Starting phenix.real_space_refine
on Sat Aug 23 04:52:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jwg_36682/08_2025/8jwg_36682_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jwg_36682/08_2025/8jwg_36682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jwg_36682/08_2025/8jwg_36682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jwg_36682/08_2025/8jwg_36682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jwg_36682/08_2025/8jwg_36682_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jwg_36682/08_2025/8jwg_36682_neut.cif"
  }
  resolution = 3.54
  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=  -0.003 sd=   0.054
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: 5
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    6241      2.51       5
     N    1583      2.21       5
     O    1750      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 9620
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1192, 9594
          Classifications: {'peptide': 1192}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 26, 'TRANS': 1165}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'YMZ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.84, per 1000 atoms: 0.19
  Number of scatterers: 9620
  At special positions: 0
  Unit cell: (71.5, 111.1, 143, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     F       6      9.00
     O    1750      8.00
     N    1583      7.00
     C    6241      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: 1.21
  Conformation dependent library (CDL) restraints added in 286.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2262

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 4 sheets defined
      64.8% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 39
      removed outlier: 3.528A  pdb=" N   LEU A  31 " --> pdb=" O   SER A  27 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ASN A  37 " --> pdb=" O   ARG A  33 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   GLU A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 63
      removed outlier: 3.890A  pdb=" N   LEU A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A  57 " --> pdb=" O   HIS A  53 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   PHE A  58 " --> pdb=" O   ARG A  54 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   SER A  60 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A  62 " --> pdb=" O   PHE A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 69
      removed outlier: 5.121A  pdb=" N   SER A  67 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 86
      removed outlier: 3.726A  pdb=" N   SER A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   GLY A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   VAL A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 136
      removed outlier: 3.503A  pdb=" N   ILE A  95 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ILE A 101 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   SER A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   TYR A 114 " --> pdb=" O   MET A 110 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 118 " --> pdb=" O   TYR A 114 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 146
    Processing helix  chain 'A' and resid 148 through 163
      removed outlier: 3.805A  pdb=" N   ARG A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ASP A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   PHE A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 191
      removed outlier: 4.065A  pdb=" N   ILE A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   ILE A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   PHE A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   THR A 175 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TYR A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 199
    Processing helix  chain 'A' and resid 202 through 240
      removed outlier: 3.662A  pdb=" N   LYS A 215 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ASN A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   THR A 230 " --> pdb=" O   TYR A 226 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY A 240 " --> pdb=" O   GLU A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 248
    Processing helix  chain 'A' and resid 250 through 305
      removed outlier: 3.519A  pdb=" N   LEU A 254 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LYS A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   PHE A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   TYR A 264 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   HIS A 278 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ILE A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASN A 283 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   GLY A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ILE A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   LEU A 287 " --> pdb=" O   ASN A 283 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A 288 " --> pdb=" O   GLY A 284 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ALA A 305 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 318
