond pdb=" C   ALA A 126 "
       pdb=" N   VAL A 127 "
    ideal  model  delta    sigma   weight residual
    1.334  1.267  0.068 1.25e-02 6.40e+03 2.94e+01
  bond pdb=" O3A ANP A1303 "
       pdb=" PB  ANP A1303 "
    ideal  model  delta    sigma   weight residual
    1.700  1.592  0.108 2.00e-02 2.50e+03 2.92e+01
  bond pdb=" O3A ANP A1304 "
       pdb=" PB  ANP A1304 "
    ideal  model  delta    sigma   weight residual
    1.700  1.606  0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" C   VAL A 127 "
       pdb=" O   VAL A 127 "
    ideal  model  delta    sigma   weight residual
    1.237  1.191  0.046 1.13e-02 7.83e+03 1.64e+01
  bond pdb=" C4  ANP A1303 "
       pdb=" C5  ANP A1303 "
    ideal  model  delta    sigma   weight residual
    1.387  1.464 -0.077 2.00e-02 2.50e+03 1.50e+01
  ... (remaining 9585 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.02: 12860
        4.02 -     8.03: 113
        8.03 -    12.05: 19
       12.05 -    16.07: 5
       16.07 -    20.08: 5
  Bond angle restraints: 13002
  Sorted by residual:
  angle pdb=" N   GLN A 130 "
        pdb=" CA  GLN A 130 "
        pdb=" C   GLN A 130 "
      ideal   model   delta    sigma   weight residual
     108.42   89.36   19.06 1.54e+00 4.22e-01 1.53e+02
  angle pdb=" N   GLN A 130 "
        pdb=" CA  GLN A 130 "
        pdb=" CB  GLN A 130 "
      ideal   model   delta    sigma   weight residual
     111.56  129.54  -17.98 1.52e+00 4.33e-01 1.40e+02
  angle pdb=" N   ALA A1125 "
        pdb=" CA  ALA A1125 "
        pdb=" C   ALA A1125 "
      ideal   model   delta    sigma   weight residual
     108.20   88.12   20.08 1.71e+00 3.42e-01 1.38e+02
  angle pdb=" N   TYR A 123 "
        pdb=" CA  TYR A 123 "
        pdb=" C   TYR A 123 "
      ideal   model   delta    sigma   weight residual
     111.02  124.97  -13.95 1.22e+00 6.72e-01 1.31e+02
  angle pdb=" C   LYS A 122 "
        pdb=" CA  LYS A 122 "
        pdb=" CB  LYS A 122 "
      ideal   model   delta    sigma   weight residual
     110.90  127.80  -16.90 1.58e+00 4.01e-01 1.14e+02
  ... (remaining 12997 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.77: 5660
       31.77 -    63.55: 96
       63.55 -    95.32: 22
       95.32 -   127.09: 0
      127.09 -   158.87: 2
  Dihedral angle restraints: 5780
    sinusoidal: 2292
      harmonic: 3488
  Sorted by residual:
  dihedral pdb=" C   SER A 681 "
           pdb=" N   SER A 681 "
           pdb=" CA  SER A 681 "
           pdb=" CB  SER A 681 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -162.82   40.22     0      2.50e+00 1.60e-01 2.59e+02
  dihedral pdb=" N   SER A 681 "
           pdb=" C   SER A 681 "
           pdb=" CA  SER A 681 "
           pdb=" CB  SER A 681 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  159.39  -36.59     0      2.50e+00 1.60e-01 2.14e+02
  dihedral pdb=" C   LYS A 122 "
           pdb=" N   LYS A 122 "
           pdb=" CA  LYS A 122 "
           pdb=" CB  LYS A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -148.01   25.41     0      2.50e+00 1.60e-01 1.03e+02
  ... (remaining 5777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.339: 1491
       0.339 -    0.677: 4
       0.677 -    1.016: 4
       1.016 -    1.355: 0
       1.355 -    1.693: 1
  Chirality restraints: 1500
  Sorted by residual:
  chirality pdb=" CA  SER A 681 "
            pdb=" N   SER A 681 "
            pdb=" C   SER A 681 "
            pdb=" CB  SER A 681 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.82    1.69 2.00e-01 2.50e+01 7.17e+01
  chirality pdb=" CA  LYS A 122 "
            pdb=" N   LYS A 122 "
            pdb=" C   LYS A 122 "
            pdb=" CB  LYS A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.58    0.93 2.00e-01 2.50e+01 2.17e+01
  chirality pdb=" CA  ALA A 118 "
            pdb=" N   ALA A 118 "
            pdb=" C   ALA A 118 "
            pdb=" CB  ALA A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.74    0.74 2.00e-01 2.50e+01 1.39e+01
  ... (remaining 1497 not shown)

  Planarity restraints: 1642
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  55 "    0.050 5.00e-02 4.00e+02   7.39e-02 8.73e+00
