Starting phenix.real_space_refine
on Sun Aug 24 13:23:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wy9_37920/08_2025/8wy9_37920.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wy9_37920/08_2025/8wy9_37920.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wy9_37920/08_2025/8wy9_37920.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wy9_37920/08_2025/8wy9_37920.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wy9_37920/08_2025/8wy9_37920.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wy9_37920/08_2025/8wy9_37920.map"
  }
  resolution = 2.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.048
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      75      5.16       5
     C   13028      2.51       5
     N    3257      2.21       5
     O    3769      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20129
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 932, 7786
          Classifications: {'peptide': 932}
          Link IDs: {'PTRANS': 19, 'TRANS': 912}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 7869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 940, 7869
          Classifications: {'peptide': 940}
          Link IDs: {'PTRANS': 19, 'TRANS': 920}
          Chain breaks: 7
    Chain: "C"
      Number of atoms: 2225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2225
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 10, 'TRANS': 261}
    Chain: "D"
      Number of atoms: 2249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2249
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 10, 'TRANS': 264}
  Time building chain proxies: 4.49, per 1000 atoms: 0.22
  Number of scatterers: 20129
  At special positions: 0
  Unit cell: (100.067, 126.531, 180.286, 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      75     16.00
     O    3769      8.00
     N    3257      7.00
     C   13028      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.45
  Conformation dependent library (CDL) restraints added in 803.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4614

  Finding SS restraints...
    Secondary structure from input PDB file:
      150 helices and 7 sheets defined
      70.6% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 40
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 4.031A  pdb=" N   SER A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 71
      removed outlier: 3.707A  pdb=" N   LEU A  62 " --> pdb=" O   GLN A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 96
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 96 through 109
      removed outlier: 3.597A  pdb=" N   PHE A 100 " --> pdb=" O   GLY A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 124
      removed outlier: 3.745A  pdb=" N   ASP A 119 " --> pdb=" O   ASN A 115 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET A 124 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 146
    Processing helix  chain 'A' and resid 154 through 158
    Processing helix  chain 'A' and resid 179 through 183
      removed outlier: 3.522A  pdb=" N   ASN A 182 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 183 " --> pdb=" O   GLY A 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 179 through 183'
    Processing helix  chain 'A' and resid 186 through 192
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 197 through 211
    Processing helix  chain 'A' and resid 222 through 234
      removed outlier: 3.793A  pdb=" N   LYS A 234 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 264
    Processing helix  chain 'A' and resid 271 through 275
    Processing helix  chain 'A' and resid 281 through 295
      removed outlier: 3.553A  pdb=" N   VAL A 289 " --> pdb=" O   ARG A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 317
    Processing helix  chain 'A' and resid 318 through 322
    Processing helix  chain 'A' and resid 326 through 328
      No H-bonds generated for 'chain 'A' and resid 326 through 328'
    Processing helix  chain 'A' and resid 329 through 334
    Processing helix  chain 'A' and resid 355 through 366
    Processing helix  chain 'A' and resid 366 through 372
      removed outlier: 4.035A  pdb=" N   ARG A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 391
    Processing helix  chain 'A' and resid 417 through 427
    Processing helix  chain 'A' and resid 431 through 445
    Processing helix  chain 'A' and resid 447 through 462
    Processing helix  chain 'A' and resid 469 through 494
    Processing helix  chain 'A' and resid 508 through 520
    Processing helix  chain 'A' and resid 532 through 539
    Processing helix  chain 'A' and resid 540 through 547
      removed outlier: 3.773A  pdb=" N   PHE A 544 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 572
    Processing helix  chain 'A' and resid 579 through 598
    Processing helix  chain 'A' and resid 600 through 604
    Processing helix  chain 'A' and resid 605 through 628
      removed outlier: 3.856A  pdb=" N   THR A 628 " --> pdb=" O   GLU A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 659
    Processing helix  chain 'A' and resid 660 through 671
    Processing helix  chain 'A' and resid 672 through 676
    Processing helix  chain 'A' and resid 680 through 699
    Processing helix  chain 'A' and resid 705 through 723
      removed outlier: 3.837A  pdb=" N   GLN A 711 " --> pdb=" O   VAL A 707 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   SER A 714 " --> pdb=" O   THR A 710 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLU A 715 " --> pdb=" O   GLN A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 726
      No H-bonds generated for 'chain 'A' and resid 724 through 726'
    Processing helix  chain 'A' and resid 729 through 743
    Processing helix  chain 'A' and resid 750 through 765
      removed outlier: 4.288A  pdb=" N   CYS A 764 " --> pdb=" O   ARG A 760 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASN A 765 " --> pdb=" O   LEU A 761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 786
    Processing helix  chain 'A' and resid 800 through 810
    Processing helix  chain 'A' and resid 817 through 826
      removed outlier: 3.521A  pdb=" N   CYS A 826 " --> pdb=" O   GLU A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 841
      removed outlier: 3.724A  pdb=" N   ILE A 835 " --> pdb=" O   LYS A 831 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LYS A 840 " --> pdb=" O   ASP A 836 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LEU A 841 " --> pdb=" O   PHE A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 857
      removed outlier: 3.905A  pdb=" N   HIS A 852 " --> pdb=" O   ASN A 848 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU A 853 " --> pdb=" O   ALA A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 872
    Processing helix  chain 'A' and resid 878 through 897
      removed outlier: 3.670A  pdb=" N   ILE A 897 " --> pdb=" O   LYS A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 922
      removed outlier: 4.020A  pdb=" N   PHE A 916 " --> pdb=" O   TYR A 912 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY A 917 " --> pdb=" O   MET A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 934
      removed outlier: 4.058A  pdb=" N   GLU A 931 " --> pdb=" O   SER A 928 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ILE A 934 " --> pdb=" O   GLU A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 937 through 945
    Processing helix  chain 'A' and resid 950 through 954
      removed outlier: 3.866A  pdb=" N   LYS A 953 " --> pdb=" O   ASP A 950 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 954 " --> pdb=" O   TYR A 951 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 950 through 954'
    Processing helix  chain 'A' and resid 955 through 956
      No H-bonds generated for 'chain 'A' and resid 955 through 956'
    Processing helix  chain 'A' and resid 957 through 962
      removed outlier: 3.955A  pdb=" N   ASN A 961 " --> pdb=" O   SER A 957 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 962 " --> pdb=" O   TRP A 958 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 957 through 962'
    Processing helix  chain 'A' and resid 963 through 974
      removed outlier: 4.321A  pdb=" N   LYS A 974 " --> pdb=" O   ILE A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 976 through 991
    Processing helix  chain 'A' and resid 994 through 1004
    Processing helix  chain 'B' and resid 9 through 21
    Processing helix  chain 'B' and resid 23 through 39
    Processing helix  chain 'B' and resid 47 through 53
      removed outlier: 3.947A  pdb=" N   SER B  51 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 72
      removed outlier: 3.784A  pdb=" N   LEU B  62 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 95
      removed outlier: 3.569A  pdb=" N   TYR B  84 " --> pdb=" O   SER B  80 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU B  85 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 96 through 109
    Processing helix  chain 'B' and resid 115 through 124
      removed outlier: 3.592A  pdb=" N   ASP B 119 " --> pdb=" O   ASN B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 145
    Processing helix  chain 'B' and resid 154 through 160
      removed outlier: 3.901A  pdb=" N   VAL B 158 " --> pdb=" O   ALA B 154 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA B 159 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASN B 160 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 154 through 160'
    Processing helix  chain 'B' and resid 186 through 192
    Processing helix  chain 'B' and resid 192 through 197
    Processing helix  chain 'B' and resid 197 through 211
    Processing helix  chain 'B' and resid 222 through 234
      removed outlier: 3.566A  pdb=" N   LYS B 234 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 264
    Processing helix  chain 'B' and resid 272 through 274
      No H-bonds generated for 'chain 'B' and resid 272 through 274'
    Processing helix  chain 'B' and resid 281 through 298
    Processing helix  chain 'B' and resid 307 through 317
    Processing helix  chain 'B' and resid 318 through 322
    Processing helix  chain 'B' and resid 326 through 334
      removed outlier: 3.604A  pdb=" N   LYS B 331 " --> pdb=" O   LYS B 327 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   HIS B 332 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 366
