Starting phenix.real_space_refine
on Wed Mar  4 00:15:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e1a_30938/03_2026/7e1a_30938.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e1a_30938/03_2026/7e1a_30938.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e1a_30938/03_2026/7e1a_30938.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e1a_30938/03_2026/7e1a_30938.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e1a_30938/03_2026/7e1a_30938.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e1a_30938/03_2026/7e1a_30938.map"
  }
  resolution = 3.66
  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=   0.006 sd=   0.079
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5951      2.51       5
     N    1566      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9284
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "U"
      Number of atoms: 9249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1189, 9249
          Classifications: {'peptide': 1189}
          Link IDs: {'PTRANS': 32, 'TRANS': 1156}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'TCH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.10, per 1000 atoms: 0.23
  Number of scatterers: 9284
  At special positions: 0
  Unit cell: (93.28, 94.34, 161.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    1712      8.00
     N    1566      7.00
     C    5951      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: 0.63
  Conformation dependent library (CDL) restraints added in 470.6 milliseconds
  

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2190

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 4 sheets defined
      48.5% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'U' and resid 63 through 74
      removed outlier: 3.778A  pdb=" N   CYS U  68 " --> pdb=" O   VAL U  64 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ALA U  69 " --> pdb=" O   GLY U  65 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE U  70 " --> pdb=" O   SER U  66 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   HIS U  72 " --> pdb=" O   CYS U  68 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 79 through 84
    Processing helix  chain 'U' and resid 88 through 102
      removed outlier: 3.506A  pdb=" N   TYR U  93 " --> pdb=" O   VAL U  89 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN U 101 " --> pdb=" O   LEU U  97 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   ILE U 102 " --> pdb=" O   GLN U  98 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 134 through 139
      removed outlier: 3.831A  pdb=" N   ILE U 139 " --> pdb=" O   GLU U 135 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 163 through 168
      removed outlier: 3.717A  pdb=" N   ALA U 168 " --> pdb=" O   VAL U 164 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 170 through 181
      removed outlier: 3.544A  pdb=" N   PHE U 179 " --> pdb=" O   ARG U 175 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 186 through 191
      removed outlier: 3.926A  pdb=" N   PHE U 190 " --> pdb=" O   GLU U 186 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 194 through 199
      removed outlier: 3.777A  pdb=" N   LEU U 198 " --> pdb=" O   SER U 194 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 227 through 236
      removed outlier: 3.805A  pdb=" N   LEU U 232 " --> pdb=" O   ILE U 228 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LEU U 233 " --> pdb=" O   CYS U 229 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLY U 234 " --> pdb=" O   GLY U 230 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 249 through 254
    Processing helix  chain 'U' and resid 256 through 264
      removed outlier: 4.143A  pdb=" N   GLY U 260 " --> pdb=" O   ALA U 256 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER U 262 " --> pdb=" O   THR U 258 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   VAL U 263 " --> pdb=" O   ILE U 259 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   SER U 264 " --> pdb=" O   GLY U 260 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 267 through 275
      removed outlier: 3.902A  pdb=" N   LYS U 272 " --> pdb=" O   ASP U 268 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   ALA U 273 " --> pdb=" O   TYR U 269 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR U 274 " --> pdb=" O   GLU U 270 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ALA U 275 " --> pdb=" O   LEU U 271 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 276 through 285
      removed outlier: 4.284A  pdb=" N   VAL U 280 " --> pdb=" O   LYS U 276 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ASP U 282 " --> pdb=" O   GLY U 278 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL U 284 " --> pdb=" O   VAL U 280 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 287 through 295
      removed outlier: 3.645A  pdb=" N   VAL U 291 " --> pdb=" O   SER U 287 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE U 294 " --> pdb=" O   THR U 290 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 301 through 306
      removed outlier: 3.748A  pdb=" N   LYS U 306 " --> pdb=" O   GLU U 302 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 307 through 309
      No H-bonds generated for 'chain 'U' and resid 307 through 309'
    Processing helix  chain 'U' and resid 315 through 324
      removed outlier: 3.504A  pdb=" N   GLY U 319 " --> pdb=" O   GLY U 315 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL U 321 " --> pdb=" O   ARG U 317 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 329 through 351
      removed outlier: 3.981A  pdb=" N   PHE U 334 " --> pdb=" O   TRP U 330 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU U 335 " --> pdb=" O   CYS U 331 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TYR U 343 " --> pdb=" O   LEU U 339 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU U 347 " --> pdb=" O   TYR U 343 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU U 349 " --> pdb=" O   SER U 345 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 366 through 372
      removed outlier: 4.175A  pdb=" N   ASN U 372 " --> pdb=" O   VAL U 368 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 373 through 375
      No H-bonds generated for 'chain 'U' and resid 373 through 375'
    Processing helix  chain 'U' and resid 380 through 389
      removed outlier: 4.065A  pdb=" N   ALA U 384 " --> pdb=" O   LEU U 380 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   GLY U 386 " --> pdb=" O   ALA U 382 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 392 through 397
    Processing helix  chain 'U' and resid 462 through 467
      removed outlier: 4.006A  pdb=" N   LEU U 467 " --> pdb=" O   THR U 463 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 468 through 470
      No H-bonds generated for 'chain 'U' and resid 468 through 470'
    Processing helix  chain 'U' and resid 490 through 498
      removed outlier: 4.568A  pdb=" N   ASP U 496 " --> pdb=" O   GLN U 492 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLN U 497 " --> pdb=" O   TRP U 493 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE U 498 " --> pdb=" O   LEU U 494 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 511 through 516
      removed outlier: 3.635A  pdb=" N   ILE U 516 " --> pdb=" O   ILE U 512 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 517 through 519
      No H-bonds generated for 'chain 'U' and resid 517 through 519'
    Processing helix  chain 'U' and resid 524 through 535
      removed outlier: 4.588A  pdb=" N   GLN U 530 " --> pdb=" O   GLU U 526 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ALA U 531 " --> pdb=" O   ASP U 527 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA U 532 " --> pdb=" O   ILE U 528 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 538 through 543
      removed outlier: 4.105A  pdb=" N   MET U 542 " --> pdb=" O   TYR U 538 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 550 through 554
      removed outlier: 4.204A  pdb=" N   GLY U 553 " --> pdb=" O   THR U 550 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU U 554 " --> pdb=" O   LEU U 551 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 550 through 554'
    Processing helix  chain 'U' and resid 563 through 574
      removed outlier: 3.691A  pdb=" N   VAL U 567 " --> pdb=" O   GLN U 563 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA U 570 " --> pdb=" O   ARG U 566 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 590 through 602
      removed outlier: 3.980A  pdb=" N   ALA U 595 " --> pdb=" O   ASN U 591 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET U 596 " --> pdb=" O   GLU U 592 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 650 through 658
      removed outlier: 3.518A  pdb=" N   THR U 655 " --> pdb=" O   PHE U 651 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   LEU U 656 " --> pdb=" O   THR U 652 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 742 through 748
    Processing helix  chain 'U' and resid 749 through 752
      removed outlier: 3.761A  pdb=" N   TRP U 752 " --> pdb=" O   ALA U 749 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 749 through 752'