        pdb=" N   PRO A  56 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A  56 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A  56 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 681 "    0.046 5.00e-02 4.00e+02   6.87e-02 7.55e+00
        pdb=" N   PRO A 682 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 682 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 682 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 377 "   -0.043 5.00e-02 4.00e+02   6.49e-02 6.74e+00
        pdb=" N   PRO A 378 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 378 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 378 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1639 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1860
        2.77 -     3.30: 8303
        3.30 -     3.83: 14099
        3.83 -     4.37: 16958
        4.37 -     4.90: 28146
  Nonbonded interactions: 69366
  Sorted by model distance:
  nonbonded pdb=" N   GLN A 130 "
            pdb=" O   GLN A 130 "
     model   vdw
     2.237 2.496
  nonbonded pdb=" O   SER A 681 "
            pdb=" N   GLU A 683 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" OH  TYR A 644 "
            pdb=" O   HIS A 865 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG  SER A 697 "
            pdb=" O   ALA A 744 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   THR A 395 "
            pdb=" OG  SER A 570 "
     model   vdw
     2.295 3.040
  ... (remaining 69361 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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.280
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
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      :  0.007   0.440   9591  Z= 0.530
  Angle     :  1.136  20.084  13002  Z= 0.673
  Chirality :  0.083   1.693   1500
  Planarity :  0.007   0.074   1642
  Dihedral  : 13.301 158.867   3552
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.63 %
  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 aren not related in a simple way.
  whole: -6.18 (0.16), residues: 1213
  helix: -4.61 (0.09), residues: 623
  sheet: -3.55 (0.48), residues: 89
  loop : -3.26 (0.22), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 653 
 TYR   0.018   0.002   TYR A 463 
 PHE   0.024   0.002   PHE A1061 
 TRP   0.024   0.002   TRP A 684 
 HIS   0.005   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 9590)
  covalent geometry    : angle       1.13627 (13002)
  hydrogen bonds       : bond        0.33114 (  226)
  hydrogen bonds       : angle      10.54072 (  627)
  Misc. bond           : bond        0.43985 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLN cc_start: 0.8530 (mm110) cc_final: 0.8227 (mm110)
REVERT: A  149 SER cc_start: 0.9054 (m) cc_final: 0.8751 (t)
REVERT: A  157 ASP cc_start: 0.7757 (t0) cc_final: 0.7522 (t0)
REVERT: A  266 MET cc_start: 0.8396 (ttp) cc_final: 0.8163 (ttm)
REVERT: A  300 ASP cc_start: 0.7749 (p0) cc_final: 0.7061 (t0)
REVERT: A  437 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8550 (mmmm)
REVERT: A  646 TYR cc_start: 0.8832 (m-80) cc_final: 0.8424 (m-80)
REVERT: A  708 MET cc_start: 0.8782 (tmm) cc_final: 0.8516 (tmm)
REVERT: A  819 LEU cc_start: 0.9338 (tp) cc_final: 0.8937 (tt)
REVERT: A  905 ARG cc_start: 0.8136 (tmt170) cc_final: 0.7759 (tmt170)
REVERT: A  908 TYR cc_start: 0.8373 (m-10) cc_final: 0.8085 (m-10)
REVERT: A 1041 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8156 (tp40)
REVERT: A 1060 ARG cc_start: 0.7788 (mtm180) cc_final: 0.7480 (mtm-85)
REVERT: A 1079 LEU cc_start: 0.9199 (mt) cc_final: 0.8994 (mm)
REVERT: A 1083 SER cc_start: 0.8689 (t) cc_final: 0.8312 (t)
REVERT: A 1148 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8436 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.1223
  time to fit residues: 39.6462
Evaluate side-chains
  128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
A  51 HIS
A 483 HIS
A 585 HIS
A 602 GLN
A 625 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.162159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.115900 restraints weight = 15237.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.119312 restraints weight = 8769.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.121682 restraints weight = 6002.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.123220 restraints weight = 4651.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.124134 restraints weight = 3940.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9591  Z= 0.174