      removed outlier: 3.557A  pdb=" N   SER A 318 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 315 through 318'
    Processing helix  chain 'A' and resid 319 through 330
      removed outlier: 3.779A  pdb=" N   LEU A 323 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LEU A 324 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   MET A 330 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 335
    Processing helix  chain 'A' and resid 336 through 358
      removed outlier: 3.773A  pdb=" N   GLU A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   ILE A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 444 through 448
    Processing helix  chain 'A' and resid 449 through 456
    Processing helix  chain 'A' and resid 472 through 477
      removed outlier: 3.886A  pdb=" N   TYR A 477 " --> pdb=" O   ASN A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 489
      removed outlier: 5.077A  pdb=" N   LEU A 485 " --> pdb=" O   SER A 481 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU A 486 " --> pdb=" O   LEU A 482 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA A 487 " --> pdb=" O   LYS A 483 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLU A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 523
    Processing helix  chain 'A' and resid 529 through 539
      removed outlier: 4.194A  pdb=" N   VAL A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ASP A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL A 539 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 546
    Processing helix  chain 'A' and resid 564 through 579
    Processing helix  chain 'A' and resid 594 through 607
      removed outlier: 3.754A  pdb=" N   GLU A 598 " --> pdb=" O   ASP A 594 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN A 607 " --> pdb=" O   LYS A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 626
      removed outlier: 3.560A  pdb=" N   THR A 625 " --> pdb=" O   ARG A 622 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A 626 " --> pdb=" O   LEU A 623 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 622 through 626'
    Processing helix  chain 'A' and resid 676 through 681
      removed outlier: 4.001A  pdb=" N   MET A 680 " --> pdb=" O   HIS A 676 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LYS A 681 " --> pdb=" O   ASP A 677 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 676 through 681'
    Processing helix  chain 'A' and resid 685 through 694
    Processing helix  chain 'A' and resid 772 through 783
      removed outlier: 4.063A  pdb=" N   ILE A 778 " --> pdb=" O   ASN A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 803
      removed outlier: 3.532A  pdb=" N   VAL A 789 " --> pdb=" O   TYR A 785 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR A 790 " --> pdb=" O   LYS A 786 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE A 791 " --> pdb=" O   LYS A 787 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ILE A 792 " --> pdb=" O   ASP A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 816
      removed outlier: 3.767A  pdb=" N   LEU A 808 " --> pdb=" O   PRO A 804 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG A 812 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   TYR A 813 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 849
      removed outlier: 3.961A  pdb=" N   ASN A 826 " --> pdb=" O   ASN A 822 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ILE A 832 " --> pdb=" O   ASN A 828 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   TYR A 833 " --> pdb=" O   LYS A 829 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE A 834 " --> pdb=" O   TYR A 830 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE A 843 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 873
      removed outlier: 4.286A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL A 859 " --> pdb=" O   ILE A 855 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLU A 860 " --> pdb=" O   GLY A 856 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ARG A 865 " --> pdb=" O   LYS A 861 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ARG A 866 " --> pdb=" O   THR A 862 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LEU A 872 " --> pdb=" O   PHE A 868 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   TYR A 873 " --> pdb=" O   GLU A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 875 through 881
      removed outlier: 3.850A  pdb=" N   PHE A 879 " --> pdb=" O   GLU A 875 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN A 881 " --> pdb=" O   SER A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 885 through 905
      removed outlier: 3.808A  pdb=" N   ILE A 893 " --> pdb=" O   LEU A 889 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN A 894 " --> pdb=" O   SER A 890 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   VAL A 897 " --> pdb=" O   ILE A 893 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 904 " --> pdb=" O   LEU A 900 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL A 905 " --> pdb=" O   LYS A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 908 through 927