    Processing helix  chain 'U' and resid 756 through 764
      removed outlier: 3.730A  pdb=" N   GLY U 761 " --> pdb=" O   VAL U 757 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA U 762 " --> pdb=" O   GLY U 758 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL U 764 " --> pdb=" O   VAL U 760 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 768 through 780
      removed outlier: 3.692A  pdb=" N   PHE U 774 " --> pdb=" O   PRO U 770 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU U 780 " --> pdb=" O   PHE U 776 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 787 through 819
      removed outlier: 3.807A  pdb=" N   GLN U 791 " --> pdb=" O   ASP U 787 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ARG U 792 " --> pdb=" O   LYS U 788 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN U 796 " --> pdb=" O   ARG U 792 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU U 800 " --> pdb=" O   ASN U 796 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU U 801 " --> pdb=" O   GLY U 797 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE U 802 " --> pdb=" O   VAL U 798 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   VAL U 803 " --> pdb=" O   CYS U 799 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA U 804 " --> pdb=" O   LEU U 800 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   SER U 809 " --> pdb=" O   MET U 805 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU U 810 " --> pdb=" O   GLY U 806 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE U 811 " --> pdb=" O   CYS U 807 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLN U 813 " --> pdb=" O   SER U 809 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU U 815 " --> pdb=" O   PHE U 811 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLN U 816 " --> pdb=" O   THR U 812 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLY U 817 " --> pdb=" O   GLN U 813 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA U 819 " --> pdb=" O   LEU U 815 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 829 through 839
    Processing helix  chain 'U' and resid 843 through 847
      removed outlier: 3.589A  pdb=" N   TRP U 846 " --> pdb=" O   ASP U 843 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 859 through 864
      removed outlier: 3.849A  pdb=" N   THR U 863 " --> pdb=" O   THR U 859 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 872 through 877
      removed outlier: 3.739A  pdb=" N   ILE U 876 " --> pdb=" O   ALA U 872 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY U 877 " --> pdb=" O   GLY U 873 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 872 through 877'
    Processing helix  chain 'U' and resid 880 through 888
      removed outlier: 3.624A  pdb=" N   THR U 884 " --> pdb=" O   VAL U 880 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   VAL U 886 " --> pdb=" O   SER U 882 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL U 888 " --> pdb=" O   THR U 884 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 888 through 896
      removed outlier: 3.562A  pdb=" N   ILE U 892 " --> pdb=" O   VAL U 888 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE U 896 " --> pdb=" O   ILE U 892 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 900 through 906
      removed outlier: 4.020A  pdb=" N   ILE U 904 " --> pdb=" O   LEU U 900 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU U 905 " --> pdb=" O   SER U 901 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 907 through 913
      removed outlier: 3.529A  pdb=" N   ALA U 912 " --> pdb=" O   PHE U 908 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 918 through 923
    Processing helix  chain 'U' and resid 929 through 934
    Processing helix  chain 'U' and resid 935 through 940
      removed outlier: 3.921A  pdb=" N   ILE U 939 " --> pdb=" O   MET U 935 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 946 through 951
      removed outlier: 3.603A  pdb=" N   VAL U 950 " --> pdb=" O   ASN U 946 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 957 through 965
      removed outlier: 4.539A  pdb=" N   LEU U 963 " --> pdb=" O   PHE U 959 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU U 964 " --> pdb=" O   ILE U 960 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR U 965 " --> pdb=" O   GLU U 961 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 982 through 987
      removed outlier: 3.679A  pdb=" N   PHE U 987 " --> pdb=" O   PHE U 983 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 994 through 1010
      removed outlier: 3.659A  pdb=" N   SER U 999 " --> pdb=" O   ALA U 995 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TYR U1000 " --> pdb=" O   ASN U 996 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR U1002 " --> pdb=" O   ALA U 998 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER U1008 " --> pdb=" O   GLY U1004 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ASN U1009 " --> pdb=" O   TYR U1005 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1013 through 1015
      No H-bonds generated for 'chain 'U' and resid 1013 through 1015'
    Processing helix  chain 'U' and resid 1016 through 1022
      removed outlier: 3.728A  pdb=" N   VAL U1020 " --> pdb=" O   TYR U1016 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE U1021 " --> pdb=" O   VAL U1017 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1025 through 1036
      removed outlier: 3.622A  pdb=" N   ALA U1030 " --> pdb=" O   LEU U1026 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LEU U1031 " --> pdb=" O   SER U1027 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA U1034 " --> pdb=" O   ALA U1030 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1041 through 1056
      removed outlier: 3.735A  pdb=" N   ILE U1046 " --> pdb=" O   ALA U1042 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   SER U1047 " --> pdb=" O   LYS U1043 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ARG U1050 " --> pdb=" O   ILE U1046 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   PHE U1051 " --> pdb=" O   SER U1047 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN U1053 " --> pdb=" O   ALA U1049 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   LEU U1054 " --> pdb=" O   ARG U1050 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1120 through 1125
    Processing helix  chain 'U' and resid 1143 through 1147
    Processing helix  chain 'U' and resid 1148 through 1153
    Processing helix  chain 'U' and resid 1170 through 1175
      removed outlier: 3.564A  pdb=" N   ILE U1174 " --> pdb=" O   ILE U1170 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1176 through 1178
      No H-bonds generated for 'chain 'U' and resid 1176 through 1178'
    Processing helix  chain 'U' and resid 1185 through 1195
      removed outlier: 4.143A  pdb=" N   ILE U1189 " --> pdb=" O   MET U1185 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ALA U1190 " --> pdb=" O   GLU U1186 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA U1192 " --> pdb=" O   VAL U1188 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS U1193 " --> pdb=" O   ILE U1189 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1199 through 1204
      removed outlier: 3.757A  pdb=" N   LEU U1204 " --> pdb=" O   PHE U1200 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1220 through 1234
      removed outlier: 4.231A  pdb=" N   ARG U1226 " --> pdb=" O   GLY U1222 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ILE U1227 " --> pdb=" O   GLU U1223 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ALA U1228 " --> pdb=" O   LYS U1224 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA U1230 " --> pdb=" O   ARG U1226 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA U1232 " --> pdb=" O   ALA U1228 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL U1234 " --> pdb=" O   ALA U1230 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1252 through 1264
      removed outlier: 3.559A  pdb=" N   GLN U1258 " --> pdb=" O   GLU U1254 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL U1259 " --> pdb=" O   LYS U1255 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ALA U1260 " --> pdb=" O   THR U1256 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1299 through 1303
      removed outlier: 3.608A  pdb=" N   LEU U1303 " --> pdb=" O   HIS U1300 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1308 through 1314
    Processing sheet with id=AA1, first strand: chain 'U' and resid 420 through 422
    Processing sheet with id=AA2, first strand: chain 'U' and resid 426 through 427
      removed outlier: 3.618A  pdb=" N   PHE U 427 " --> pdb=" O   LEU U 438 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   LEU U 438 " --> pdb=" O   PHE U 427 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'U' and resid 500 through 501
      removed outlier: 5.843A  pdb=" N   LEU U 580 " --> pdb=" O   ILE U 611 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'U' and resid 1156 through 1159
      removed outlier: 7.111A  pdb=" N   GLY U1157 " --> pdb=" O   LEU U1241 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    193 hydrogen bonds defined for protein.