  Angle     :  0.688  12.140  13002  Z= 0.358
  Chirality :  0.044   0.175   1500
  Planarity :  0.005   0.059   1642
  Dihedral  : 10.602 135.997   1471
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.16 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.62 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.10 (0.19), residues: 1213
  helix: -3.71 (0.14), residues: 630
  sheet: -2.96 (0.58), residues: 67
  loop : -2.81 (0.23), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 992 
 TYR   0.026   0.002   TYR A1241 
 PHE   0.024   0.002   PHE A1031 
 TRP   0.023   0.002   TRP A 684 
 HIS   0.005   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 9590)
  covalent geometry    : angle       0.68773 (13002)
  hydrogen bonds       : bond        0.04578 (  226)
  hydrogen bonds       : angle       5.90464 (  627)
  Misc. bond           : bond        0.00204 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLN cc_start: 0.8724 (mm110) cc_final: 0.8330 (mm110)
REVERT: A  147 SER cc_start: 0.8982 (m) cc_final: 0.8521 (p)
REVERT: A  549 VAL cc_start: 0.8573 (p) cc_final: 0.8049 (m)
REVERT: A  642 LEU cc_start: 0.8928 (tp) cc_final: 0.8705 (mm)
REVERT: A  646 TYR cc_start: 0.8789 (m-80) cc_final: 0.8492 (m-80)
REVERT: A  653 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6839 (mtm110)
REVERT: A  799 ASP cc_start: 0.8317 (t0) cc_final: 0.8042 (t0)
REVERT: A  827 ILE cc_start: 0.9113 (mm) cc_final: 0.8782 (mt)
REVERT: A  905 ARG cc_start: 0.8195 (tmt170) cc_final: 0.7971 (tmt170)
REVERT: A  975 ARG cc_start: 0.7703 (tmm-80) cc_final: 0.7392 (ttm170)
REVERT: A 1063 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8363 (t0)
REVERT: A 1216 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7785 (mt)
  outliers start: 20
  outliers final: 6
  residues processed: 162
  average time/residue: 0.0973
  time to fit residues: 21.6810
Evaluate side-chains
  121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue 1063 ASP
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 99 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 59 optimal weight:    8.9990
   chunk 6 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0770
   chunk 98 optimal weight:    8.9990
   overall best weight:    1.5744

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
A1041 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.161792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112807 restraints weight = 15609.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.116125 restraints weight = 9494.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.118393 restraints weight = 6772.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.119749 restraints weight = 5383.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.120848 restraints weight = 4664.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9591  Z= 0.174
  Angle     :  0.654  13.682  13002  Z= 0.340
  Chirality :  0.043   0.145   1500
  Planarity :  0.004   0.057   1642
  Dihedral  :  9.643 143.897   1471
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.76 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.44 (0.21), residues: 1213
  helix: -3.13 (0.16), residues: 630
  sheet: -2.89 (0.53), residues: 79
  loop : -2.47 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1223 
 TYR   0.018   0.002   TYR A1241 
 PHE   0.020   0.002   PHE A 386 
 TRP   0.020   0.001   TRP A 684 
 HIS   0.008   0.001   HIS A 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9590)
  covalent geometry    : angle       0.65365 (13002)
  hydrogen bonds       : bond        0.04121 (  226)
  hydrogen bonds       : angle       5.32572 (  627)
  Misc. bond           : bond        0.00111 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLN cc_start: 0.8767 (mm110) cc_final: 0.8306 (mm110)
REVERT: A  147 SER cc_start: 0.9057 (m) cc_final: 0.8696 (p)
REVERT: A  549 VAL cc_start: 0.8446 (p) cc_final: 0.7983 (m)
REVERT: A  560 HIS cc_start: 0.7137 (t-170) cc_final: 0.6909 (t70)