      removed outlier: 3.595A  pdb=" N   SER A 912 " --> pdb=" O   ILE A 908 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   MET A 922 " --> pdb=" O   PHE A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 945
      removed outlier: 3.599A  pdb=" N   ALA A 933 " --> pdb=" O   CYS A 929 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   VAL A 935 " --> pdb=" O   ILE A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 962
      removed outlier: 3.981A  pdb=" N   GLU A 960 " --> pdb=" O   SER A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 992
      removed outlier: 3.649A  pdb=" N   GLU A 988 " --> pdb=" O   PHE A 984 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   PHE A 990 " --> pdb=" O   ILE A 986 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   TYR A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ASN A 992 " --> pdb=" O   GLU A 988 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1008 through 1035
      removed outlier: 4.512A  pdb=" N   TYR A1015 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASN A1017 " --> pdb=" O   ILE A1013 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   LYS A1018 " --> pdb=" O   ASP A1014 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   GLY A1019 " --> pdb=" O   TYR A1015 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ARG A1022 " --> pdb=" O   LYS A1018 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TRP A1031 " --> pdb=" O   ASN A1027 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLN A1035 " --> pdb=" O   TRP A1031 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1055
      removed outlier: 3.874A  pdb=" N   LEU A1052 " --> pdb=" O   PHE A1048 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE A1053 " --> pdb=" O   GLY A1049 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LYS A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ARG A1055 " --> pdb=" O   PHE A1051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1059 through 1081
      removed outlier: 4.122A  pdb=" N   PHE A1063 " --> pdb=" O   LEU A1059 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR A1069 " --> pdb=" O   LYS A1065 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   PHE A1070 " --> pdb=" O   SER A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1087 through 1098
      removed outlier: 3.859A  pdb=" N   GLU A1095 " --> pdb=" O   LYS A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1099 through 1102
    Processing helix  chain 'A' and resid 1169 through 1175
    Processing helix  chain 'A' and resid 1243 through 1248
      removed outlier: 3.648A  pdb=" N   LEU A1247 " --> pdb=" O   ASN A1243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1270
    Processing helix  chain 'A' and resid 1277 through 1288
      removed outlier: 3.698A  pdb=" N   LYS A1286 " --> pdb=" O   LYS A1282 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   PHE A1287 " --> pdb=" O   ARG A1283 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ALA A1288 " --> pdb=" O   VAL A1284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1293 through 1297
      removed outlier: 4.026A  pdb=" N   LEU A1297 " --> pdb=" O   ILE A1294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1310
    Processing helix  chain 'A' and resid 1313 through 1328
      removed outlier: 3.698A  pdb=" N   LYS A1317 " --> pdb=" O   SER A1313 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ARG A1328 " --> pdb=" O   ARG A1324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1343 through 1360
      removed outlier: 3.896A  pdb=" N   LYS A1360 " --> pdb=" O   ASP A1356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1371 through 1376
    Processing helix  chain 'A' and resid 1410 through 1417
    Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 408
      removed outlier: 8.062A  pdb=" N   LYS A 407 " --> pdb=" O   THR A 616 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 458
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1150 through 1151
      removed outlier: 5.212A  pdb=" N   ILE A1128 " --> pdb=" O   LEU A1233 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU A1233 " --> pdb=" O   ILE A1128 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASP A1130 " --> pdb=" O   GLU A1231 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1332 through 1334
      removed outlier: 6.214A  pdb=" N   THR A1157 " --> pdb=" O   THR A1367 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ALA A1158 " --> pdb=" O   VAL A1382 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   PHE A1384 " --> pdb=" O   ALA A1158 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   VAL A1160 " --> pdb=" O   PHE A1384 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASN A1385 " --> pdb=" O   PHE A1393 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE A1393 " --> pdb=" O   ASN A1385 " (cutoff:3.500A)