    Processing helix  chain 'B' and resid 366 through 372
      removed outlier: 3.579A  pdb=" N   ARG B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 391
    Processing helix  chain 'B' and resid 417 through 427
    Processing helix  chain 'B' and resid 431 through 445
    Processing helix  chain 'B' and resid 447 through 462
    Processing helix  chain 'B' and resid 468 through 493
    Processing helix  chain 'B' and resid 508 through 519
    Processing helix  chain 'B' and resid 523 through 525
      No H-bonds generated for 'chain 'B' and resid 523 through 525'
    Processing helix  chain 'B' and resid 526 through 531
    Processing helix  chain 'B' and resid 532 through 539
    Processing helix  chain 'B' and resid 540 through 547
      removed outlier: 4.420A  pdb=" N   PHE B 544 " --> pdb=" O   ILE B 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 558
    Processing helix  chain 'B' and resid 559 through 563
      removed outlier: 3.634A  pdb=" N   ASN B 563 " --> pdb=" O   GLU B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 598
    Processing helix  chain 'B' and resid 600 through 604
    Processing helix  chain 'B' and resid 605 through 635
    Processing helix  chain 'B' and resid 648 through 659
    Processing helix  chain 'B' and resid 660 through 671
    Processing helix  chain 'B' and resid 672 through 676
    Processing helix  chain 'B' and resid 680 through 700
    Processing helix  chain 'B' and resid 705 through 723
      removed outlier: 3.862A  pdb=" N   GLN B 711 " --> pdb=" O   VAL B 707 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   SER B 714 " --> pdb=" O   THR B 710 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU B 715 " --> pdb=" O   GLN B 711 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 724 through 726
      No H-bonds generated for 'chain 'B' and resid 724 through 726'
    Processing helix  chain 'B' and resid 729 through 743
    Processing helix  chain 'B' and resid 750 through 762
    Processing helix  chain 'B' and resid 768 through 786
    Processing helix  chain 'B' and resid 800 through 812
      removed outlier: 4.040A  pdb=" N   TYR B 804 " --> pdb=" O   TYR B 800 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY B 805 " --> pdb=" O   SER B 801 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE B 811 " --> pdb=" O   LEU B 807 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 826
    Processing helix  chain 'B' and resid 831 through 839
      removed outlier: 3.599A  pdb=" N   ILE B 835 " --> pdb=" O   LYS B 831 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 841 through 845
    Processing helix  chain 'B' and resid 846 through 856
      removed outlier: 3.530A  pdb=" N   SER B 855 " --> pdb=" O   SER B 851 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   PHE B 856 " --> pdb=" O   HIS B 852 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 861 through 872
    Processing helix  chain 'B' and resid 878 through 895
    Processing helix  chain 'B' and resid 912 through 922
    Processing helix  chain 'B' and resid 929 through 934
      removed outlier: 3.564A  pdb=" N   GLU B 932 " --> pdb=" O   LYS B 929 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE B 934 " --> pdb=" O   GLU B 931 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 937 through 945
      removed outlier: 3.535A  pdb=" N   ASP B 941 " --> pdb=" O   ASP B 937 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASP B 945 " --> pdb=" O   ASP B 941 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 950 through 954
    Processing helix  chain 'B' and resid 955 through 956
      No H-bonds generated for 'chain 'B' and resid 955 through 956'
    Processing helix  chain 'B' and resid 957 through 962
      removed outlier: 4.054A  pdb=" N   ASN B 961 " --> pdb=" O   SER B 957 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 963 through 972
    Processing helix  chain 'B' and resid 976 through 991
    Processing helix  chain 'B' and resid 993 through 1003
      removed outlier: 3.930A  pdb=" N   TYR B1003 " --> pdb=" O   ILE B 999 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 40
    Processing helix  chain 'C' and resid 47 through 53
      removed outlier: 3.791A  pdb=" N   SER C  51 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 72
    Processing helix  chain 'C' and resid 80 through 96
      removed outlier: 3.706A  pdb=" N   LEU C  85 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
      Proline residue:  C  88  - end of helix
    Processing helix  chain 'C' and resid 96 through 109
    Processing helix  chain 'C' and resid 115 through 124
      removed outlier: 3.769A  pdb=" N   ASP C 119 " --> pdb=" O   ASN C 115 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   MET C 124 " --> pdb=" O   LYS C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 146
    Processing helix  chain 'C' and resid 179 through 183
      removed outlier: 3.596A  pdb=" N   VAL C 183 " --> pdb=" O   GLY C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 192
    Processing helix  chain 'C' and resid 192 through 197
    Processing helix  chain 'C' and resid 197 through 211
    Processing helix  chain 'C' and resid 222 through 235
      removed outlier: 3.707A  pdb=" N   LYS C 234 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU C 235 " --> pdb=" O   TRP C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 264
      removed outlier: 3.525A  pdb=" N   TYR C 260 " --> pdb=" O   GLU C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 275
    Processing helix  chain 'C' and resid 281 through 297
      removed outlier: 3.851A  pdb=" N   ARG C 285 " --> pdb=" O   ASP C 281 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL C 289 " --> pdb=" O   ARG C 285 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 24 through 39
      removed outlier: 3.936A  pdb=" N   GLU D  28 " --> pdb=" O   ASN D  24 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   CYS D  29 " --> pdb=" O   ASN D  25 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASN D  39 " --> pdb=" O   GLU D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 54
      removed outlier: 3.993A  pdb=" N   SER D  51 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   SER D  54 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 72
      removed outlier: 3.769A  pdb=" N   LEU D  62 " --> pdb=" O   GLN D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 96
      removed outlier: 3.898A  pdb=" N   LEU D  85 " --> pdb=" O   SER D  81 " (cutoff:3.500A)
      Proline residue:  D  88  - end of helix
    Processing helix  chain 'D' and resid 96 through 109
    Processing helix  chain 'D' and resid 115 through 124
      removed outlier: 3.873A  pdb=" N   ASP D 119 " --> pdb=" O   ASN D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 136 through 146
    Processing helix  chain 'D' and resid 154 through 158
    Processing helix  chain 'D' and resid 179 through 183
    Processing helix  chain 'D' and resid 186 through 192
    Processing helix  chain 'D' and resid 192 through 197
    Processing helix  chain 'D' and resid 197 through 211
    Processing helix  chain 'D' and resid 222 through 233
    Processing helix  chain 'D' and resid 254 through 263
    Processing helix  chain 'D' and resid 271 through 275
    Processing helix  chain 'D' and resid 281 through 296
      removed outlier: 4.065A  pdb=" N   ARG D 285 " --> pdb=" O   ASP D 281 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL D 289 " --> pdb=" O   ARG D 285 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU D 292 " --> pdb=" O   ALA D 288 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152
      removed outlier: 6.332A  pdb=" N   SER A 150 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LYS A 169 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ILE A 152 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   HIS A 128 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ILE A 213 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   ILE A 246 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   PHE A 245 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340
    Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152
      removed outlier: 3.808A  pdb=" N   HIS B 128 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   ILE B 213 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   ILE B 246 " --> pdb=" O   ILE B 213 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   PHE B 215 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   PHE B 245 " --> pdb=" O   ILE B 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340
    Processing sheet with id=AA5, first strand: chain 'B' and resid 646 through 647
    Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152
      removed outlier: 6.045A  pdb=" N   SER C 150 " --> pdb=" O   LEU C 167 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LYS C 169 " --> pdb=" O   SER C 150 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE C 152 " --> pdb=" O   LYS C 169 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   HIS C 128 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ILE C 213 " --> pdb=" O   PHE C 244 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   ILE C 246 " --> pdb=" O   ILE C 213 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   PHE C 215 " --> pdb=" O   ILE C 246 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   PHE C 245 " --> pdb=" O   ILE C 269 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152
      removed outlier: 6.125A  pdb=" N   SER D 150 " --> pdb=" O   LEU D 167 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LYS D 169 " --> pdb=" O   SER D 150 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ILE D 152 " --> pdb=" O   LYS D 169 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   HIS D 128 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ILE D 213 " --> pdb=" O   PHE D 244 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ILE D 246 " --> pdb=" O   ILE D 213 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   PHE D 215 " --> pdb=" O   ILE D 246 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   PHE D 245 " --> pdb=" O   ILE D 269 " (cutoff:3.500A)

    1092 hydrogen bonds defined for protein.