REVERT: A  799 ASP cc_start: 0.8354 (t0) cc_final: 0.7980 (t0)
REVERT: A  905 ARG cc_start: 0.8281 (tmt170) cc_final: 0.8057 (tmt170)
REVERT: A  975 ARG cc_start: 0.7800 (tmm-80) cc_final: 0.7412 (ttm170)
REVERT: A 1028 PHE cc_start: 0.8493 (m-80) cc_final: 0.8208 (m-80)
REVERT: A 1063 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8406 (t0)
REVERT: A 1195 MET cc_start: 0.7012 (mmm) cc_final: 0.6765 (mmt)
  outliers start: 25
  outliers final: 15
  residues processed: 149
  average time/residue: 0.1110
  time to fit residues: 22.3468
Evaluate side-chains
  131 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  625 HIS
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain A residue  920 SER
Chi-restraints excluded: chain A residue 1063 ASP
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1210 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 56 optimal weight:   20.0000
   chunk 33 optimal weight:    0.0870
   chunk 91 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0370
   chunk 40 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.7638

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.164154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.116154 restraints weight = 15512.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.119547 restraints weight = 9236.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.121892 restraints weight = 6497.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.123420 restraints weight = 5140.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.124213 restraints weight = 4420.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9591  Z= 0.111
  Angle     :  0.596  14.222  13002  Z= 0.306
  Chirality :  0.041   0.155   1500
  Planarity :  0.004   0.050   1642
  Dihedral  :  9.068 142.667   1471
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.17 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.92 (0.22), residues: 1213
  helix: -2.61 (0.18), residues: 622
  sheet: -2.75 (0.52), residues: 79
  loop : -2.36 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 600 
 TYR   0.013   0.001   TYR A 646 
 PHE   0.020   0.001   PHE A 386 
 TRP   0.012   0.001   TRP A 684 
 HIS   0.004   0.001   HIS A 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9590)
  covalent geometry    : angle       0.59591 (13002)
  hydrogen bonds       : bond        0.03088 (  226)
  hydrogen bonds       : angle       4.75453 (  627)
  Misc. bond           : bond        0.00265 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.8788 (t80) cc_final: 0.8369 (t80)
REVERT: A  147 SER cc_start: 0.9076 (m) cc_final: 0.8761 (p)
REVERT: A  518 MET cc_start: 0.8248 (mmm) cc_final: 0.7907 (mmm)
REVERT: A  799 ASP cc_start: 0.8289 (t0) cc_final: 0.7896 (t0)
REVERT: A  905 ARG cc_start: 0.8241 (tmt170) cc_final: 0.8028 (tmt170)
REVERT: A  975 ARG cc_start: 0.7610 (tmm-80) cc_final: 0.7289 (tpp-160)
REVERT: A 1022 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7618 (ttm170)
REVERT: A 1079 LEU cc_start: 0.8997 (mt) cc_final: 0.8584 (tt)
REVERT: A 1102 ILE cc_start: 0.8300 (mt) cc_final: 0.8004 (tt)
REVERT: A 1123 ARG cc_start: 0.7252 (mtm180) cc_final: 0.6511 (ptp-170)
REVERT: A 1195 MET cc_start: 0.6934 (mmm) cc_final: 0.6543 (mmt)
  outliers start: 22
  outliers final: 15
  residues processed: 140
  average time/residue: 0.0997
  time to fit residues: 19.5042
Evaluate side-chains
  125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ASP
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  625 HIS
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain A residue  920 SER
Chi-restraints excluded: chain A residue 1022 ARG
Chi-restraints excluded: chain A residue 1210 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 98 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.157497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.108968 restraints weight = 15290.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112179 restraints weight = 9014.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.114341 restraints weight = 6291.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.115715 restraints weight = 4980.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.116554 restraints weight = 4292.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060   9591  Z= 0.295