    435 hydrogen bonds defined for protein.
    1272 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 0.93 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: 2971
        1.34 -     1.46: 1725
        1.46 -     1.58: 5037
        1.58 -     1.69: 0
        1.69 -     1.81: 67
  Bond restraints: 9800
  Sorted by residual:
  bond pdb=" CAR YMZ A1500 "
       pdb=" NAP YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.298  1.374 -0.076 2.00e-02 2.50e+03 1.45e+01
  bond pdb=" CAJ YMZ A1500 "
       pdb=" CAU YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.414  1.372  0.042 2.00e-02 2.50e+03 4.52e+00
  bond pdb=" CAS YMZ A1500 "
       pdb=" CAW YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.518  1.560 -0.042 2.00e-02 2.50e+03 4.50e+00
  bond pdb=" CAN YMZ A1500 "
       pdb=" NAQ YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.457  1.415  0.042 2.00e-02 2.50e+03 4.31e+00
  bond pdb=" CAZ YMZ A1500 "
       pdb=" FAE YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.340  1.378 -0.038 2.00e-02 2.50e+03 3.56e+00
  ... (remaining 9795 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 12420
        1.34 -     2.69: 670
        2.69 -     4.03: 79
        4.03 -     5.38: 31
        5.38 -     6.72: 12
  Bond angle restraints: 13212
  Sorted by residual:
  angle pdb=" C   ASN A 440 "
        pdb=" N   ASP A 441 "
        pdb=" CA  ASP A 441 "
      ideal   model   delta    sigma   weight residual
     122.08  128.80   -6.72 1.47e+00 4.63e-01 2.09e+01
  angle pdb=" C   ALA A 821 "
        pdb=" N   ASN A 822 "
        pdb=" CA  ASN A 822 "
      ideal   model   delta    sigma   weight residual
     121.54  127.62   -6.08 1.91e+00 2.74e-01 1.01e+01
  angle pdb=" N   LEU A1001 "
        pdb=" CA  LEU A1001 "
        pdb=" C   LEU A1001 "
      ideal   model   delta    sigma   weight residual
     112.72  108.74    3.98 1.28e+00 6.10e-01 9.67e+00
  angle pdb=" CA  ASN A1106 "
        pdb=" CB  ASN A1106 "
        pdb=" CG  ASN A1106 "
      ideal   model   delta    sigma   weight residual
     112.60  115.57   -2.97 1.00e+00 1.00e+00 8.79e+00
  angle pdb=" C   SER A1105 "
        pdb=" N   ASN A1106 "
        pdb=" CA  ASN A1106 "
      ideal   model   delta    sigma   weight residual
     122.61  127.03   -4.42 1.56e+00 4.11e-01 8.04e+00
  ... (remaining 13207 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 5720
       17.92 -    35.84: 175
       35.84 -    53.76: 18
       53.76 -    71.68: 2
       71.68 -    89.60: 3
  Dihedral angle restraints: 5918
    sinusoidal: 2413
      harmonic: 3505
  Sorted by residual:
  dihedral pdb=" CA  TYR A1004 "
           pdb=" C   TYR A1004 "
           pdb=" N   PHE A1005 "
           pdb=" CA  PHE A1005 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.98   21.02     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  ARG A 776 "
           pdb=" C   ARG A 776 "
           pdb=" N   ILE A 777 "
           pdb=" CA  ILE A 777 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.44   20.56     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  ARG A 428 "
           pdb=" C   ARG A 428 "
           pdb=" N   LEU A 429 "
           pdb=" CA  LEU A 429 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.62   20.38     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 5915 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 994
       0.037 -    0.074: 376
       0.074 -    0.111: 105
       0.111 -    0.148: 33
       0.148 -    0.185: 6
  Chirality restraints: 1514
  Sorted by residual:
  chirality pdb=" CB  ILE A 437 "
            pdb=" CA  ILE A 437 "
            pdb=" CG1 ILE A 437 "
            pdb=" CG2 ILE A 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CA  ASN A 440 "
            pdb=" N   ASN A 440 "
            pdb=" C   ASN A 440 "
            pdb=" CB  ASN A 440 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.83e-01
  chirality pdb=" CAX YMZ A1500 "
            pdb=" CAO YMZ A1500 "
            pdb=" CAW YMZ A1500 "
            pdb=" NAQ YMZ A1500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.39   -2.56    0.17 2.00e-01 2.50e+01 6.83e-01
  ... (remaining 1511 not shown)

  Planarity restraints: 1638
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 290 "   -0.019 2.00e-02 2.50e+03   1.38e-02 3.82e+00
        pdb=" CG  TYR A 290 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 290 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 290 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 290 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 290 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 290 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 290 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1257 "   -0.032 5.00e-02 4.00e+02   4.88e-02 3.81e+00
        pdb=" N   PRO A1258 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A1258 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1258 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  71 "   -0.031 5.00e-02 4.00e+02   4.64e-02 3.45e+00