    3171 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: 3.73

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6376
        1.34 -     1.46: 5165
        1.46 -     1.58: 8927
        1.58 -     1.70: 0
        1.70 -     1.82: 126
  Bond restraints: 20594
  Sorted by residual:
  bond pdb=" CB  PRO B 506 "
       pdb=" CG  PRO B 506 "
    ideal  model  delta    sigma   weight residual
    1.492  1.557 -0.065 5.00e-02 4.00e+02 1.70e+00
  bond pdb=" CB  GLU A 510 "
       pdb=" CG  GLU A 510 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.64e+00
  bond pdb=" CG  PRO A  74 "
       pdb=" CD  PRO A  74 "
    ideal  model  delta    sigma   weight residual
    1.503  1.463  0.040 3.40e-02 8.65e+02 1.36e+00
  bond pdb=" CB  PRO A  74 "
       pdb=" CG  PRO A  74 "
    ideal  model  delta    sigma   weight residual
    1.492  1.547 -0.055 5.00e-02 4.00e+02 1.21e+00
  bond pdb=" CB  ASN B 797 "
       pdb=" CG  ASN B 797 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  ... (remaining 20589 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 27543
        2.23 -     4.46: 190
        4.46 -     6.69: 23
        6.69 -     8.92: 5
        8.92 -    11.15: 4
  Bond angle restraints: 27765
  Sorted by residual:
  angle pdb=" N   PRO A  74 "
        pdb=" CD  PRO A  74 "
        pdb=" CG  PRO A  74 "
      ideal   model   delta    sigma   weight residual
     103.20   97.54    5.66 1.50e+00 4.44e-01 1.43e+01
  angle pdb=" CA  PRO A  74 "
        pdb=" N   PRO A  74 "
        pdb=" CD  PRO A  74 "
      ideal   model   delta    sigma   weight residual
     112.00  107.00    5.00 1.40e+00 5.10e-01 1.27e+01
  angle pdb=" CA  LEU B 838 "
        pdb=" CB  LEU B 838 "
        pdb=" CG  LEU B 838 "
      ideal   model   delta    sigma   weight residual
     116.30  127.45  -11.15 3.50e+00 8.16e-02 1.02e+01
  angle pdb=" CB  GLU A 510 "
        pdb=" CG  GLU A 510 "
        pdb=" CD  GLU A 510 "
      ideal   model   delta    sigma   weight residual
     112.60  117.57   -4.97 1.70e+00 3.46e-01 8.55e+00
  angle pdb=" CA  GLU A 510 "
        pdb=" CB  GLU A 510 "
        pdb=" CG  GLU A 510 "
      ideal   model   delta    sigma   weight residual
     114.10  119.85   -5.75 2.00e+00 2.50e-01 8.26e+00
  ... (remaining 27760 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 10325
       17.83 -    35.66: 1445
       35.66 -    53.49: 399
       53.49 -    71.31: 79
       71.31 -    89.14: 21
  Dihedral angle restraints: 12269
    sinusoidal: 5093
      harmonic: 7176
  Sorted by residual:
  dihedral pdb=" CA  GLU A 923 "
           pdb=" C   GLU A 923 "
           pdb=" N   GLU A 924 "
           pdb=" CA  GLU A 924 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.67   19.33     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  TYR D 166 "
           pdb=" C   TYR D 166 "
           pdb=" N   LEU D 167 "
           pdb=" CA  LEU D 167 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.20   18.80     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  TYR A 166 "
           pdb=" C   TYR A 166 "
           pdb=" N   LEU A 167 "
           pdb=" CA  LEU A 167 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.31   18.69     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 12266 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 2451
       0.049 -    0.099: 437
       0.099 -    0.148: 67
       0.148 -    0.197: 0
       0.197 -    0.246: 2
  Chirality restraints: 2957
  Sorted by residual:
  chirality pdb=" CG  LEU A 966 "
            pdb=" CB  LEU A 966 "
            pdb=" CD1 LEU A 966 "
            pdb=" CD2 LEU A 966 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CG  LEU B 363 "
            pdb=" CB  LEU B 363 "
            pdb=" CD1 LEU B 363 "
            pdb=" CD2 LEU B 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CG  LEU D 228 "
            pdb=" CB  LEU D 228 "
            pdb=" CD1 LEU D 228 "
            pdb=" CD2 LEU D 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.40e-01
  ... (remaining 2954 not shown)

  Planarity restraints: 3536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  73 "   -0.041 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO A  74 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A  74 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  74 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 744 "    0.036 5.00e-02 4.00e+02   5.42e-02 4.71e+00
        pdb=" N   PRO B 745 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 745 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 745 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 510 "    0.009 2.00e-02 2.50e+03   1.81e-02 3.28e+00
        pdb=" CD  GLU A 510 "   -0.031 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 510 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 510 "    0.011 2.00e-02 2.50e+03
  ... (remaining 3533 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 307
        2.65 -     3.21: 18648
        3.21 -     3.77: 33334
        3.77 -     4.34: 47436
        4.34 -     4.90: 75015
  Nonbonded interactions: 174740
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 470 "
            pdb=" OG  SER A 474 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" O   TYR B 313 "
            pdb=" OG  SER B 317 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OH  TYR A 324 "
            pdb=" OD1 ASP A 590 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   TYR C 197 "
            pdb=" OG  SER C 201 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OG  SER A  37 "
            pdb=" O   MET A 124 "
     model   vdw
     2.190 3.040
  ... (remaining 174735 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 22 through 399 or resid 406 through 493 or resid 504 throu \ 
gh 565 or resid 579 through 786 or resid 793 through 1005))
  selection = (chain 'B' and (resid 22 through 462 or resid 468 through 629 or resid 645 throu \ 
gh 700 or resid 703 through 1005))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'D' and resid 26 through 297)
}

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 individual isotropic
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:             9.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     18.460
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  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:6.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
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      :  0.002   0.065  20594  Z= 0.108
  Angle     :  0.508  11.154  27765  Z= 0.268
  Chirality :  0.038   0.246   2957
  Planarity :  0.003   0.060   3536
  Dihedral  : 17.958  89.142   7655
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 26.86 %
    Favored  : 69.67 %
  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 aren not related in a simple way.