  Angle     :  0.738  15.136  13002  Z= 0.380
  Chirality :  0.047   0.142   1500
  Planarity :  0.004   0.056   1642
  Dihedral  :  9.348 142.965   1471
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 14.58 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.98 (0.21), residues: 1213
  helix: -2.71 (0.18), residues: 633
  sheet: -2.74 (0.57), residues: 66
  loop : -2.34 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1029 
 TYR   0.015   0.002   TYR A 417 
 PHE   0.025   0.002   PHE A 386 
 TRP   0.029   0.002   TRP A 684 
 HIS   0.006   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00672 ( 9590)
  covalent geometry    : angle       0.73791 (13002)
  hydrogen bonds       : bond        0.04483 (  226)
  hydrogen bonds       : angle       5.38389 (  627)
  Misc. bond           : bond        0.00514 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 111
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 SER cc_start: 0.8975 (m) cc_final: 0.8729 (p)
REVERT: A  708 MET cc_start: 0.8555 (tmm) cc_final: 0.8149 (tmm)
REVERT: A  799 ASP cc_start: 0.8340 (t0) cc_final: 0.8010 (t0)
REVERT: A  975 ARG cc_start: 0.7868 (tmm-80) cc_final: 0.7368 (tpp-160)
REVERT: A 1022 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7646 (ttm170)
REVERT: A 1195 MET cc_start: 0.7034 (mmm) cc_final: 0.6395 (mmt)
  outliers start: 37
  outliers final: 30
  residues processed: 137
  average time/residue: 0.0969
  time to fit residues: 18.8338
Evaluate side-chains
  133 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  207 TYR
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  833 SER
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  920 SER
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue  967 VAL
Chi-restraints excluded: chain A residue 1022 ARG
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1210 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0070
   chunk 37 optimal weight:    5.9990
   chunk 110 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0170
   chunk 117 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0980
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
A 233 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.166375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.117323 restraints weight = 15480.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.120823 restraints weight = 9140.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.123135 restraints weight = 6374.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.124750 restraints weight = 5059.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.125582 restraints weight = 4354.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   9591  Z= 0.100
  Angle     :  0.581  14.658  13002  Z= 0.299
  Chirality :  0.041   0.202   1500
  Planarity :  0.004   0.046   1642
  Dihedral  :  8.634 137.611   1471
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.74 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.43 (0.22), residues: 1213
  helix: -2.19 (0.19), residues: 626
  sheet: -2.64 (0.56), residues: 68
  loop : -2.17 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 600 
 TYR   0.017   0.001   TYR A 595 
 PHE   0.034   0.001   PHE A1031 
 TRP   0.007   0.001   TRP A 778 
 HIS   0.002   0.000   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9590)
  covalent geometry    : angle       0.58065 (13002)
  hydrogen bonds       : bond        0.02695 (  226)
  hydrogen bonds       : angle       4.42219 (  627)
  Misc. bond           : bond        0.00494 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.8794 (t80) cc_final: 0.8312 (t80)
REVERT: A  147 SER cc_start: 0.9039 (m) cc_final: 0.8713 (p)
REVERT: A  799 ASP cc_start: 0.8213 (t0) cc_final: 0.7939 (t0)
REVERT: A  975 ARG cc_start: 0.7716 (tmm-80) cc_final: 0.7391 (ttm170)
REVERT: A 1022 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7680 (ttm170)
REVERT: A 1079 LEU cc_start: 0.9006 (mt) cc_final: 0.8604 (tt)
REVERT: A 1195 MET cc_start: 0.7074 (mmm) cc_final: 0.6868 (mmt)
  outliers start: 21
  outliers final: 12