        pdb=" N   PRO A  72 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A  72 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  72 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1635 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1463
        2.76 -     3.29: 9996
        3.29 -     3.83: 14263
        3.83 -     4.36: 17239
        4.36 -     4.90: 29001
  Nonbonded interactions: 71962
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 822 "
            pdb=" ND2 ASN A 826 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OD2 ASP A 144 "
            pdb=" OH  TYR A 430 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   PRO A 338 "
            pdb=" OG1 THR A 341 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   LYS A 220 "
            pdb=" OG  SER A 223 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" NE  ARG A1116 "
            pdb=" OD2 ASP A1246 "
     model   vdw
     2.267 3.120
  ... (remaining 71957 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.890
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
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      :  0.005   0.076   9800  Z= 0.213
  Angle     :  0.721   6.724  13212  Z= 0.399
  Chirality :  0.044   0.185   1514
  Planarity :  0.004   0.049   1638
  Dihedral  :  9.433  89.598   3656
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  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: -3.71 (0.20), residues: 1178
  helix: -1.90 (0.16), residues: 658
  sheet: -3.26 (0.73), residues: 34
  loop : -3.12 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 575 
 TYR   0.033   0.002   TYR A 290 
 PHE   0.030   0.002   PHE A 926 
 TRP   0.012   0.001   TRP A 186 
 HIS   0.010   0.002   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 9800)
  covalent geometry    : angle       0.72058 (13212)
  hydrogen bonds       : bond        0.16035 (  435)
  hydrogen bonds       : angle       5.93708 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.8162 (tpp) cc_final: 0.7929 (tpp)
REVERT: A  358 ASN cc_start: 0.6861 (m-40) cc_final: 0.6537 (t0)
REVERT: A  793 PHE cc_start: 0.6511 (t80) cc_final: 0.6228 (t80)
REVERT: A  880 ASP cc_start: 0.8342 (t70) cc_final: 0.8010 (t0)
REVERT: A 1308 TYR cc_start: 0.7718 (m-80) cc_final: 0.7478 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1041
  time to fit residues: 34.4473
Evaluate side-chains
  110 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:   20.0000
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 ASN
A 884 ASN
A 894 ASN
A 994 HIS
A 998 ASN
A1318 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.163272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.121487 restraints weight = 17930.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.126528 restraints weight = 7174.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.129529 restraints weight = 3935.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.131262 restraints weight = 2723.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.132258 restraints weight = 2209.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.3491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9800  Z= 0.217
  Angle     :  0.745  10.939  13212  Z= 0.396
  Chirality :  0.049   0.187   1514
  Planarity :  0.005   0.056   1638
  Dihedral  :  5.964  53.769   1307
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.03 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.85 (0.21), residues: 1178
  helix: -1.06 (0.17), residues: 697
  sheet: -3.15 (0.62), residues: 46
  loop : -3.04 (0.24), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1371 
 TYR   0.023   0.002   TYR A 290 
 PHE   0.024   0.002   PHE A 257 
 TRP   0.021   0.003   TRP A 186 
 HIS   0.006   0.001   HIS A 898 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 9800)
  covalent geometry    : angle       0.74526 (13212)
  hydrogen bonds       : bond        0.06385 (  435)
  hydrogen bonds       : angle       4.85680 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.8548 (tpp) cc_final: 0.8126 (tpp)
REVERT: A  358 ASN cc_start: 0.7615 (m-40) cc_final: 0.6901 (t0)
REVERT: A  690 MET cc_start: 0.5251 (mmm) cc_final: 0.4628 (ptp)
REVERT: A  793 PHE cc_start: 0.7108 (t80) cc_final: 0.6773 (t80)
REVERT: A 1397 HIS cc_start: 0.8220 (t70) cc_final: 0.7358 (p-80)
  outliers start: 23
  outliers final: 17
  residues processed: 140
  average time/residue: 0.0847
  time to fit residues: 16.6801
Evaluate side-chains
  116 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  408 THR
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  855 ILE
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  926 PHE
Chi-restraints excluded: chain A residue  944 MET
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1320 ILE