  whole:  0.70 (0.17), residues: 2383
  helix:  0.91 (0.13), residues: 1496
  sheet: -0.82 (0.67), residues: 40
  loop : -0.09 (0.20), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 145 
 TYR   0.021   0.001   TYR A 709 
 PHE   0.016   0.001   PHE A 943 
 TRP   0.010   0.001   TRP A 757 
 HIS   0.003   0.001   HIS B 978 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (20594)
  covalent geometry    : angle       0.50833 (27765)
  hydrogen bonds       : bond        0.16799 ( 1092)
  hydrogen bonds       : angle       6.03114 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 227
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7572 (mt-10)
REVERT: A  989 LYS cc_start: 0.8244 (mptt) cc_final: 0.7871 (mptt)
REVERT: B  776 ASP cc_start: 0.8208 (t70) cc_final: 0.7930 (t0)
REVERT: B  913 MET cc_start: 0.7842 (ptm) cc_final: 0.7476 (pmm)
REVERT: D  216 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8587 (pp)
  outliers start: 77
  outliers final: 57
  residues processed: 298
  average time/residue: 0.5557
  time to fit residues: 188.3257
Evaluate side-chains
  253 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 195
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  370 ARG
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  615 SER
Chi-restraints excluded: chain A residue  674 ASP
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  711 GLN
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  814 ASN
Chi-restraints excluded: chain A residue  826 CYS
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  175 ARG
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  297 GLN
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  379 GLU
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  553 ASP
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  674 ASP
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  770 SER
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue  794 VAL
Chi-restraints excluded: chain B residue  814 ASN
Chi-restraints excluded: chain B residue 1003 TYR
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  201 SER
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   55 ASP
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain D residue  160 ASN
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  225 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 216 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 194 optimal weight:    4.9990
   chunk 227 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0270
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.2980
   chunk 103 optimal weight:    3.9990
   chunk 235 optimal weight:    0.0980
   overall best weight:    0.3838

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

Flipped N/Q/H residues before XYZ refinement:
A 339 HIS
A 391 ASN
A 475 GLN
A 711 GLN
A 797 ASN
A 834 GLN
** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 236 GLN
D 278 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.141298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.098874 restraints weight = 31401.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.14
r_work: 0.3262 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  20594  Z= 0.120
  Angle     :  0.515   9.999  27765  Z= 0.274
  Chirality :  0.040   0.167   2957
  Planarity :  0.004   0.051   3536
  Dihedral  :  6.563  64.016   2755
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.06 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.17), residues: 2383
  helix:  1.19 (0.13), residues: 1506
  sheet: -1.20 (0.62), residues: 32
  loop :  0.03 (0.20), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 677 
 TYR   0.011   0.001   TYR A 472 
 PHE   0.012   0.001   PHE A 856 
 TRP   0.011   0.001   TRP A 757 
 HIS   0.004   0.001   HIS B 978 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (20594)
  covalent geometry    : angle       0.51549 (27765)
  hydrogen bonds       : bond        0.04156 ( 1092)
  hydrogen bonds       : angle       4.69251 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 223
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7783 (mt-10)
REVERT: A  348 ARG cc_start: 0.8344 (ttm170) cc_final: 0.7960 (ttt180)
REVERT: A  377 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7292 (mt0)
REVERT: A  525 ASP cc_start: 0.8621 (m-30) cc_final: 0.8405 (m-30)
REVERT: A  714 SER cc_start: 0.8985 (t) cc_final: 0.8763 (p)
REVERT: A  965 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8494 (tptt)
REVERT: A  975 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7213 (t-90)
REVERT: A  989 LYS cc_start: 0.8211 (mptt) cc_final: 0.7979 (mmmm)
REVERT: A  995 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8127 (tpm170)
REVERT: B  181 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8116 (pm20)
REVERT: B  491 GLN cc_start: 0.7434 (tm-30) cc_final: 0.7187 (tm-30)
REVERT: B  526 ASP cc_start: 0.8333 (t0) cc_final: 0.8112 (t70)
REVERT: B  634 LEU cc_start: 0.8037 (mm) cc_final: 0.7797 (mt)
REVERT: B  776 ASP cc_start: 0.8530 (t70) cc_final: 0.8278 (t0)
REVERT: B  913 MET cc_start: 0.8148 (ptm) cc_final: 0.7712 (pmm)
REVERT: C  262 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8437 (mm-30)
REVERT: D   81 SER cc_start: 0.8877 (m) cc_final: 0.8508 (p)
REVERT: D  216 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8353 (pp)
REVERT: D  227 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7974 (mtm)
REVERT: D  237 LYS cc_start: 0.8509 (tptp) cc_final: 0.8239 (tptp)
REVERT: D  238 ASP cc_start: 0.8798 (m-30) cc_final: 0.8538 (m-30)
  outliers start: 92
  outliers final: 31
  residues processed: 298
  average time/residue: 0.5705
  time to fit residues: 193.6011
Evaluate side-chains
  242 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 204
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  674 ASP
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  953 LYS
Chi-restraints excluded: chain A residue  965 LYS
Chi-restraints excluded: chain A residue  975 HIS
Chi-restraints excluded: chain A residue  995 ARG
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  160 ASN
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  794 VAL
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  160 ASN
Chi-restraints excluded: chain D residue  204 MET
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  227 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 81 optimal weight:    8.9990
   chunk 23 optimal weight:    0.6980
   chunk 179 optimal weight:    5.9990
   chunk 156 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 221 optimal weight:    0.9990
   chunk 227 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
A 475 GLN
C 236 GLN
D 278 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.140270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.097453 restraints weight = 31512.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.15
r_work: 0.3240 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  20594  Z= 0.143
  Angle     :  0.505  10.074  27765  Z= 0.266
  Chirality :  0.040   0.170   2957
  Planarity :  0.003   0.046   3536
  Dihedral  :  5.185  57.658   2684
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 24.34 %
    Favored  : 71.11 %
  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 aren not related in a simple way.