  residues processed: 135
  average time/residue: 0.0947
  time to fit residues: 17.8697
Evaluate side-chains
  121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  767 MET
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain A residue  896 CYS
Chi-restraints excluded: chain A residue 1022 ARG
Chi-restraints excluded: chain A residue 1210 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0040
   chunk 107 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 104 optimal weight:    5.9990
   overall best weight:    0.7194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.164512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.116762 restraints weight = 15027.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.120259 restraints weight = 8395.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.122634 restraints weight = 5686.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.124193 restraints weight = 4406.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.124983 restraints weight = 3749.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.4554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9591  Z= 0.106
  Angle     :  0.569   9.308  13002  Z= 0.295
  Chirality :  0.041   0.209   1500
  Planarity :  0.004   0.057   1642
  Dihedral  :  8.319 138.181   1471
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.14 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.20 (0.23), residues: 1213
  helix: -1.94 (0.20), residues: 630
  sheet: -2.58 (0.53), residues: 77
  loop : -2.12 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 600 
 TYR   0.012   0.001   TYR A 646 
 PHE   0.022   0.001   PHE A1031 
 TRP   0.004   0.001   TRP A 108 
 HIS   0.002   0.001   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9590)
  covalent geometry    : angle       0.56855 (13002)
  hydrogen bonds       : bond        0.02906 (  226)
  hydrogen bonds       : angle       4.31034 (  627)
  Misc. bond           : bond        0.00304 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.8797 (t80) cc_final: 0.8382 (t80)
REVERT: A  147 SER cc_start: 0.9041 (m) cc_final: 0.8730 (p)
REVERT: A  364 ASN cc_start: 0.7688 (t0) cc_final: 0.7143 (t0)
REVERT: A  684 TRP cc_start: 0.6720 (p-90) cc_final: 0.6216 (p90)
REVERT: A  799 ASP cc_start: 0.8236 (t0) cc_final: 0.7998 (t0)
REVERT: A  975 ARG cc_start: 0.7750 (tmm-80) cc_final: 0.7334 (tpp-160)
REVERT: A 1022 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7605 (ttm170)
REVERT: A 1079 LEU cc_start: 0.9018 (mt) cc_final: 0.8610 (tt)
REVERT: A 1195 MET cc_start: 0.7081 (mmm) cc_final: 0.6785 (mmt)
  outliers start: 21
  outliers final: 14
  residues processed: 134
  average time/residue: 0.1031
  time to fit residues: 19.4190
Evaluate side-chains
  126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  406 LYS
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  767 MET
Chi-restraints excluded: chain A residue  920 SER
Chi-restraints excluded: chain A residue  967 VAL
Chi-restraints excluded: chain A residue 1022 ARG
Chi-restraints excluded: chain A residue 1140 THR
Chi-restraints excluded: chain A residue 1210 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 102 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0980
   chunk 26 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.166330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.116533 restraints weight = 15420.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.120137 restraints weight = 8813.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.122668 restraints weight = 6074.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.124264 restraints weight = 4743.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.125330 restraints weight = 4078.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.4690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9591  Z= 0.103
  Angle     :  0.572   9.175  13002  Z= 0.292
  Chirality :  0.041   0.202   1500
  Planarity :  0.004   0.043   1642
  Dihedral  :  8.153 137.757   1471
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.94 %
    Favored  : 79.31 %
  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 aren not related in a simple way.