    561 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: 1.38

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2349
        1.33 -     1.45: 1944
        1.45 -     1.57: 5082
        1.57 -     1.69: 1
        1.69 -     1.81: 89
  Bond restraints: 9465
  Sorted by residual:
  bond pdb=" C   ALA U 214 "
       pdb=" N   ASP U 215 "
    ideal  model  delta    sigma   weight residual
    1.335  1.269  0.065 1.42e-02 4.96e+03 2.12e+01
  bond pdb=" O3S TCH U1401 "
       pdb=" S26 TCH U1401 "
    ideal  model  delta    sigma   weight residual
    1.475  1.549 -0.074 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" CG1 ILE U 171 "
       pdb=" CD1 ILE U 171 "
    ideal  model  delta    sigma   weight residual
    1.513  1.376  0.137 3.90e-02 6.57e+02 1.23e+01
  bond pdb=" CG1 ILE U 245 "
       pdb=" CD1 ILE U 245 "
    ideal  model  delta    sigma   weight residual
    1.513  1.382  0.131 3.90e-02 6.57e+02 1.13e+01
  bond pdb=" CB  VAL U1024 "
       pdb=" CG2 VAL U1024 "
    ideal  model  delta    sigma   weight residual
    1.521  1.419  0.102 3.30e-02 9.18e+02 9.62e+00
  ... (remaining 9460 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.03: 12690
        5.03 -    10.07: 102
       10.07 -    15.10: 13
       15.10 -    20.14: 0
       20.14 -    25.17: 1
  Bond angle restraints: 12806
  Sorted by residual:
  angle pdb=" N   VAL U 152 "
        pdb=" CA  VAL U 152 "
        pdb=" C   VAL U 152 "
      ideal   model   delta    sigma   weight residual
     113.20  104.66    8.54 9.60e-01 1.09e+00 7.91e+01
  angle pdb=" C   HIS U1013 "
        pdb=" N   PHE U1014 "
        pdb=" CA  PHE U1014 "
      ideal   model   delta    sigma   weight residual
     120.82  131.96  -11.14 1.50e+00 4.44e-01 5.52e+01
  angle pdb=" N   ILE U 158 "
        pdb=" CA  ILE U 158 "
        pdb=" C   ILE U 158 "
      ideal   model   delta    sigma   weight residual
     113.53  106.72    6.81 9.80e-01 1.04e+00 4.83e+01
  angle pdb=" N   ILE U 221 "
        pdb=" CA  ILE U 221 "
        pdb=" C   ILE U 221 "
      ideal   model   delta    sigma   weight residual
     111.91  105.90    6.01 8.90e-01 1.26e+00 4.56e+01
  angle pdb=" N   VAL U1017 "
        pdb=" CA  VAL U1017 "
        pdb=" C   VAL U1017 "
      ideal   model   delta    sigma   weight residual
     112.96  106.66    6.30 1.00e+00 1.00e+00 3.97e+01
  ... (remaining 12801 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.42: 5084
       15.42 -    30.84: 471
       30.84 -    46.25: 112
       46.25 -    61.67: 4
       61.67 -    77.09: 15
  Dihedral angle restraints: 5686
    sinusoidal: 2275
      harmonic: 3411
  Sorted by residual:
  dihedral pdb=" CA  PRO U1039 "
           pdb=" C   PRO U1039 "
           pdb=" N   SER U1040 "
           pdb=" CA  SER U1040 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.85  -31.15     0      5.00e+00 4.00e-02 3.88e+01
  dihedral pdb=" CA  ARG U 181 "
           pdb=" C   ARG U 181 "
           pdb=" N   ILE U 182 "
           pdb=" CA  ILE U 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.73   30.27     0      5.00e+00 4.00e-02 3.67e+01
  dihedral pdb=" CA  ILE U 362 "
           pdb=" C   ILE U 362 "
           pdb=" N   PHE U 363 "
           pdb=" CA  PHE U 363 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.24   29.76     0      5.00e+00 4.00e-02 3.54e+01
  ... (remaining 5683 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 989
       0.063 -    0.126: 380
       0.126 -    0.189: 66
       0.189 -    0.251: 20
       0.251 -    0.314: 7
  Chirality restraints: 1462
  Sorted by residual:
  chirality pdb=" CB  VAL U 764 "
            pdb=" CA  VAL U 764 "
            pdb=" CG1 VAL U 764 "
            pdb=" CG2 VAL U 764 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CB  ILE U 221 "
            pdb=" CA  ILE U 221 "
            pdb=" CG1 ILE U 221 "
            pdb=" CG2 ILE U 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CB  VAL U 248 "
            pdb=" CA  VAL U 248 "
            pdb=" CG1 VAL U 248 "
            pdb=" CG2 VAL U 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 1459 not shown)

  Planarity restraints: 1631
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C23 TCH U1401 "    0.142 2.00e-02 2.50e+03   1.65e-01 3.39e+02
        pdb=" C24 TCH U1401 "   -0.054 2.00e-02 2.50e+03
        pdb=" C25 TCH U1401 "    0.198 2.00e-02 2.50e+03
        pdb=" N24 TCH U1401 "   -0.270 2.00e-02 2.50e+03
        pdb=" O24 TCH U1401 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS U 969 "    0.051 5.00e-02 4.00e+02   7.57e-02 9.16e+00
        pdb=" N   PRO U 970 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO U 970 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO U 970 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN U  76 "    0.050 5.00e-02 4.00e+02   7.51e-02 9.03e+00
        pdb=" N   PRO U  77 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO U  77 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO U  77 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1628 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2053
        2.77 -     3.30: 8542
        3.30 -     3.83: 14514
        3.83 -     4.37: 16969
        4.37 -     4.90: 28369
  Nonbonded interactions: 70447
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP U 864 "
            pdb=" OG  SER U1047 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   SER U 809 "
            pdb=" OG  SER U 809 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OH  TYR U 145 "
            pdb=" O2S TCH U1401 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG1 THR U 355 "
            pdb=" OG1 THR U 358 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   THR U 155 "
            pdb=" OG1 THR U 155 "
     model   vdw
     2.262 3.040
  ... (remaining 70442 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:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.530
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
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      :  0.014   0.563   9466  Z= 0.794
  Angle     :  1.391  25.169  12806  Z= 0.775
  Chirality :  0.069   0.314   1462
  Planarity :  0.009   0.165   1631
  Dihedral  : 13.322  77.090   3496
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.65 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.91 %
    Favored  : 90.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.43 (0.15), residues: 1185
  helix: -4.74 (0.08), residues: 637
  sheet: -4.05 (0.64), residues: 37
  loop : -3.46 (0.22), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG U 832 
 TYR   0.034   0.004   TYR U 178 
 PHE   0.031   0.004   PHE U 363 
 TRP   0.035   0.003   TRP U 314 
 HIS   0.022   0.003   HIS U  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.01250 ( 9465)
  covalent geometry    : angle       1.39056 (12806)
  hydrogen bonds       : bond        0.31785 (  193)
  hydrogen bonds       : angle      11.04683 (  561)
  Misc. bond           : bond        0.56330 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 209
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: U  123 MET cc_start: 0.3728 (mtp) cc_final: 0.2894 (ttm)
REVERT: U  183 MET cc_start: 0.8632 (mmm) cc_final: 0.8097 (mmm)
REVERT: U  205 ASP cc_start: 0.8685 (t0) cc_final: 0.8439 (t0)
REVERT: U  217 MET cc_start: 0.8143 (tpp) cc_final: 0.7781 (tpt)
REVERT: U  252 ILE cc_start: 0.7727 (tt) cc_final: 0.6929 (mt)
REVERT: U  442 ASN cc_start: 0.8085 (m-40) cc_final: 0.7851 (m-40)
REVERT: U  453 LEU cc_start: 0.7903 (tm) cc_final: 0.7688 (tt)
REVERT: U  478 MET cc_start: 0.7594 (ppp) cc_final: 0.6892 (ppp)
REVERT: U  492 GLN cc_start: 0.8508 (mm110) cc_final: 0.7674 (tm-30)
REVERT: U  600 VAL cc_start: 0.8954 (t) cc_final: 0.8745 (t)
REVERT: U  863 THR cc_start: 0.8222 (m) cc_final: 0.7953 (t)
REVERT: U  891 ILE cc_start: 0.8531 (mm) cc_final: 0.8174 (mt)
REVERT: U  921 MET cc_start: 0.7516 (tmt) cc_final: 0.6862 (tmt)
REVERT: U 1111 PHE cc_start: 0.8693 (m-10) cc_final: 0.8158 (m-10)
REVERT: U 1299 THR cc_start: 0.4668 (OUTLIER) cc_final: 0.4309 (m)
  outliers start: 8
  outliers final: 1
  residues processed: 216
  average time/residue: 0.1151
  time to fit residues: 32.9510
Evaluate side-chains
  123 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue  768 VAL
Chi-restraints excluded: chain U residue 1299 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 117 optimal weight:   10.0000
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
U 492 GLN
U 503 GLN
U 515 ASN
U 605 GLN
U 640 HIS
U 842 GLN