  whole:  1.06 (0.17), residues: 2383
  helix:  1.23 (0.13), residues: 1519
  sheet: -1.51 (0.63), residues: 32
  loop : -0.03 (0.20), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 677 
 TYR   0.018   0.001   TYR A 755 
 PHE   0.015   0.001   PHE B 699 
 TRP   0.014   0.001   TRP A 757 
 HIS   0.004   0.001   HIS A 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (20594)
  covalent geometry    : angle       0.50506 (27765)
  hydrogen bonds       : bond        0.03891 ( 1092)
  hydrogen bonds       : angle       4.51994 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 226
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8797 (t0)
REVERT: A  377 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7373 (mt0)
REVERT: A  525 ASP cc_start: 0.8685 (m-30) cc_final: 0.8390 (m-30)
REVERT: A  714 SER cc_start: 0.8999 (t) cc_final: 0.8775 (p)
REVERT: A  740 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7951 (tp)
REVERT: A  915 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7788 (p)
REVERT: A  965 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8423 (tptp)
REVERT: A  976 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6215 (ptp)
REVERT: A  995 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8073 (tpm170)
REVERT: B  181 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8097 (pm20)
REVERT: B  526 ASP cc_start: 0.8355 (t0) cc_final: 0.8145 (t70)
REVERT: B  557 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8360 (tmmm)
REVERT: B  776 ASP cc_start: 0.8518 (t70) cc_final: 0.8276 (t0)
REVERT: B  913 MET cc_start: 0.8197 (ptm) cc_final: 0.7814 (pmm)
REVERT: B  936 MET cc_start: 0.3960 (OUTLIER) cc_final: 0.3551 (mpp)
REVERT: C   32 GLU cc_start: 0.7942 (tp30) cc_final: 0.7658 (tp30)
REVERT: C  145 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.7053 (mpp80)
REVERT: D   81 SER cc_start: 0.8800 (m) cc_final: 0.8467 (p)
REVERT: D  105 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8197 (ttpt)
REVERT: D  181 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.7919 (pm20)
REVERT: D  227 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7989 (mtm)
REVERT: D  228 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8704 (mm)
REVERT: D  233 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7791 (ptp90)
REVERT: D  237 LYS cc_start: 0.8481 (tptp) cc_final: 0.8182 (tptp)
REVERT: D  238 ASP cc_start: 0.8797 (m-30) cc_final: 0.8516 (m-30)
REVERT: D  278 ASN cc_start: 0.7977 (t0) cc_final: 0.7267 (m110)
  outliers start: 101
  outliers final: 31
  residues processed: 302
  average time/residue: 0.6332
  time to fit residues: 217.0543
Evaluate side-chains
  252 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 205
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  674 ASP
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  915 THR
Chi-restraints excluded: chain A residue  953 LYS
Chi-restraints excluded: chain A residue  965 LYS
Chi-restraints excluded: chain A residue  976 MET
Chi-restraints excluded: chain A residue  979 HIS
Chi-restraints excluded: chain A residue  995 ARG
Chi-restraints excluded: chain A residue 1004 PHE
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  557 LYS
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  846 SER
Chi-restraints excluded: chain B residue  936 MET
Chi-restraints excluded: chain B residue 1003 TYR
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue  145 ARG
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  105 LYS
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  160 ASN
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  204 MET
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  227 MET
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain D residue  233 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 122 optimal weight:    0.8980
   chunk 237 optimal weight:    0.0870
   chunk 195 optimal weight:    1.9990
   chunk 238 optimal weight:    1.9990
   chunk 214 optimal weight:    0.8980
   chunk 131 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 217 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.9160

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
A 475 GLN
C 236 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.140722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.097805 restraints weight = 31571.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.16
r_work: 0.3231 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  20594  Z= 0.147
  Angle     :  0.504  10.607  27765  Z= 0.264
  Chirality :  0.040   0.163   2957
  Planarity :  0.003   0.044   3536
  Dihedral  :  5.092  58.753   2679
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 23.70 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.17), residues: 2383
  helix:  1.24 (0.13), residues: 1525
  sheet: -1.72 (0.62), residues: 32
  loop : -0.03 (0.20), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 677 
 TYR   0.040   0.001   TYR A 951 
 PHE   0.015   0.001   PHE B 699 
 TRP   0.016   0.001   TRP B 958 
 HIS   0.005   0.001   HIS A 979 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (20594)
  covalent geometry    : angle       0.50438 (27765)
  hydrogen bonds       : bond        0.03688 ( 1092)
  hydrogen bonds       : angle       4.43977 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 103
    poor density    : 219
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8318 (pttp)
REVERT: A  377 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7364 (mt0)
REVERT: A  525 ASP cc_start: 0.8750 (m-30) cc_final: 0.8428 (m-30)
REVERT: A  714 SER cc_start: 0.9004 (t) cc_final: 0.8768 (p)
REVERT: A  740 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7935 (tp)
REVERT: A  875 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7517 (p0)
REVERT: A  915 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7793 (p)
REVERT: A  936 MET cc_start: 0.6157 (mmm) cc_final: 0.5617 (mmm)
REVERT: A  965 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8424 (tptp)
REVERT: A  975 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6981 (t-90)
REVERT: A  976 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6398 (ptt)
REVERT: A  989 LYS cc_start: 0.8545 (mmmm) cc_final: 0.7851 (mptt)
REVERT: A  995 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8076 (tpm170)
REVERT: B  181 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8113 (pm20)
REVERT: B  491 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7315 (tm-30)
REVERT: B  557 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8398 (tmmm)
REVERT: B  626 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: B  776 ASP cc_start: 0.8537 (t70) cc_final: 0.8304 (t0)
REVERT: B  913 MET cc_start: 0.8203 (ptm) cc_final: 0.7782 (pmm)
REVERT: B  936 MET cc_start: 0.3953 (OUTLIER) cc_final: 0.3441 (mpp)
REVERT: B 1001 MET cc_start: 0.8640 (mtm) cc_final: 0.8316 (ttp)
REVERT: C  145 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.7049 (mpp80)
REVERT: D   81 SER cc_start: 0.8781 (m) cc_final: 0.8459 (p)
REVERT: D  105 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8207 (ttpt)
REVERT: D  181 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.7921 (pm20)
REVERT: D  227 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8029 (mtm)
REVERT: D  233 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7766 (ptp90)
REVERT: D  237 LYS cc_start: 0.8509 (tptp) cc_final: 0.8200 (tptp)
REVERT: D  238 ASP cc_start: 0.8816 (m-30) cc_final: 0.8540 (m-30)
REVERT: D  267 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8444 (mtp85)
  outliers start: 103
  outliers final: 37
  residues processed: 296
  average time/residue: 0.6286
  time to fit residues: 211.9571
Evaluate side-chains
  263 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 208
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  674 ASP
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  813 LYS
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  875 ASP
Chi-restraints excluded: chain A residue  915 THR
Chi-restraints excluded: chain A residue  953 LYS
Chi-restraints excluded: chain A residue  965 LYS
Chi-restraints excluded: chain A residue  975 HIS
Chi-restraints excluded: chain A residue  976 MET
Chi-restraints excluded: chain A residue  995 ARG
Chi-restraints excluded: chain A residue 1004 PHE
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  160 ASN
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  379 GLU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  491 GLN
Chi-restraints excluded: chain B residue  557 LYS
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  846 SER
Chi-restraints excluded: chain B residue  936 MET
Chi-restraints excluded: chain B residue  976 MET
Chi-restraints excluded: chain B residue 1003 TYR
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue  145 ARG
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  105 LYS
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  160 ASN
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  204 MET
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  227 MET
Chi-restraints excluded: chain D residue  233 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 167 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 128 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 185 optimal weight:   10.0000
   chunk 121 optimal weight:    0.5980
   chunk 176 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 159 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
A 475 GLN
A 829 GLN
A 832 GLN
C 236 GLN
D 202 ASN
D 278 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.139779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.096877 restraints weight = 31533.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 2.17
r_work: 0.3223 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  20594  Z= 0.172