  whole: -2.96 (0.23), residues: 1213
  helix: -1.74 (0.20), residues: 627
  sheet: -2.24 (0.58), residues: 68
  loop : -2.06 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 600 
 TYR   0.011   0.001   TYR A 646 
 PHE   0.031   0.001   PHE A1031 
 TRP   0.004   0.001   TRP A 933 
 HIS   0.002   0.000   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9590)
  covalent geometry    : angle       0.57157 (13002)
  hydrogen bonds       : bond        0.02733 (  226)
  hydrogen bonds       : angle       4.20201 (  627)
  Misc. bond           : bond        0.00249 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.8769 (t80) cc_final: 0.8289 (t80)
REVERT: A  147 SER cc_start: 0.9043 (m) cc_final: 0.8731 (p)
REVERT: A  364 ASN cc_start: 0.7928 (t0) cc_final: 0.7490 (t0)
REVERT: A  683 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7311 (pt0)
REVERT: A  799 ASP cc_start: 0.8194 (t0) cc_final: 0.7980 (t0)
REVERT: A  898 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8642 (tm-30)
REVERT: A  975 ARG cc_start: 0.7799 (tmm-80) cc_final: 0.7438 (ttm170)
REVERT: A 1022 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7651 (ttm170)
REVERT: A 1079 LEU cc_start: 0.9052 (mt) cc_final: 0.8566 (tt)
REVERT: A 1148 GLN cc_start: 0.8445 (tp-100) cc_final: 0.8199 (tp-100)
REVERT: A 1195 MET cc_start: 0.7128 (mmm) cc_final: 0.6872 (mmt)
REVERT: A 1210 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8438 (mp)
  outliers start: 27
  outliers final: 21
  residues processed: 133
  average time/residue: 0.0926
  time to fit residues: 17.8163
Evaluate side-chains
  135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  406 LYS
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  767 MET
Chi-restraints excluded: chain A residue  833 SER
Chi-restraints excluded: chain A residue  896 CYS
Chi-restraints excluded: chain A residue  920 SER
Chi-restraints excluded: chain A residue  967 VAL
Chi-restraints excluded: chain A residue 1022 ARG
Chi-restraints excluded: chain A residue 1140 THR
Chi-restraints excluded: chain A residue 1210 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0770
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 64 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0010
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.1748

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.163000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.115185 restraints weight = 15118.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.118610 restraints weight = 8498.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.120895 restraints weight = 5786.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.122447 restraints weight = 4525.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.123409 restraints weight = 3860.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.4766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9591  Z= 0.135
  Angle     :  0.587   8.627  13002  Z= 0.301
  Chirality :  0.042   0.202   1500
  Planarity :  0.004   0.039   1642
  Dihedral  :  8.152 139.441   1471
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.45 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.92 (0.23), residues: 1213
  helix: -1.71 (0.20), residues: 627
  sheet: -2.26 (0.58), residues: 67
  loop : -2.03 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 600 
 TYR   0.014   0.001   TYR A 646 
 PHE   0.028   0.001   PHE A1031 
 TRP   0.005   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9590)
  covalent geometry    : angle       0.58715 (13002)
  hydrogen bonds       : bond        0.03116 (  226)
  hydrogen bonds       : angle       4.34376 (  627)
  Misc. bond           : bond        0.00235 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.8831 (t80) cc_final: 0.8416 (t80)
REVERT: A  147 SER cc_start: 0.9044 (m) cc_final: 0.8722 (p)
REVERT: A  364 ASN cc_start: 0.7975 (t0) cc_final: 0.7563 (t0)
REVERT: A  489 LEU cc_start: 0.7497 (pp) cc_final: 0.6852 (mm)
REVERT: A  799 ASP cc_start: 0.8231 (t0) cc_final: 0.8001 (t0)
REVERT: A  975 ARG cc_start: 0.7759 (tmm-80) cc_final: 0.7373 (ttm170)
REVERT: A 1022 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7575 (ttm170)
REVERT: A 1057 MET cc_start: 0.7963 (mmt) cc_final: 0.7552 (mmt)
REVERT: A 1148 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8097 (tp-100)
REVERT: A 1195 MET cc_start: 0.7033 (mmm) cc_final: 0.6753 (mmt)
REVERT: A 1210 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8454 (mp)
  outliers start: 28
  outliers final: 23
  residues processed: 127
  average time/residue: 0.0945
  time to fit residues: 17.4644
Evaluate side-chains
  130 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  406 LYS
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  767 MET
Chi-restraints excluded: chain A residue  896 CYS
Chi-restraints excluded: chain A residue  913 SER
Chi-restraints excluded: chain A residue  920 SER
Chi-restraints excluded: chain A residue  967 VAL
Chi-restraints excluded: chain A residue 1022 ARG
Chi-restraints excluded: chain A residue 1140 THR