U1142 HIS
U1196 GLN
U1258 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.180081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.126985 restraints weight = 13926.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.122351 restraints weight = 9403.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.122820 restraints weight = 9796.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125372 restraints weight = 6949.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.125238 restraints weight = 5275.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9466  Z= 0.170
  Angle     :  0.730  18.746  12806  Z= 0.374
  Chirality :  0.044   0.159   1462
  Planarity :  0.005   0.046   1631
  Dihedral  :  8.272  87.609   1359
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 13.46 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.59 (0.18), residues: 1185
  helix: -3.99 (0.12), residues: 645
  sheet: -3.58 (0.76), residues: 37
  loop : -3.14 (0.24), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG U1268 
 TYR   0.014   0.002   TYR U 274 
 PHE   0.011   0.001   PHE U 811 
 TRP   0.013   0.001   TRP U 189 
 HIS   0.004   0.001   HIS U1013 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 9465)
  covalent geometry    : angle       0.73032 (12806)
  hydrogen bonds       : bond        0.04256 (  193)
  hydrogen bonds       : angle       6.04392 (  561)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 0.373 
Fit side-chains
REVERT: U  132 LEU cc_start: 0.8253 (tp) cc_final: 0.7551 (tp)
REVERT: U  157 TYR cc_start: 0.8462 (t80) cc_final: 0.8228 (t80)
REVERT: U  174 MET cc_start: 0.8318 (ttm) cc_final: 0.8115 (ttm)
REVERT: U  177 PHE cc_start: 0.7987 (t80) cc_final: 0.7661 (t80)
REVERT: U  217 MET cc_start: 0.8016 (tpp) cc_final: 0.7648 (tpt)
REVERT: U  232 LEU cc_start: 0.8816 (tt) cc_final: 0.8341 (mm)
REVERT: U  335 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6888 (mt)
REVERT: U  380 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8401 (tt)
REVERT: U  413 LEU cc_start: 0.8854 (tt) cc_final: 0.8332 (mp)
REVERT: U  414 ASP cc_start: 0.7811 (p0) cc_final: 0.7509 (t0)
REVERT: U  443 MET cc_start: 0.8500 (ppp) cc_final: 0.8010 (ppp)
REVERT: U  453 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7659 (tt)
REVERT: U  492 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7649 (tm-30)
REVERT: U  503 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8664 (tp40)
REVERT: U  629 PHE cc_start: 0.7138 (p90) cc_final: 0.6414 (p90)
REVERT: U  643 LEU cc_start: 0.6385 (tp) cc_final: 0.6102 (tp)
REVERT: U  823 SER cc_start: 0.8904 (t) cc_final: 0.8697 (t)
REVERT: U  891 ILE cc_start: 0.8156 (mm) cc_final: 0.7897 (mt)
REVERT: U  928 ARG cc_start: 0.7261 (ttt180) cc_final: 0.6992 (ttt180)
REVERT: U 1111 PHE cc_start: 0.8529 (m-10) cc_final: 0.7879 (m-10)
REVERT: U 1146 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8185 (mmtt)
REVERT: U 1202 MET cc_start: 0.5171 (mmm) cc_final: 0.4173 (mtm)
REVERT: U 1224 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8208 (mtmm)
REVERT: U 1271 ILE cc_start: 0.9263 (mm) cc_final: 0.8949 (mm)
REVERT: U 1304 MET cc_start: 0.7424 (mpt) cc_final: 0.7068 (mpp)
  outliers start: 31
  outliers final: 9
  residues processed: 162
  average time/residue: 0.0891
  time to fit residues: 20.2847
Evaluate side-chains
  130 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue  145 TYR
Chi-restraints excluded: chain U residue  335 LEU
Chi-restraints excluded: chain U residue  371 LEU
Chi-restraints excluded: chain U residue  380 LEU
Chi-restraints excluded: chain U residue  453 LEU
Chi-restraints excluded: chain U residue  454 VAL
Chi-restraints excluded: chain U residue  503 GLN
Chi-restraints excluded: chain U residue  567 VAL
Chi-restraints excluded: chain U residue  580 LEU
Chi-restraints excluded: chain U residue  619 THR
Chi-restraints excluded: chain U residue  757 VAL
Chi-restraints excluded: chain U residue  768 VAL
Chi-restraints excluded: chain U residue  888 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 77 optimal weight:    0.8980
   chunk 116 optimal weight:   30.0000
   chunk 109 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
U 442 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.178468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.126859 restraints weight = 13890.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.120684 restraints weight = 10238.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.121509 restraints weight = 9654.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.122426 restraints weight = 6826.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.123815 restraints weight = 5934.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   9466  Z= 0.204
  Angle     :  0.717  18.819  12806  Z= 0.359
  Chirality :  0.044   0.134   1462
  Planarity :  0.004   0.040   1631
  Dihedral  :  7.805  82.246   1358
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 13.87 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.14 (0.20), residues: 1185
  helix: -3.58 (0.15), residues: 650
  sheet: -3.81 (0.72), residues: 42
  loop : -2.91 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG U 928 
 TYR   0.012   0.002   TYR U 178 
 PHE   0.011   0.001   PHE U 363 
 TRP   0.010   0.001   TRP U  60 
 HIS   0.003   0.001   HIS U1142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 9465)
  covalent geometry    : angle       0.71653 (12806)
  hydrogen bonds       : bond        0.04000 (  193)
  hydrogen bonds       : angle       5.67260 (  561)
  Misc. bond           : bond        0.00162 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 123
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: U  177 PHE cc_start: 0.8036 (t80) cc_final: 0.7734 (t80)
REVERT: U  217 MET cc_start: 0.8116 (tpp) cc_final: 0.7655 (tpt)
REVERT: U  335 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6900 (mt)
REVERT: U  359 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8876 (tt)
REVERT: U  380 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8421 (tt)
REVERT: U  413 LEU cc_start: 0.8839 (tt) cc_final: 0.8416 (mp)
REVERT: U  414 ASP cc_start: 0.7965 (p0) cc_final: 0.7690 (t0)
REVERT: U  453 LEU cc_start: 0.7943 (tm) cc_final: 0.7694 (tt)
REVERT: U  629 PHE cc_start: 0.7058 (p90) cc_final: 0.6349 (p90)
REVERT: U  743 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7922 (mmm-85)
REVERT: U  891 ILE cc_start: 0.8311 (mm) cc_final: 0.8071 (mt)
REVERT: U 1111 PHE cc_start: 0.8544 (m-10) cc_final: 0.7854 (m-10)
REVERT: U 1202 MET cc_start: 0.5172 (mmm) cc_final: 0.3936 (mtm)
REVERT: U 1224 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8263 (mtmt)
REVERT: U 1271 ILE cc_start: 0.9194 (mm) cc_final: 0.8788 (mm)
REVERT: U 1304 MET cc_start: 0.7658 (mpt) cc_final: 0.7310 (mpp)
  outliers start: 42
  outliers final: 19
  residues processed: 157
  average time/residue: 0.0870
  time to fit residues: 19.7212
Evaluate side-chains
  133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   66 SER
Chi-restraints excluded: chain U residue   79 VAL
Chi-restraints excluded: chain U residue  145 TYR
Chi-restraints excluded: chain U residue  244 VAL
Chi-restraints excluded: chain U residue  263 VAL
Chi-restraints excluded: chain U residue  335 LEU
Chi-restraints excluded: chain U residue  359 LEU
Chi-restraints excluded: chain U residue  371 LEU
Chi-restraints excluded: chain U residue  380 LEU
Chi-restraints excluded: chain U residue  454 VAL
Chi-restraints excluded: chain U residue  479 VAL
Chi-restraints excluded: chain U residue  540 PHE
Chi-restraints excluded: chain U residue  548 PHE
Chi-restraints excluded: chain U residue  567 VAL
Chi-restraints excluded: chain U residue  580 LEU
Chi-restraints excluded: chain U residue  757 VAL
Chi-restraints excluded: chain U residue  768 VAL
Chi-restraints excluded: chain U residue  834 PHE
Chi-restraints excluded: chain U residue  888 VAL
Chi-restraints excluded: chain U residue 1013 HIS
Chi-restraints excluded: chain U residue 1014 PHE
Chi-restraints excluded: chain U residue 1079 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 81 optimal weight:    0.4980
   chunk 76 optimal weight:    0.5980
   chunk 92 optimal weight:    0.6980
   chunk 105 optimal weight:    5.9990
   chunk 93 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 117 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 110 optimal weight:   10.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 640 HIS