  Angle     :  0.519  10.646  27765  Z= 0.271
  Chirality :  0.040   0.140   2957
  Planarity :  0.003   0.045   3536
  Dihedral  :  4.928  59.450   2674
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 24.02 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.17), residues: 2383
  helix:  1.23 (0.13), residues: 1525
  sheet: -1.68 (0.64), residues: 32
  loop : -0.06 (0.20), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 677 
 TYR   0.023   0.001   TYR A 951 
 PHE   0.014   0.001   PHE B 699 
 TRP   0.017   0.001   TRP B 958 
 HIS   0.012   0.001   HIS A 979 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (20594)
  covalent geometry    : angle       0.51870 (27765)
  hydrogen bonds       : bond        0.03772 ( 1092)
  hydrogen bonds       : angle       4.43290 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 219
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8329 (pttp)
REVERT: A  377 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7368 (mt0)
REVERT: A  525 ASP cc_start: 0.8773 (m-30) cc_final: 0.8442 (m-30)
REVERT: A  740 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7929 (tp)
REVERT: A  784 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7138 (tm-30)
REVERT: A  802 ARG cc_start: 0.8475 (ptt180) cc_final: 0.8192 (ppt170)
REVERT: A  915 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7758 (p)
REVERT: A  936 MET cc_start: 0.6283 (mmm) cc_final: 0.5936 (mmm)
REVERT: A  965 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8423 (tptp)
REVERT: A  989 LYS cc_start: 0.8637 (mmmm) cc_final: 0.8356 (mmmm)
REVERT: A  995 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8031 (tpm170)
REVERT: A  999 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7250 (mt)
REVERT: B  181 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8128 (pm20)
REVERT: B  491 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7336 (tm-30)
REVERT: B  557 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8437 (tmmm)
REVERT: B  626 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8176 (mm-30)
REVERT: B  744 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8833 (t80)
REVERT: B  776 ASP cc_start: 0.8564 (t70) cc_final: 0.8333 (t0)
REVERT: B  913 MET cc_start: 0.8218 (ptm) cc_final: 0.7803 (pmm)
REVERT: B  936 MET cc_start: 0.3981 (OUTLIER) cc_final: 0.3429 (mpp)
REVERT: C  145 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.7040 (mpp80)
REVERT: C  165 ARG cc_start: 0.7472 (ptm160) cc_final: 0.7268 (ptm160)
REVERT: D   81 SER cc_start: 0.8796 (m) cc_final: 0.8482 (p)
REVERT: D  105 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8219 (ttpt)
REVERT: D  181 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.7945 (pm20)
REVERT: D  227 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8061 (mtm)
REVERT: D  233 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7776 (ptp90)
REVERT: D  237 LYS cc_start: 0.8543 (tptp) cc_final: 0.8261 (tptp)
REVERT: D  238 ASP cc_start: 0.8859 (m-30) cc_final: 0.8612 (m-30)
  outliers start: 98
  outliers final: 42
  residues processed: 294
  average time/residue: 0.5930
  time to fit residues: 198.2193
Evaluate side-chains
  263 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 203
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  674 ASP
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  784 GLU
Chi-restraints excluded: chain A residue  813 LYS
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain A residue  915 THR
Chi-restraints excluded: chain A residue  953 LYS
Chi-restraints excluded: chain A residue  965 LYS
Chi-restraints excluded: chain A residue  995 ARG
Chi-restraints excluded: chain A residue  999 ILE
Chi-restraints excluded: chain A residue 1004 PHE
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  160 ASN
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  379 GLU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  491 GLN
Chi-restraints excluded: chain B residue  557 LYS
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  730 GLU
Chi-restraints excluded: chain B residue  744 PHE
Chi-restraints excluded: chain B residue  846 SER
Chi-restraints excluded: chain B residue  936 MET
Chi-restraints excluded: chain B residue  976 MET
Chi-restraints excluded: chain B residue 1003 TYR
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue  145 ARG
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  105 LYS
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  204 MET
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  227 MET
Chi-restraints excluded: chain D residue  233 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 149 optimal weight:    0.9980
   chunk 206 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 210 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 204 optimal weight:    0.0980
   chunk 85 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 155 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
A 475 GLN
C 236 GLN
D 202 ASN
D 278 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.141066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.098577 restraints weight = 31422.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.16
r_work: 0.3230 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  20594  Z= 0.125
  Angle     :  0.502  11.026  27765  Z= 0.261
  Chirality :  0.039   0.158   2957
  Planarity :  0.003   0.048   3536
  Dihedral  :  4.832  59.428   2672
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 24.61 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.17), residues: 2383
  helix:  1.31 (0.13), residues: 1529
  sheet: -1.74 (0.60), residues: 44
  loop : -0.01 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 677 
 TYR   0.022   0.001   TYR A 709 
 PHE   0.014   0.001   PHE B 699 
 TRP   0.019   0.001   TRP B 958 
 HIS   0.015   0.001   HIS A 979 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (20594)
  covalent geometry    : angle       0.50232 (27765)
  hydrogen bonds       : bond        0.03461 ( 1092)
  hydrogen bonds       : angle       4.35076 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 220
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8306 (pttp)
REVERT: A  377 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7407 (mt0)
REVERT: A  525 ASP cc_start: 0.8812 (m-30) cc_final: 0.8463 (m-30)
REVERT: A  740 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7951 (tp)
REVERT: A  784 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7065 (tm-30)
REVERT: A  839 PHE cc_start: 0.8535 (t80) cc_final: 0.8290 (t80)
REVERT: A  915 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7776 (p)
REVERT: A  939 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7006 (mm110)
REVERT: A  965 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8468 (tptt)
REVERT: A  989 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8333 (mmmm)
REVERT: A  995 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8179 (tpm170)
REVERT: B  181 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8132 (pm20)
REVERT: B  491 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7413 (tm-30)
REVERT: B  626 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8189 (mm-30)
REVERT: B  744 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8841 (t80)
REVERT: B  776 ASP cc_start: 0.8556 (t70) cc_final: 0.8329 (t0)
REVERT: B  913 MET cc_start: 0.8184 (ptm) cc_final: 0.7763 (pmm)
REVERT: B  936 MET cc_start: 0.3927 (OUTLIER) cc_final: 0.3296 (mpp)
REVERT: C  145 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.7035 (mpp80)
REVERT: C  262 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8599 (mm-30)
REVERT: D  181 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.7920 (pm20)
REVERT: D  227 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8105 (mtm)
REVERT: D  233 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7782 (ptp90)
REVERT: D  237 LYS cc_start: 0.8579 (tptp) cc_final: 0.8275 (tptp)
REVERT: D  238 ASP cc_start: 0.8822 (m-30) cc_final: 0.8560 (m-30)
  outliers start: 89
  outliers final: 41
  residues processed: 288
  average time/residue: 0.5647
  time to fit residues: 184.7519
Evaluate side-chains
  259 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 202
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  674 ASP
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  784 GLU
Chi-restraints excluded: chain A residue  813 LYS
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain A residue  915 THR
Chi-restraints excluded: chain A residue  939 GLN
Chi-restraints excluded: chain A residue  965 LYS
Chi-restraints excluded: chain A residue  995 ARG
Chi-restraints excluded: chain A residue 1004 PHE
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  160 ASN
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  379 GLU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  491 GLN
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  730 GLU
Chi-restraints excluded: chain B residue  744 PHE
Chi-restraints excluded: chain B residue  846 SER
Chi-restraints excluded: chain B residue  936 MET
Chi-restraints excluded: chain B residue  976 MET
Chi-restraints excluded: chain B residue 1000 LEU
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  145 ARG
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  204 MET
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  227 MET
Chi-restraints excluded: chain D residue  233 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 186 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 127 optimal weight:    4.9990
   chunk 12 optimal weight:    0.2980
   chunk 55 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 163 optimal weight:    0.9980
   chunk 165 optimal weight:    0.6980
   chunk 187 optimal weight:    4.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