Chi-restraints excluded: chain A residue 1210 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 120 optimal weight:    7.9990
   chunk 14 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 96 optimal weight:    0.3980
   chunk 91 optimal weight:    0.1980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.163456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.115481 restraints weight = 15089.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.118911 restraints weight = 8460.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.121257 restraints weight = 5780.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.122816 restraints weight = 4490.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.123594 restraints weight = 3834.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.4860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9591  Z= 0.124
  Angle     :  0.585   8.717  13002  Z= 0.298
  Chirality :  0.042   0.200   1500
  Planarity :  0.003   0.037   1642
  Dihedral  :  8.054 139.362   1471
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.45 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.78 (0.23), residues: 1213
  helix: -1.58 (0.20), residues: 629
  sheet: -2.12 (0.57), residues: 65
  loop : -2.02 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 600 
 TYR   0.019   0.001   TYR A 595 
 PHE   0.027   0.001   PHE A1031 
 TRP   0.005   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9590)
  covalent geometry    : angle       0.58510 (13002)
  hydrogen bonds       : bond        0.02991 (  226)
  hydrogen bonds       : angle       4.33357 (  627)
  Misc. bond           : bond        0.00228 (    1)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.8854 (t80) cc_final: 0.8424 (t80)
REVERT: A  147 SER cc_start: 0.9039 (m) cc_final: 0.8705 (p)
REVERT: A  364 ASN cc_start: 0.8019 (t0) cc_final: 0.7614 (t0)
REVERT: A  489 LEU cc_start: 0.7557 (pp) cc_final: 0.6940 (mm)
REVERT: A  799 ASP cc_start: 0.8234 (t0) cc_final: 0.7982 (t0)
REVERT: A  975 ARG cc_start: 0.7816 (tmm-80) cc_final: 0.7344 (tpp-160)
REVERT: A 1022 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7458 (ttm170)
REVERT: A 1026 MET cc_start: 0.7454 (mmp) cc_final: 0.7107 (mmp)
REVERT: A 1057 MET cc_start: 0.7969 (mmt) cc_final: 0.7561 (mmt)
REVERT: A 1070 MET cc_start: 0.6009 (mmp) cc_final: 0.5664 (mmm)
REVERT: A 1148 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8138 (tp-100)
REVERT: A 1195 MET cc_start: 0.7088 (mmm) cc_final: 0.6810 (mmt)
REVERT: A 1210 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8481 (mp)
  outliers start: 26
  outliers final: 23
  residues processed: 127
  average time/residue: 0.0872
  time to fit residues: 16.2566
Evaluate side-chains
  133 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  406 LYS
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  767 MET
Chi-restraints excluded: chain A residue  920 SER
Chi-restraints excluded: chain A residue  967 VAL
Chi-restraints excluded: chain A residue 1022 ARG
Chi-restraints excluded: chain A residue 1140 THR
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1210 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 116 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0270
   chunk 41 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0070
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.4458

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.166572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.119353 restraints weight = 15024.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.122987 restraints weight = 8306.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.125403 restraints weight = 5549.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.126910 restraints weight = 4323.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.127903 restraints weight = 3688.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.5063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9591  Z= 0.092
  Angle     :  0.556   8.236  13002  Z= 0.283
  Chirality :  0.040   0.203   1500
  Planarity :  0.003   0.036   1642
  Dihedral  :  7.740 136.446   1471
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.86 %
    Favored  : 79.00 %
  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 aren not related in a simple way.
  whole: -2.49 (0.23), residues: 1213
  helix: -1.22 (0.21), residues: 614
  sheet: -2.07 (0.55), residues: 66
  loop : -2.03 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1193 
 TYR   0.013   0.001   TYR A1241 
 PHE   0.025   0.001   PHE A1031 
 TRP   0.004   0.000   TRP A 108 
 HIS   0.002   0.000   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 9590)
  covalent geometry    : angle       0.55617 (13002)
  hydrogen bonds       : bond        0.02535 (  226)
  hydrogen bonds       : angle       4.11477 (  627)
  Misc. bond           : bond        0.00208 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1602.75 seconds
wall clock time: 28 minutes 16.21 seconds (1696.21 seconds total)