U 842 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.180465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.127932 restraints weight = 14134.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.124824 restraints weight = 8785.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.124607 restraints weight = 10482.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.125957 restraints weight = 6679.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.126638 restraints weight = 5397.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9466  Z= 0.113
  Angle     :  0.656  19.201  12806  Z= 0.319
  Chirality :  0.041   0.136   1462
  Planarity :  0.003   0.031   1631
  Dihedral  :  7.142  82.898   1358
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.40 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.63 (0.21), residues: 1185
  helix: -3.19 (0.16), residues: 651
  sheet: -3.33 (0.94), residues: 31
  loop : -2.70 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG U 743 
 TYR   0.012   0.001   TYR U 157 
 PHE   0.013   0.001   PHE U 363 
 TRP   0.006   0.001   TRP U 314 
 HIS   0.003   0.001   HIS U1013 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9465)
  covalent geometry    : angle       0.65631 (12806)
  hydrogen bonds       : bond        0.03108 (  193)
  hydrogen bonds       : angle       5.11356 (  561)
  Misc. bond           : bond        0.00084 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: U  154 ILE cc_start: 0.8345 (tp) cc_final: 0.8031 (tp)
REVERT: U  177 PHE cc_start: 0.7797 (t80) cc_final: 0.7453 (t80)
REVERT: U  197 GLU cc_start: 0.8128 (tp30) cc_final: 0.7646 (tp30)
REVERT: U  217 MET cc_start: 0.7741 (tpp) cc_final: 0.7317 (tpt)
REVERT: U  232 LEU cc_start: 0.8726 (tt) cc_final: 0.8178 (mm)
REVERT: U  290 THR cc_start: 0.9145 (p) cc_final: 0.8925 (t)
REVERT: U  322 MET cc_start: 0.6988 (tmm) cc_final: 0.6638 (tpp)
REVERT: U  335 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6832 (mt)
REVERT: U  413 LEU cc_start: 0.8886 (tt) cc_final: 0.8415 (mp)
REVERT: U  414 ASP cc_start: 0.7982 (p0) cc_final: 0.7734 (t0)
REVERT: U  453 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7619 (tt)
REVERT: U  629 PHE cc_start: 0.7112 (p90) cc_final: 0.6534 (p90)
REVERT: U  743 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.6851 (mpp-170)
REVERT: U  910 PHE cc_start: 0.8069 (m-10) cc_final: 0.7787 (m-10)
REVERT: U 1111 PHE cc_start: 0.8572 (m-10) cc_final: 0.7991 (m-10)
REVERT: U 1175 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.6557 (mmtm)
REVERT: U 1202 MET cc_start: 0.5705 (mmm) cc_final: 0.4510 (mtm)
REVERT: U 1224 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8092 (mtmt)
REVERT: U 1304 MET cc_start: 0.7828 (mpt) cc_final: 0.7460 (mpp)
  outliers start: 29
  outliers final: 11
  residues processed: 139
  average time/residue: 0.0872
  time to fit residues: 17.2524
Evaluate side-chains
  111 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue  145 TYR
Chi-restraints excluded: chain U residue  335 LEU
Chi-restraints excluded: chain U residue  453 LEU
Chi-restraints excluded: chain U residue  454 VAL
Chi-restraints excluded: chain U residue  479 VAL
Chi-restraints excluded: chain U residue  580 LEU
Chi-restraints excluded: chain U residue  757 VAL
Chi-restraints excluded: chain U residue  768 VAL
Chi-restraints excluded: chain U residue  888 VAL
Chi-restraints excluded: chain U residue 1013 HIS
Chi-restraints excluded: chain U residue 1014 PHE
Chi-restraints excluded: chain U residue 1079 ASP
Chi-restraints excluded: chain U residue 1121 THR
Chi-restraints excluded: chain U residue 1175 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 40 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 114 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 111 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 104 optimal weight:    0.4980
   chunk 36 optimal weight:   10.0000
   overall best weight:    2.0584

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

Flipped N/Q/H residues before XYZ refinement:
U 170 GLN
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 842 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.177145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.125898 restraints weight = 14157.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.120344 restraints weight = 10568.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.121531 restraints weight = 9159.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.122108 restraints weight = 6642.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.122883 restraints weight = 5875.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9466  Z= 0.191
  Angle     :  0.688  17.286  12806  Z= 0.338
  Chirality :  0.044   0.183   1462
  Planarity :  0.004   0.033   1631
  Dihedral  :  7.219  79.215   1358
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 17.91 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.43 (0.21), residues: 1185
  helix: -3.08 (0.16), residues: 652
  sheet: -3.52 (0.92), residues: 30
  loop : -2.51 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG U 299 
 TYR   0.014   0.002   TYR U 274 
 PHE   0.011   0.001   PHE U 235 
 TRP   0.011   0.001   TRP U 314 
 HIS   0.002   0.001   HIS U 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 9465)
  covalent geometry    : angle       0.68807 (12806)
  hydrogen bonds       : bond        0.03413 (  193)
  hydrogen bonds       : angle       5.17394 (  561)
  Misc. bond           : bond        0.00152 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 107
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: U  123 MET cc_start: 0.1997 (mmp) cc_final: 0.0926 (mmm)
REVERT: U  154 ILE cc_start: 0.8329 (tp) cc_final: 0.8004 (tp)
REVERT: U  177 PHE cc_start: 0.7995 (t80) cc_final: 0.7672 (t80)
REVERT: U  197 GLU cc_start: 0.8127 (tp30) cc_final: 0.7680 (tp30)
REVERT: U  205 ASP cc_start: 0.8642 (t0) cc_final: 0.8378 (t0)
REVERT: U  217 MET cc_start: 0.8180 (tpp) cc_final: 0.7572 (tpt)
REVERT: U  290 THR cc_start: 0.9113 (p) cc_final: 0.8898 (t)
REVERT: U  335 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6996 (mt)
REVERT: U  380 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8266 (tt)
REVERT: U  413 LEU cc_start: 0.8927 (tt) cc_final: 0.8440 (mp)
REVERT: U  414 ASP cc_start: 0.7988 (p0) cc_final: 0.7718 (t0)
REVERT: U  453 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7695 (tt)
REVERT: U  629 PHE cc_start: 0.7060 (p90) cc_final: 0.6433 (p90)
REVERT: U  890 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8533 (mmm)
REVERT: U 1111 PHE cc_start: 0.8648 (m-10) cc_final: 0.8160 (m-10)
REVERT: U 1224 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8080 (tmtt)
REVERT: U 1304 MET cc_start: 0.7792 (mpt) cc_final: 0.7452 (mpp)
  outliers start: 41
  outliers final: 24
  residues processed: 139
  average time/residue: 0.0825
  time to fit residues: 16.5985
Evaluate side-chains
  131 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   64 VAL
Chi-restraints excluded: chain U residue   66 SER
Chi-restraints excluded: chain U residue  145 TYR
Chi-restraints excluded: chain U residue  182 ILE
Chi-restraints excluded: chain U residue  244 VAL
Chi-restraints excluded: chain U residue  263 VAL
Chi-restraints excluded: chain U residue  335 LEU
Chi-restraints excluded: chain U residue  371 LEU
Chi-restraints excluded: chain U residue  380 LEU
Chi-restraints excluded: chain U residue  453 LEU
Chi-restraints excluded: chain U residue  454 VAL
Chi-restraints excluded: chain U residue  479 VAL
Chi-restraints excluded: chain U residue  524 THR
Chi-restraints excluded: chain U residue  567 VAL
Chi-restraints excluded: chain U residue  580 LEU
Chi-restraints excluded: chain U residue  757 VAL
Chi-restraints excluded: chain U residue  768 VAL
Chi-restraints excluded: chain U residue  834 PHE
Chi-restraints excluded: chain U residue  839 MET
Chi-restraints excluded: chain U residue  888 VAL
Chi-restraints excluded: chain U residue  890 MET
Chi-restraints excluded: chain U residue  913 LEU
Chi-restraints excluded: chain U residue  917 THR
Chi-restraints excluded: chain U residue 1013 HIS
Chi-restraints excluded: chain U residue 1014 PHE
Chi-restraints excluded: chain U residue 1121 THR
Chi-restraints excluded: chain U residue 1139 ILE
Chi-restraints excluded: chain U residue 1175 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 94 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 103 optimal weight:   20.0000
   chunk 112 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0770
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