A 475 GLN
C 226 ASN
C 236 GLN
D 202 ASN
D 278 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.140551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.097858 restraints weight = 31486.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.15
r_work: 0.3230 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  20594  Z= 0.153
  Angle     :  0.515  10.938  27765  Z= 0.267
  Chirality :  0.040   0.168   2957
  Planarity :  0.003   0.051   3536
  Dihedral  :  4.839  59.666   2672
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 24.52 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.17), residues: 2383
  helix:  1.29 (0.13), residues: 1528
  sheet: -1.76 (0.65), residues: 32
  loop : -0.04 (0.21), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 677 
 TYR   0.015   0.001   TYR A 951 
 PHE   0.015   0.001   PHE B 699 
 TRP   0.021   0.001   TRP B 958 
 HIS   0.014   0.001   HIS A 979 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (20594)
  covalent geometry    : angle       0.51468 (27765)
  hydrogen bonds       : bond        0.03574 ( 1092)
  hydrogen bonds       : angle       4.36076 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 213
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8268 (pttp)
REVERT: A  366 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7440 (p)
REVERT: A  377 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7395 (mt0)
REVERT: A  525 ASP cc_start: 0.8803 (m-30) cc_final: 0.8447 (m-30)
REVERT: A  740 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7908 (tp)
REVERT: A  784 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7169 (tm-30)
REVERT: A  802 ARG cc_start: 0.8474 (ptt180) cc_final: 0.8186 (ppt170)
REVERT: A  939 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6991 (mm110)
REVERT: A  965 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8479 (tptt)
REVERT: A  975 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6915 (t-90)
REVERT: A  989 LYS cc_start: 0.8631 (mmmm) cc_final: 0.7982 (mptt)
REVERT: A  995 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8173 (tpm170)
REVERT: B  181 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8110 (pm20)
REVERT: B  491 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7409 (tm-30)
REVERT: B  626 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8157 (mm-30)
REVERT: B  744 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8828 (t80)
REVERT: B  776 ASP cc_start: 0.8571 (t70) cc_final: 0.8336 (t0)
REVERT: B  913 MET cc_start: 0.8222 (ptm) cc_final: 0.7804 (pmm)
REVERT: B  936 MET cc_start: 0.4009 (OUTLIER) cc_final: 0.3404 (mpp)
REVERT: C  145 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7047 (mpp80)
REVERT: C  262 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8579 (mm-30)
REVERT: D  181 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.7912 (pm20)
REVERT: D  227 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8066 (mtm)
REVERT: D  233 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7768 (ptp90)
  outliers start: 93
  outliers final: 43
  residues processed: 287
  average time/residue: 0.5740
  time to fit residues: 187.4956
Evaluate side-chains
  260 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 200
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  674 ASP
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  784 GLU
Chi-restraints excluded: chain A residue  813 LYS
Chi-restraints excluded: chain A residue  814 ASN
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  939 GLN
Chi-restraints excluded: chain A residue  965 LYS
Chi-restraints excluded: chain A residue  975 HIS
Chi-restraints excluded: chain A residue  995 ARG
Chi-restraints excluded: chain A residue 1004 PHE
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  160 ASN
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  379 GLU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  491 GLN
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  730 GLU
Chi-restraints excluded: chain B residue  744 PHE
Chi-restraints excluded: chain B residue  846 SER
Chi-restraints excluded: chain B residue  936 MET
Chi-restraints excluded: chain B residue  976 MET
Chi-restraints excluded: chain B residue 1001 MET
Chi-restraints excluded: chain B residue 1003 TYR
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  145 ARG
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  204 MET
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  227 MET
Chi-restraints excluded: chain D residue  233 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 143 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 173 optimal weight:   10.0000
   chunk 218 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 121 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 150 optimal weight:    2.9990
   chunk 239 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 339 HIS
A 391 ASN
A 475 GLN
C 226 ASN
C 236 GLN
D 202 ASN
D 278 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.135844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.091869 restraints weight = 30951.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.21
r_work: 0.3103 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  20594  Z= 0.219
  Angle     :  0.561  11.340  27765  Z= 0.291
  Chirality :  0.042   0.166   2957
  Planarity :  0.003   0.053   3536
  Dihedral  :  4.952  59.741   2672
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 24.70 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.17), residues: 2383
  helix:  1.16 (0.13), residues: 1524
  sheet: -2.22 (0.54), residues: 20
  loop : -0.04 (0.20), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 677 
 TYR   0.018   0.002   TYR A 951 
 PHE   0.015   0.002   PHE A 856 
 TRP   0.028   0.002   TRP B 958 
 HIS   0.015   0.001   HIS A 979 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (20594)
  covalent geometry    : angle       0.56065 (27765)
  hydrogen bonds       : bond        0.03939 ( 1092)
  hydrogen bonds       : angle       4.48867 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 211
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8237 (pttp)
REVERT: A  366 SER cc_start: 0.7383 (OUTLIER) cc_final: 0.7180 (p)
REVERT: A  377 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7277 (mt0)
REVERT: A  398 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7480 (mppt)
REVERT: A  525 ASP cc_start: 0.8809 (m-30) cc_final: 0.8474 (m-30)
REVERT: A  784 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7268 (tm-30)
REVERT: A  802 ARG cc_start: 0.8464 (ptt180) cc_final: 0.8227 (ppt170)
REVERT: A  965 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8521 (tptt)
REVERT: A  975 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6889 (t-90)
REVERT: A  989 LYS cc_start: 0.8681 (mmmm) cc_final: 0.7986 (mptt)
REVERT: A  995 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8021 (tpm170)
REVERT: B  181 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8083 (pm20)
REVERT: B  491 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7415 (tm-30)
REVERT: B  626 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8109 (mm-30)
REVERT: B  744 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8829 (t80)
REVERT: B  776 ASP cc_start: 0.8579 (t70) cc_final: 0.8365 (t0)
REVERT: B  913 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7795 (pmm)
REVERT: B  936 MET cc_start: 0.4029 (OUTLIER) cc_final: 0.3370 (mpp)
REVERT: C  145 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6937 (mpp80)
REVERT: D  145 ARG cc_start: 0.7899 (mmt90) cc_final: 0.7570 (mmt90)
REVERT: D  181 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.7913 (pm20)
REVERT: D  227 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8002 (mtm)
REVERT: D  228 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8649 (mm)
REVERT: D  233 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7850 (ptp90)
REVERT: D  278 ASN cc_start: 0.7995 (t0) cc_final: 0.7254 (m110)
  outliers start: 92
  outliers final: 41
  residues processed: 283
  average time/residue: 0.5562
  time to fit residues: 178.0533
Evaluate side-chains
  261 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 202
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  674 ASP
Chi-restraints excluded: chain A residue  727 LYS
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  784 GLU
Chi-restraints excluded: chain A residue  813 LYS
Chi-restraints excluded: chain A residue  814 ASN
Chi-restraints excluded: chain A residue  826 CYS
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  965 LYS
Chi-restraints excluded: chain A residue  975 HIS
Chi-restraints excluded: chain A residue  995 ARG
Chi-restraints excluded: chain A residue 1004 PHE
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  379 GLU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  491 GLN
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  730 GLU
Chi-restraints excluded: chain B residue  744 PHE
Chi-restraints excluded: chain B residue  913 MET
Chi-restraints excluded: chain B residue  936 MET
Chi-restraints excluded: chain B residue  976 MET
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  145 ARG
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  227 MET
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain D residue  233 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 195 optimal weight:    1.9990
   chunk 141 optimal weight:    0.0670
   chunk 25 optimal weight:    3.9990
   chunk 164 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 127 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 121 optimal weight:    0.7980
   chunk 101 optimal weight:    0.0980
   chunk 222 optimal weight:    1.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A 339 HIS
A 391 ASN
A 475 GLN