Chi-restraints excluded: chain A residue 1412 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 90 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.161441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.119557 restraints weight = 18016.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.124472 restraints weight = 7202.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.127486 restraints weight = 3967.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.129250 restraints weight = 2735.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.130141 restraints weight = 2222.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9800  Z= 0.185
  Angle     :  0.682  10.667  13212  Z= 0.357
  Chirality :  0.046   0.159   1514
  Planarity :  0.004   0.055   1638
  Dihedral  :  5.634  47.663   1307
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.82 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.34 (0.22), residues: 1178
  helix: -0.66 (0.18), residues: 709
  sheet: -2.52 (0.67), residues: 46
  loop : -2.91 (0.25), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 575 
 TYR   0.021   0.002   TYR A 290 
 PHE   0.018   0.002   PHE A 941 
 TRP   0.015   0.003   TRP A 186 
 HIS   0.006   0.001   HIS A 898 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 9800)
  covalent geometry    : angle       0.68227 (13212)
  hydrogen bonds       : bond        0.06122 (  435)
  hydrogen bonds       : angle       4.56743 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 ASN cc_start: 0.7814 (m-40) cc_final: 0.6900 (t0)
REVERT: A  399 LEU cc_start: 0.7511 (tp) cc_final: 0.7175 (mm)
REVERT: A  542 HIS cc_start: 0.6331 (p-80) cc_final: 0.5837 (p-80)
REVERT: A  690 MET cc_start: 0.5411 (mmm) cc_final: 0.4679 (ptp)
REVERT: A  793 PHE cc_start: 0.7364 (t80) cc_final: 0.7045 (t80)
REVERT: A 1150 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7748 (t)
REVERT: A 1397 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7425 (p-80)
  outliers start: 28
  outliers final: 21
  residues processed: 123
  average time/residue: 0.0872
  time to fit residues: 15.1711
Evaluate side-chains
  116 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  855 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  926 PHE
Chi-restraints excluded: chain A residue 1064 MET
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1320 ILE
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1412 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 853 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.162997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.120594 restraints weight = 17487.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.125417 restraints weight = 6967.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.128474 restraints weight = 3826.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.130278 restraints weight = 2643.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.131283 restraints weight = 2137.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9800  Z= 0.159
  Angle     :  0.638   9.655  13212  Z= 0.334
  Chirality :  0.045   0.154   1514
  Planarity :  0.004   0.045   1638
  Dihedral  :  5.346  41.540   1307
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 12.48 %
    Favored  : 84.54 %
  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: -1.85 (0.23), residues: 1178
  helix: -0.27 (0.19), residues: 702
  sheet: -1.62 (0.75), residues: 45
  loop : -2.78 (0.25), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 575 
 TYR   0.018   0.001   TYR A 290 
 PHE   0.016   0.001   PHE A1033 
 TRP   0.012   0.002   TRP A 186 
 HIS   0.005   0.001   HIS A 898 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9800)
  covalent geometry    : angle       0.63791 (13212)
  hydrogen bonds       : bond        0.05655 (  435)
  hydrogen bonds       : angle       4.40729 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 LEU cc_start: 0.7590 (tp) cc_final: 0.7199 (mm)
REVERT: A  690 MET cc_start: 0.5428 (mmm) cc_final: 0.4802 (ptm)
REVERT: A  793 PHE cc_start: 0.7342 (t80) cc_final: 0.7034 (t80)
REVERT: A 1150 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7740 (t)
REVERT: A 1231 GLU cc_start: 0.7252 (mp0) cc_final: 0.6034 (mp0)
REVERT: A 1242 TYR cc_start: 0.5920 (m-80) cc_final: 0.5415 (m-10)
REVERT: A 1397 HIS cc_start: 0.8118 (t70) cc_final: 0.7417 (p-80)
  outliers start: 32
  outliers final: 23
  residues processed: 128
  average time/residue: 0.0759
  time to fit residues: 13.9374
Evaluate side-chains
  126 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  855 ILE
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  926 PHE
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1171 MET
Chi-restraints excluded: chain A residue 1412 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 96 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 109 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.162453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.120819 restraints weight = 18152.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.125820 restraints weight = 7218.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.128880 restraints weight = 3940.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.130546 restraints weight = 2720.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 74)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.131678 restraints weight = 2216.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.4803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9800  Z= 0.129