U 497 GLN
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 842 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.181462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.130445 restraints weight = 14089.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.127188 restraints weight = 9501.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.127762 restraints weight = 9901.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.128226 restraints weight = 6817.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.128718 restraints weight = 5686.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9466  Z= 0.105
  Angle     :  0.637  17.675  12806  Z= 0.304
  Chirality :  0.041   0.180   1462
  Planarity :  0.003   0.031   1631
  Dihedral  :  6.708  81.123   1358
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 19.13 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.00 (0.22), residues: 1185
  helix: -2.73 (0.17), residues: 648
  sheet: -3.04 (0.88), residues: 34
  loop : -2.33 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG U1265 
 TYR   0.017   0.001   TYR U 274 
 PHE   0.012   0.001   PHE U 363 
 TRP   0.010   0.001   TRP U 493 
 HIS   0.003   0.000   HIS U1013 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9465)
  covalent geometry    : angle       0.63682 (12806)
  hydrogen bonds       : bond        0.02691 (  193)
  hydrogen bonds       : angle       4.75097 (  561)
  Misc. bond           : bond        0.00098 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.341 
Fit side-chains
REVERT: U  154 ILE cc_start: 0.8340 (tp) cc_final: 0.8035 (tp)
REVERT: U  177 PHE cc_start: 0.7769 (t80) cc_final: 0.7424 (t80)
REVERT: U  197 GLU cc_start: 0.8076 (tp30) cc_final: 0.7521 (tp30)
REVERT: U  205 ASP cc_start: 0.8673 (t0) cc_final: 0.8442 (t0)
REVERT: U  217 MET cc_start: 0.7689 (tpp) cc_final: 0.7214 (tpt)
REVERT: U  232 LEU cc_start: 0.8740 (tt) cc_final: 0.8196 (mm)
REVERT: U  290 THR cc_start: 0.9096 (p) cc_final: 0.8878 (t)
REVERT: U  362 ILE cc_start: 0.8953 (pp) cc_final: 0.8663 (pt)
REVERT: U  413 LEU cc_start: 0.8742 (tt) cc_final: 0.8336 (mp)
REVERT: U  414 ASP cc_start: 0.7848 (p0) cc_final: 0.7593 (t0)
REVERT: U  443 MET cc_start: 0.8464 (ppp) cc_final: 0.7900 (ppp)
REVERT: U  453 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7733 (tt)
REVERT: U  596 MET cc_start: 0.9011 (mmm) cc_final: 0.8805 (mmm)
REVERT: U  629 PHE cc_start: 0.7092 (p90) cc_final: 0.6517 (p90)
REVERT: U  890 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8385 (mmm)
REVERT: U  910 PHE cc_start: 0.8110 (m-10) cc_final: 0.7847 (m-10)
REVERT: U 1111 PHE cc_start: 0.8609 (m-10) cc_final: 0.8151 (m-10)
REVERT: U 1202 MET cc_start: 0.5371 (mmm) cc_final: 0.4098 (mtm)
REVERT: U 1221 ARG cc_start: 0.8164 (ptt-90) cc_final: 0.7874 (ptt-90)
REVERT: U 1224 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8013 (tmtt)
REVERT: U 1304 MET cc_start: 0.7732 (mpt) cc_final: 0.7521 (mpp)
  outliers start: 33
  outliers final: 21
  residues processed: 142
  average time/residue: 0.0779
  time to fit residues: 16.3095
Evaluate side-chains
  123 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   56 SER
Chi-restraints excluded: chain U residue  145 TYR
Chi-restraints excluded: chain U residue  171 ILE
Chi-restraints excluded: chain U residue  176 LYS
Chi-restraints excluded: chain U residue  182 ILE
Chi-restraints excluded: chain U residue  368 VAL
Chi-restraints excluded: chain U residue  403 ILE
Chi-restraints excluded: chain U residue  422 PHE
Chi-restraints excluded: chain U residue  453 LEU
Chi-restraints excluded: chain U residue  454 VAL
Chi-restraints excluded: chain U residue  479 VAL
Chi-restraints excluded: chain U residue  580 LEU
Chi-restraints excluded: chain U residue  587 SER
Chi-restraints excluded: chain U residue  617 LEU
Chi-restraints excluded: chain U residue  757 VAL
Chi-restraints excluded: chain U residue  811 PHE
Chi-restraints excluded: chain U residue  834 PHE
Chi-restraints excluded: chain U residue  890 MET
Chi-restraints excluded: chain U residue 1013 HIS
Chi-restraints excluded: chain U residue 1014 PHE
Chi-restraints excluded: chain U residue 1121 THR
Chi-restraints excluded: chain U residue 1139 ILE
Chi-restraints excluded: chain U residue 1285 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0670
   chunk 115 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    1.4126

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

Flipped N/Q/H residues before XYZ refinement:
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.179365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.128525 restraints weight = 14066.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.123864 restraints weight = 9953.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.124812 restraints weight = 10115.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.125385 restraints weight = 6977.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125889 restraints weight = 5630.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9466  Z= 0.143
  Angle     :  0.660  16.644  12806  Z= 0.314
  Chirality :  0.042   0.182   1462
  Planarity :  0.003   0.032   1631
  Dihedral  :  6.651  78.256   1357
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.64 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.89 (0.22), residues: 1185
  helix: -2.60 (0.18), residues: 652
  sheet: -2.91 (0.89), residues: 34
  loop : -2.33 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG U 487 
 TYR   0.014   0.001   TYR U 274 
 PHE   0.011   0.001   PHE U 363 
 TRP   0.025   0.001   TRP U 493 
 HIS   0.003   0.001   HIS U1013 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9465)
  covalent geometry    : angle       0.65997 (12806)
  hydrogen bonds       : bond        0.02956 (  193)
  hydrogen bonds       : angle       4.79656 (  561)
  Misc. bond           : bond        0.00119 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 110
  time to evaluate  : 0.284 
Fit side-chains
REVERT: U  154 ILE cc_start: 0.8343 (tp) cc_final: 0.8022 (tp)
REVERT: U  177 PHE cc_start: 0.7832 (t80) cc_final: 0.7479 (t80)
REVERT: U  197 GLU cc_start: 0.8150 (tp30) cc_final: 0.7652 (tp30)
REVERT: U  217 MET cc_start: 0.8044 (tpp) cc_final: 0.7428 (tpt)
REVERT: U  232 LEU cc_start: 0.8848 (tt) cc_final: 0.8299 (mm)
REVERT: U  290 THR cc_start: 0.9069 (p) cc_final: 0.8845 (t)
REVERT: U  362 ILE cc_start: 0.9012 (pp) cc_final: 0.8715 (pt)
REVERT: U  413 LEU cc_start: 0.8668 (tt) cc_final: 0.8299 (mp)
REVERT: U  443 MET cc_start: 0.8527 (ppp) cc_final: 0.7599 (ppp)
REVERT: U  453 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7742 (tt)
REVERT: U  559 MET cc_start: 0.6415 (mtt) cc_final: 0.6082 (mtt)
REVERT: U  629 PHE cc_start: 0.7014 (p90) cc_final: 0.6435 (p90)
REVERT: U  890 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8466 (mmm)
REVERT: U 1111 PHE cc_start: 0.8676 (m-10) cc_final: 0.8261 (m-10)
REVERT: U 1202 MET cc_start: 0.5440 (mmm) cc_final: 0.4248 (mtm)
REVERT: U 1224 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7875 (mtmm)
REVERT: U 1304 MET cc_start: 0.7755 (mpt) cc_final: 0.7548 (mpp)
  outliers start: 36
  outliers final: 23
  residues processed: 136
  average time/residue: 0.0885
  time to fit residues: 17.3833
Evaluate side-chains
  129 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue  145 TYR
Chi-restraints excluded: chain U residue  171 ILE
Chi-restraints excluded: chain U residue  176 LYS
Chi-restraints excluded: chain U residue  182 ILE
Chi-restraints excluded: chain U residue  244 VAL
Chi-restraints excluded: chain U residue  359 LEU
Chi-restraints excluded: chain U residue  363 PHE
Chi-restraints excluded: chain U residue  368 VAL
Chi-restraints excluded: chain U residue  453 LEU
Chi-restraints excluded: chain U residue  454 VAL
Chi-restraints excluded: chain U residue  479 VAL
Chi-restraints excluded: chain U residue  580 LEU
Chi-restraints excluded: chain U residue  587 SER
Chi-restraints excluded: chain U residue  757 VAL
Chi-restraints excluded: chain U residue  768 VAL
Chi-restraints excluded: chain U residue  775 LEU
Chi-restraints excluded: chain U residue  834 PHE
Chi-restraints excluded: chain U residue  839 MET
Chi-restraints excluded: chain U residue  888 VAL
Chi-restraints excluded: chain U residue  890 MET
Chi-restraints excluded: chain U residue  913 LEU
Chi-restraints excluded: chain U residue 1013 HIS
Chi-restraints excluded: chain U residue 1014 PHE
Chi-restraints excluded: chain U residue 1139 ILE