C 236 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.137966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.093714 restraints weight = 30692.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.24
r_work: 0.3138 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  20594  Z= 0.119
  Angle     :  0.526  11.613  27765  Z= 0.272
  Chirality :  0.040   0.184   2957
  Planarity :  0.003   0.043   3536
  Dihedral  :  4.807  61.622   2672
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 25.33 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.17), residues: 2383
  helix:  1.29 (0.13), residues: 1528
  sheet: -1.82 (0.59), residues: 44
  loop :  0.02 (0.21), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 677 
 TYR   0.015   0.001   TYR A 755 
 PHE   0.012   0.001   PHE A 839 
 TRP   0.033   0.001   TRP B 958 
 HIS   0.022   0.001   HIS A 979 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (20594)
  covalent geometry    : angle       0.52561 (27765)
  hydrogen bonds       : bond        0.03435 ( 1092)
  hydrogen bonds       : angle       4.36021 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 213
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8182 (pttp)
REVERT: A  348 ARG cc_start: 0.8241 (ttm170) cc_final: 0.8006 (ttt180)
REVERT: A  377 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7281 (mt0)
REVERT: A  525 ASP cc_start: 0.8821 (m-30) cc_final: 0.8468 (m-30)
REVERT: A  695 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8088 (tt)
REVERT: A  784 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7246 (tm-30)
REVERT: A  965 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8524 (tptt)
REVERT: A  975 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.7016 (t-90)
REVERT: A  989 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8007 (mptt)
REVERT: A  995 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8039 (tpm170)
REVERT: B  181 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8076 (pm20)
REVERT: B  491 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7421 (tm-30)
REVERT: B  626 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8043 (mm-30)
REVERT: B  744 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8883 (t80)
REVERT: B  936 MET cc_start: 0.3964 (OUTLIER) cc_final: 0.3558 (mpp)
REVERT: D  227 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7984 (mtm)
REVERT: D  233 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7840 (ptp90)
REVERT: D  278 ASN cc_start: 0.7942 (t0) cc_final: 0.7172 (m110)
  outliers start: 75
  outliers final: 36
  residues processed: 271
  average time/residue: 0.5763
  time to fit residues: 177.2053
Evaluate side-chains
  249 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 200
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  784 GLU
Chi-restraints excluded: chain A residue  813 LYS
Chi-restraints excluded: chain A residue  814 ASN
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  945 ASP
Chi-restraints excluded: chain A residue  953 LYS
Chi-restraints excluded: chain A residue  965 LYS
Chi-restraints excluded: chain A residue  975 HIS
Chi-restraints excluded: chain A residue  995 ARG
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  379 GLU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  491 GLN
Chi-restraints excluded: chain B residue  510 GLU
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  730 GLU
Chi-restraints excluded: chain B residue  744 PHE
Chi-restraints excluded: chain B residue  781 LEU
Chi-restraints excluded: chain B residue  846 SER
Chi-restraints excluded: chain B residue  936 MET
Chi-restraints excluded: chain B residue 1000 LEU
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  227 MET
Chi-restraints excluded: chain D residue  233 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 173 optimal weight:   10.0000
   chunk 204 optimal weight:    0.0970
   chunk 196 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 128 optimal weight:    0.6980
   chunk 193 optimal weight:    0.9980
   chunk 188 optimal weight:    0.7980
   chunk 79 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 190 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
A 475 GLN
C 226 ASN
C 236 GLN
D 202 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.138047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.093171 restraints weight = 31079.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.30
r_work: 0.3134 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  20594  Z= 0.122
  Angle     :  0.540  13.206  27765  Z= 0.279
  Chirality :  0.040   0.193   2957
  Planarity :  0.003   0.066   3536
  Dihedral  :  4.708  62.066   2670
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 26.18 %
    Favored  : 71.20 %
  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 aren not related in a simple way.
  whole:  1.16 (0.17), residues: 2383
  helix:  1.31 (0.13), residues: 1530
  sheet: -1.86 (0.60), residues: 44
  loop :  0.04 (0.21), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 677 
 TYR   0.028   0.001   TYR A 709 
 PHE   0.012   0.001   PHE A 856 
 TRP   0.039   0.001   TRP B 958 
 HIS   0.022   0.001   HIS A 979 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (20594)
  covalent geometry    : angle       0.54030 (27765)
  hydrogen bonds       : bond        0.03410 ( 1092)
  hydrogen bonds       : angle       4.33931 ( 3171)

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

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

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4766 Ramachandran restraints generated.
    2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 206
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8142 (pttp)
REVERT: A  348 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7979 (ttt180)
REVERT: A  377 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7255 (mt0)
REVERT: A  525 ASP cc_start: 0.8812 (m-30) cc_final: 0.8479 (m-30)
REVERT: A  695 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8073 (tt)
REVERT: A  784 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7254 (tm-30)
REVERT: A  965 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8537 (tptt)
REVERT: A  975 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6975 (t-90)
REVERT: A  995 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8028 (tpm170)
REVERT: B  181 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8060 (pm20)
REVERT: B  491 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7402 (tm-30)
REVERT: B  626 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8047 (mm-30)
REVERT: B  744 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8855 (t80)
REVERT: B  936 MET cc_start: 0.3921 (OUTLIER) cc_final: 0.3500 (mpp)
REVERT: D  227 MET cc_start: 0.8287 (tpt) cc_final: 0.7952 (mtm)
REVERT: D  233 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7825 (ptp90)
REVERT: D  278 ASN cc_start: 0.7991 (t0) cc_final: 0.7222 (m110)
  outliers start: 58
  outliers final: 32
  residues processed: 253
  average time/residue: 0.5930
  time to fit residues: 169.8032
Evaluate side-chains
  242 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 198
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  784 GLU
Chi-restraints excluded: chain A residue  813 LYS
Chi-restraints excluded: chain A residue  814 ASN
Chi-restraints excluded: chain A residue  826 CYS
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  953 LYS
Chi-restraints excluded: chain A residue  965 LYS
Chi-restraints excluded: chain A residue  975 HIS
Chi-restraints excluded: chain A residue  995 ARG
Chi-restraints excluded: chain B residue  134 TYR
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  379 GLU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  491 GLN
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  730 GLU
Chi-restraints excluded: chain B residue  744 PHE
Chi-restraints excluded: chain B residue  936 MET
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue  134 TYR
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  233 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 241
   random chunks:
   chunk 142 optimal weight:    2.9990
   chunk 219 optimal weight:    4.9990
   chunk 223 optimal weight:    0.5980
   chunk 155 optimal weight:    4.9990
   chunk 148 optimal weight:    0.9990
   chunk 152 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 167 optimal weight:    9.9990
   chunk 10 optimal weight:    0.3980
   chunk 110 optimal weight:    0.4980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
C 226 ASN
C 236 GLN
D 202 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.138250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.093243 restraints weight = 31010.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.30
r_work: 0.3136 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  20594  Z= 0.131
  Angle     :  0.534  11.851  27765  Z= 0.277
  Chirality :  0.040   0.200   2957
  Planarity :  0.003   0.042   3536
  Dihedral  :  4.682  62.005   2670
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 25.91 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.17), residues: 2383
  helix:  1.31 (0.13), residues: 1531
  sheet: -1.83 (0.60), residues: 44
  loop :  0.03 (0.21), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 677 
 TYR   0.026   0.001   TYR A 709 
 PHE   0.014   0.001   PHE A 839 
 TRP   0.039   0.001   TRP B 958 
 HIS   0.020   0.001   HIS A 979 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (20594)
  covalent geometry    : angle       0.53362 (27765)
  hydrogen bonds       : bond        0.03444 ( 1092)
  hydrogen bonds       : angle       4.32132 ( 3171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8800.27 seconds
wall clock time: 150 minutes 15.67 seconds (9015.67 seconds total)