  Angle     :  0.601  12.747  13212  Z= 0.311
  Chirality :  0.043   0.160   1514
  Planarity :  0.003   0.042   1638
  Dihedral  :  5.011  35.944   1307
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 12.94 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.23), residues: 1178
  helix:  0.08 (0.19), residues: 696
  sheet: -1.27 (0.77), residues: 45
  loop : -2.65 (0.26), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 242 
 TYR   0.014   0.001   TYR A 290 
 PHE   0.014   0.001   PHE A1033 
 TRP   0.008   0.002   TRP A1047 
 HIS   0.004   0.001   HIS A 542 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9800)
  covalent geometry    : angle       0.60146 (13212)
  hydrogen bonds       : bond        0.05087 (  435)
  hydrogen bonds       : angle       4.13552 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 107
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 LEU cc_start: 0.7620 (tp) cc_final: 0.7278 (mm)
REVERT: A  486 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7434 (tt0)
REVERT: A  542 HIS cc_start: 0.6077 (p-80) cc_final: 0.5480 (p90)
REVERT: A  578 MET cc_start: 0.4195 (ttt) cc_final: 0.3459 (mmm)
REVERT: A  690 MET cc_start: 0.5462 (mmm) cc_final: 0.4757 (ptm)
REVERT: A  793 PHE cc_start: 0.7203 (t80) cc_final: 0.6888 (t80)
REVERT: A  916 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7438 (tpp)
REVERT: A 1150 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7692 (t)
REVERT: A 1231 GLU cc_start: 0.7196 (mp0) cc_final: 0.6124 (mp0)
REVERT: A 1242 TYR cc_start: 0.6220 (m-80) cc_final: 0.5993 (m-10)
REVERT: A 1397 HIS cc_start: 0.8148 (t70) cc_final: 0.7454 (p-80)
  outliers start: 37
  outliers final: 21
  residues processed: 132
  average time/residue: 0.0764
  time to fit residues: 14.7478
Evaluate side-chains
  123 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  486 GLU
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  834 ILE
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  916 MET
Chi-restraints excluded: chain A residue  926 PHE
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1064 MET
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1171 MET
Chi-restraints excluded: chain A residue 1412 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 117 optimal weight:   20.0000
   chunk 75 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 93 optimal weight:    9.9990
   chunk 115 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 103 optimal weight:    0.5980
   chunk 80 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 146 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.159945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.117923 restraints weight = 18406.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.122747 restraints weight = 7379.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.125711 restraints weight = 4086.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.127526 restraints weight = 2852.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.128337 restraints weight = 2319.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.5090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9800  Z= 0.156
  Angle     :  0.643  12.935  13212  Z= 0.335
  Chirality :  0.044   0.211   1514
  Planarity :  0.004   0.039   1638
  Dihedral  :  4.951  28.995   1307
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.59 %
    Favored  : 82.77 %
  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: -1.33 (0.23), residues: 1178
  helix:  0.19 (0.20), residues: 688
  sheet: -1.07 (0.77), residues: 45
  loop : -2.61 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 575 
 TYR   0.018   0.001   TYR A 290 
 PHE   0.014   0.001   PHE A  78 
 TRP   0.008   0.002   TRP A 186 
 HIS   0.005   0.001   HIS A 898 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9800)
  covalent geometry    : angle       0.64253 (13212)
  hydrogen bonds       : bond        0.05440 (  435)
  hydrogen bonds       : angle       4.25130 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 100
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 LEU cc_start: 0.7750 (tp) cc_final: 0.7364 (mm)
REVERT: A  486 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7543 (tt0)
REVERT: A  488 MET cc_start: 0.5792 (ptp) cc_final: 0.5562 (ptp)
REVERT: A  542 HIS cc_start: 0.6279 (p-80) cc_final: 0.5751 (p-80)
REVERT: A  578 MET cc_start: 0.4451 (ttt) cc_final: 0.3706 (mmm)
REVERT: A  690 MET cc_start: 0.5698 (mmm) cc_final: 0.4919 (ptm)
REVERT: A  793 PHE cc_start: 0.7334 (t80) cc_final: 0.6981 (t80)
REVERT: A  916 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7447 (tpp)