Chi-restraints excluded: chain U residue 1285 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0870
   chunk 72 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 112 optimal weight:    8.9990
   chunk 91 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 107 optimal weight:   30.0000
   overall best weight:    1.6162

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

Flipped N/Q/H residues before XYZ refinement:
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 842 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.179011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.127415 restraints weight = 13988.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.122407 restraints weight = 10168.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.123388 restraints weight = 10331.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.124112 restraints weight = 7060.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.124976 restraints weight = 5851.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9466  Z= 0.157
  Angle     :  0.676  16.193  12806  Z= 0.322
  Chirality :  0.043   0.179   1462
  Planarity :  0.003   0.031   1631
  Dihedral  :  6.691  79.417   1357
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 19.64 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.79 (0.22), residues: 1185
  helix: -2.52 (0.18), residues: 652
  sheet: -2.65 (0.93), residues: 32
  loop : -2.32 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG U1221 
 TYR   0.022   0.001   TYR U 274 
 PHE   0.011   0.001   PHE U 363 
 TRP   0.022   0.001   TRP U 493 
 HIS   0.003   0.001   HIS U1013 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9465)
  covalent geometry    : angle       0.67618 (12806)
  hydrogen bonds       : bond        0.02966 (  193)
  hydrogen bonds       : angle       4.82651 (  561)
  Misc. bond           : bond        0.00132 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 107
  time to evaluate  : 0.330 
Fit side-chains
REVERT: U  123 MET cc_start: 0.0658 (mmm) cc_final: 0.0456 (mmp)
REVERT: U  154 ILE cc_start: 0.8330 (tp) cc_final: 0.8021 (tp)
REVERT: U  177 PHE cc_start: 0.7885 (t80) cc_final: 0.7529 (t80)
REVERT: U  197 GLU cc_start: 0.8160 (tp30) cc_final: 0.7682 (tp30)
REVERT: U  217 MET cc_start: 0.8011 (tpp) cc_final: 0.7389 (tpt)
REVERT: U  224 MET cc_start: 0.7671 (tpp) cc_final: 0.7446 (tpt)
REVERT: U  232 LEU cc_start: 0.8853 (tt) cc_final: 0.8371 (mm)
REVERT: U  362 ILE cc_start: 0.9015 (pp) cc_final: 0.8705 (pt)
REVERT: U  371 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8252 (mp)
REVERT: U  413 LEU cc_start: 0.8671 (tt) cc_final: 0.8217 (mp)
REVERT: U  443 MET cc_start: 0.8493 (ppp) cc_final: 0.7799 (ppp)
REVERT: U  453 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7681 (tt)
REVERT: U  461 LYS cc_start: 0.7429 (ptpp) cc_final: 0.7132 (mmmt)
REVERT: U  596 MET cc_start: 0.9016 (mmm) cc_final: 0.8780 (mmm)
REVERT: U  629 PHE cc_start: 0.7075 (p90) cc_final: 0.6469 (p90)
REVERT: U  751 GLU cc_start: 0.7108 (tp30) cc_final: 0.6871 (tp30)
REVERT: U  878 MET cc_start: 0.8325 (tpp) cc_final: 0.7232 (tmm)
REVERT: U  890 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8491 (mmm)
REVERT: U  925 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6529 (t80)
REVERT: U 1043 LYS cc_start: 0.8604 (ptmt) cc_final: 0.7928 (pttp)
REVERT: U 1111 PHE cc_start: 0.8647 (m-10) cc_final: 0.7780 (m-10)
REVERT: U 1123 ILE cc_start: 0.8895 (tp) cc_final: 0.8682 (mm)
REVERT: U 1202 MET cc_start: 0.5047 (mmm) cc_final: 0.4002 (mtm)
REVERT: U 1224 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7839 (mtmt)
REVERT: U 1304 MET cc_start: 0.7772 (mpt) cc_final: 0.7562 (mpp)
  outliers start: 42
  outliers final: 29
  residues processed: 138
  average time/residue: 0.0792
  time to fit residues: 15.9823
Evaluate side-chains
  139 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   66 SER
Chi-restraints excluded: chain U residue  145 TYR
Chi-restraints excluded: chain U residue  171 ILE
Chi-restraints excluded: chain U residue  174 MET
Chi-restraints excluded: chain U residue  176 LYS
Chi-restraints excluded: chain U residue  182 ILE
Chi-restraints excluded: chain U residue  244 VAL
Chi-restraints excluded: chain U residue  252 ILE
Chi-restraints excluded: chain U residue  263 VAL
Chi-restraints excluded: chain U residue  359 LEU
Chi-restraints excluded: chain U residue  363 PHE
Chi-restraints excluded: chain U residue  368 VAL
Chi-restraints excluded: chain U residue  371 LEU
Chi-restraints excluded: chain U residue  403 ILE
Chi-restraints excluded: chain U residue  453 LEU
Chi-restraints excluded: chain U residue  454 VAL
Chi-restraints excluded: chain U residue  479 VAL
Chi-restraints excluded: chain U residue  580 LEU
Chi-restraints excluded: chain U residue  582 LEU
Chi-restraints excluded: chain U residue  587 SER
Chi-restraints excluded: chain U residue  757 VAL
Chi-restraints excluded: chain U residue  768 VAL
Chi-restraints excluded: chain U residue  775 LEU
Chi-restraints excluded: chain U residue  834 PHE
Chi-restraints excluded: chain U residue  839 MET
Chi-restraints excluded: chain U residue  844 ILE
Chi-restraints excluded: chain U residue  888 VAL
Chi-restraints excluded: chain U residue  890 MET
Chi-restraints excluded: chain U residue  913 LEU
Chi-restraints excluded: chain U residue  925 PHE
Chi-restraints excluded: chain U residue 1013 HIS
Chi-restraints excluded: chain U residue 1014 PHE
Chi-restraints excluded: chain U residue 1285 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
U 546 GLN
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 996 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.180502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.127424 restraints weight = 13924.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.122377 restraints weight = 9355.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.123295 restraints weight = 8559.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.124296 restraints weight = 6413.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.124591 restraints weight = 5650.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9466  Z= 0.122
  Angle     :  0.659  16.362  12806  Z= 0.310
  Chirality :  0.042   0.174   1462
  Planarity :  0.003   0.032   1631
  Dihedral  :  6.485  80.119   1357
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.85 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.60 (0.23), residues: 1185
  helix: -2.33 (0.18), residues: 652
  sheet: -2.52 (0.94), residues: 32
  loop : -2.28 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG U1221 
 TYR   0.020   0.001   TYR U 274 
 PHE   0.012   0.001   PHE U 363 
 TRP   0.019   0.001   TRP U 493 
 HIS   0.004   0.001   HIS U1013 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9465)
  covalent geometry    : angle       0.65869 (12806)
  hydrogen bonds       : bond        0.02748 (  193)
  hydrogen bonds       : angle       4.67086 (  561)
  Misc. bond           : bond        0.00117 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.395 
Fit side-chains
REVERT: U  154 ILE cc_start: 0.8410 (tp) cc_final: 0.8101 (tp)
REVERT: U  177 PHE cc_start: 0.7850 (t80) cc_final: 0.7523 (t80)
REVERT: U  197 GLU cc_start: 0.8223 (tp30) cc_final: 0.7667 (tp30)
REVERT: U  217 MET cc_start: 0.7948 (tpp) cc_final: 0.7383 (tpt)
REVERT: U  232 LEU cc_start: 0.8808 (tt) cc_final: 0.8362 (mm)
REVERT: U  290 THR cc_start: 0.9215 (p) cc_final: 0.8969 (t)
REVERT: U  362 ILE cc_start: 0.8976 (pp) cc_final: 0.8639 (pt)
REVERT: U  371 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8210 (mp)
REVERT: U  413 LEU cc_start: 0.8862 (tt) cc_final: 0.8316 (mp)
REVERT: U  443 MET cc_start: 0.8766 (ppp) cc_final: 0.8204 (ppp)
REVERT: U  453 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7616 (tt)
REVERT: U  461 LYS cc_start: 0.7661 (ptpp) cc_final: 0.7227 (mmmt)
REVERT: U  478 MET cc_start: 0.7315 (ppp) cc_final: 0.6806 (ppp)
REVERT: U  559 MET cc_start: 0.6399 (mtt) cc_final: 0.5985 (mtt)
REVERT: U  596 MET cc_start: 0.9152 (mmm) cc_final: 0.8871 (mmm)
REVERT: U  629 PHE cc_start: 0.7058 (p90) cc_final: 0.6318 (p90)
REVERT: U  878 MET cc_start: 0.8201 (tpp) cc_final: 0.7185 (tmm)
REVERT: U  890 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8448 (mmm)
REVERT: U  925 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6360 (t80)
REVERT: U 1043 LYS cc_start: 0.8593 (ptmt) cc_final: 0.7914 (pttp)
REVERT: U 1111 PHE cc_start: 0.8626 (m-10) cc_final: 0.7988 (m-10)
REVERT: U 1202 MET cc_start: 0.5470 (mmm) cc_final: 0.4438 (mtm)
REVERT: U 1221 ARG cc_start: 0.8018 (ptt-90) cc_final: 0.7164 (ptt-90)
REVERT: U 1304 MET cc_start: 0.7976 (mpt) cc_final: 0.7722 (mpp)
  outliers start: 34
  outliers final: 28
  residues processed: 134
  average time/residue: 0.0811
  time to fit residues: 15.9673
Evaluate side-chains
  138 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   66 SER
Chi-restraints excluded: chain U residue  145 TYR
Chi-restraints excluded: chain U residue  171 ILE
Chi-restraints excluded: chain U residue  174 MET
Chi-restraints excluded: chain U residue  176 LYS
Chi-restraints excluded: chain U residue  252 ILE
Chi-restraints excluded: chain U residue  263 VAL
Chi-restraints excluded: chain U residue  359 LEU
Chi-restraints excluded: chain U residue  363 PHE
Chi-restraints excluded: chain U residue  368 VAL
Chi-restraints excluded: chain U residue  371 LEU
Chi-restraints excluded: chain U residue  403 ILE
Chi-restraints excluded: chain U residue  453 LEU
Chi-restraints excluded: chain U residue  454 VAL
Chi-restraints excluded: chain U residue  479 VAL
Chi-restraints excluded: chain U residue  580 LEU
Chi-restraints excluded: chain U residue  582 LEU
Chi-restraints excluded: chain U residue  587 SER
Chi-restraints excluded: chain U residue  757 VAL
Chi-restraints excluded: chain U residue  768 VAL
Chi-restraints excluded: chain U residue  775 LEU
Chi-restraints excluded: chain U residue  834 PHE
Chi-restraints excluded: chain U residue  839 MET
Chi-restraints excluded: chain U residue  844 ILE
Chi-restraints excluded: chain U residue  888 VAL
Chi-restraints excluded: chain U residue  890 MET
Chi-restraints excluded: chain U residue  913 LEU
Chi-restraints excluded: chain U residue  925 PHE
Chi-restraints excluded: chain U residue 1013 HIS
Chi-restraints excluded: chain U residue 1014 PHE
Chi-restraints excluded: chain U residue 1139 ILE
Chi-restraints excluded: chain U residue 1285 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 91 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 107 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
U 546 GLN
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.179879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.113050 restraints weight = 14054.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.116393 restraints weight = 7903.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118572 restraints weight = 5490.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.119692 restraints weight = 4440.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.120673 restraints weight = 3933.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9466  Z= 0.156
  Angle     :  0.691  15.764  12806  Z= 0.326
  Chirality :  0.043   0.185   1462
  Planarity :  0.003   0.032   1631
  Dihedral  :  6.539  79.867   1357
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.05 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.57 (0.23), residues: 1185
  helix: -2.32 (0.18), residues: 658
  sheet: -2.44 (0.95), residues: 32
  loop : -2.25 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG U1221 
 TYR   0.024   0.001   TYR U 274 
 PHE   0.011   0.001   PHE U 363 
 TRP   0.017   0.001   TRP U 493 
 HIS   0.004   0.001   HIS U1013 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9465)
  covalent geometry    : angle       0.69052 (12806)
  hydrogen bonds       : bond        0.02947 (  193)
  hydrogen bonds       : angle       4.77004 (  561)
  Misc. bond           : bond        0.00134 (    1)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.319 
Fit side-chains
REVERT: U  153 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8422 (tp)
REVERT: U  154 ILE cc_start: 0.8800 (tp) cc_final: 0.8451 (tp)
REVERT: U  177 PHE cc_start: 0.7832 (t80) cc_final: 0.7488 (t80)
REVERT: U  197 GLU cc_start: 0.8262 (tp30) cc_final: 0.7733 (tp30)
REVERT: U  217 MET cc_start: 0.8188 (tpp) cc_final: 0.7629 (tpt)
REVERT: U  232 LEU cc_start: 0.8842 (tt) cc_final: 0.8373 (mm)
REVERT: U  371 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7985 (mp)
REVERT: U  413 LEU cc_start: 0.8815 (tt) cc_final: 0.8236 (mp)
REVERT: U  443 MET cc_start: 0.8536 (ppp) cc_final: 0.8069 (ppp)
REVERT: U  461 LYS cc_start: 0.7408 (ptpp) cc_final: 0.7097 (mmmt)
REVERT: U  559 MET cc_start: 0.6553 (mtt) cc_final: 0.6134 (mtt)
REVERT: U  878 MET cc_start: 0.8221 (tpp) cc_final: 0.7085 (tmm)
REVERT: U  890 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8538 (mmm)
REVERT: U  925 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6494 (t80)
REVERT: U 1043 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8004 (pttp)
REVERT: U 1138 MET cc_start: 0.6602 (tpp) cc_final: 0.6167 (tpp)
REVERT: U 1202 MET cc_start: 0.5106 (mmm) cc_final: 0.4093 (mtm)
REVERT: U 1221 ARG cc_start: 0.7833 (ptt-90) cc_final: 0.7583 (ptt-90)
REVERT: U 1225 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8416 (tm-30)
REVERT: U 1276 ARG cc_start: 0.6801 (ptp90) cc_final: 0.6380 (ptp90)
  outliers start: 34
  outliers final: 27
  residues processed: 131
  average time/residue: 0.0801
  time to fit residues: 15.2551
Evaluate side-chains
  134 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   66 SER
Chi-restraints excluded: chain U residue  145 TYR
Chi-restraints excluded: chain U residue  153 LEU
Chi-restraints excluded: chain U residue  171 ILE
Chi-restraints excluded: chain U residue  174 MET
Chi-restraints excluded: chain U residue  176 LYS
Chi-restraints excluded: chain U residue  182 ILE
Chi-restraints excluded: chain U residue  252 ILE
Chi-restraints excluded: chain U residue  263 VAL
Chi-restraints excluded: chain U residue  359 LEU
Chi-restraints excluded: chain U residue  363 PHE
Chi-restraints excluded: chain U residue  368 VAL
Chi-restraints excluded: chain U residue  371 LEU
Chi-restraints excluded: chain U residue  403 ILE
Chi-restraints excluded: chain U residue  454 VAL
Chi-restraints excluded: chain U residue  479 VAL
Chi-restraints excluded: chain U residue  580 LEU
Chi-restraints excluded: chain U residue  582 LEU
Chi-restraints excluded: chain U residue  757 VAL
Chi-restraints excluded: chain U residue  768 VAL
Chi-restraints excluded: chain U residue  775 LEU
Chi-restraints excluded: chain U residue  834 PHE
Chi-restraints excluded: chain U residue  839 MET
Chi-restraints excluded: chain U residue  844 ILE
Chi-restraints excluded: chain U residue  888 VAL
Chi-restraints excluded: chain U residue  890 MET
Chi-restraints excluded: chain U residue  913 LEU
Chi-restraints excluded: chain U residue  925 PHE
Chi-restraints excluded: chain U residue 1013 HIS
Chi-restraints excluded: chain U residue 1014 PHE
Chi-restraints excluded: chain U residue 1285 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 73 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   chunk 97 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 95 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
U 546 GLN
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.182420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.129554 restraints weight = 13635.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.124487 restraints weight = 9604.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.124755 restraints weight = 9910.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.126180 restraints weight = 6824.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.127236 restraints weight = 5670.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.4793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9466  Z= 0.139
  Angle     :  0.693  15.881  12806  Z= 0.325
  Chirality :  0.042   0.181   1462
  Planarity :  0.003   0.032   1631
  Dihedral  :  6.470  81.083   1357
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.36 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.49 (0.23), residues: 1185
  helix: -2.24 (0.18), residues: 661
  sheet: -2.65 (0.93), residues: 34
  loop : -2.21 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG U1221 
 TYR   0.023   0.001   TYR U 274 
 PHE   0.012   0.001   PHE U 363 
 TRP   0.016   0.001   TRP U 493 
 HIS   0.004   0.001   HIS U1013 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9465)
  covalent geometry    : angle       0.69319 (12806)
  hydrogen bonds       : bond        0.02923 (  193)
  hydrogen bonds       : angle       4.78350 (  561)
  Misc. bond           : bond        0.00130 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1516.24 seconds
wall clock time: 26 minutes 49.48 seconds (1609.48 seconds total)