REVERT: A 1150 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7741 (t)
REVERT: A 1231 GLU cc_start: 0.7305 (mp0) cc_final: 0.6831 (mp0)
REVERT: A 1242 TYR cc_start: 0.6666 (m-80) cc_final: 0.6220 (m-10)
REVERT: A 1292 GLU cc_start: 0.8159 (pm20) cc_final: 0.7858 (pm20)
REVERT: A 1397 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7540 (p-80)
  outliers start: 39
  outliers final: 30
  residues processed: 126
  average time/residue: 0.0817
  time to fit residues: 15.0073
Evaluate side-chains
  129 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  486 GLU
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  834 ILE
Chi-restraints excluded: chain A residue  855 ILE
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  916 MET
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  926 PHE
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1064 MET
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1171 MET
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1412 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 18 optimal weight:    0.2980
   chunk 63 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.162651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.121462 restraints weight = 18042.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.126479 restraints weight = 7044.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.129580 restraints weight = 3807.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.131320 restraints weight = 2613.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.132177 restraints weight = 2122.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.5194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9800  Z= 0.118
  Angle     :  0.588  12.855  13212  Z= 0.303
  Chirality :  0.042   0.193   1514
  Planarity :  0.003   0.037   1638
  Dihedral  :  4.632  24.806   1307
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.80 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.24), residues: 1178
  helix:  0.45 (0.20), residues: 690
  sheet: -0.82 (0.79), residues: 45
  loop : -2.50 (0.26), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 242 
 TYR   0.013   0.001   TYR A1266 
 PHE   0.011   0.001   PHE A1033 
 TRP   0.021   0.002   TRP A 452 
 HIS   0.003   0.001   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9800)
  covalent geometry    : angle       0.58762 (13212)
  hydrogen bonds       : bond        0.04699 (  435)
  hydrogen bonds       : angle       3.95503 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7743 (mtt90)
REVERT: A  399 LEU cc_start: 0.7715 (tp) cc_final: 0.7334 (mm)
REVERT: A  486 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7456 (tt0)
REVERT: A  542 HIS cc_start: 0.6239 (p-80) cc_final: 0.5881 (p-80)
REVERT: A  578 MET cc_start: 0.4449 (ttt) cc_final: 0.3920 (mmm)
REVERT: A  690 MET cc_start: 0.5690 (mmm) cc_final: 0.4915 (ptm)
REVERT: A  793 PHE cc_start: 0.7235 (t80) cc_final: 0.6933 (t80)
REVERT: A  916 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7430 (tpp)
REVERT: A 1231 GLU cc_start: 0.7209 (mp0) cc_final: 0.6755 (mp0)
REVERT: A 1335 LEU cc_start: 0.8819 (mt) cc_final: 0.8276 (tt)
REVERT: A 1397 HIS cc_start: 0.8322 (t70) cc_final: 0.7510 (p-80)
  outliers start: 31
  outliers final: 18
  residues processed: 124
  average time/residue: 0.0794
  time to fit residues: 14.0513
Evaluate side-chains
  118 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  146 ASN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  486 GLU
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  916 MET
Chi-restraints excluded: chain A residue  926 PHE
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1171 MET
Chi-restraints excluded: chain A residue 1174 LEU
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1412 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 88 optimal weight:    0.0470
   chunk 45 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 111 optimal weight:   20.0000
   overall best weight:    1.3284

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.160698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.121894 restraints weight = 18162.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.124395 restraints weight = 7807.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.127459 restraints weight = 4281.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.127532 restraints weight = 3175.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.127814 restraints weight = 2897.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.5393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9800  Z= 0.137
  Angle     :  0.618  13.006  13212  Z= 0.320
  Chirality :  0.043   0.218   1514
  Planarity :  0.004   0.038   1638
  Dihedral  :  4.611  20.280   1307
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.62 %
    Favored  : 82.03 %
  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: -0.98 (0.24), residues: 1178
  helix:  0.45 (0.20), residues: 696
  sheet: -0.77 (0.79), residues: 45
  loop : -2.49 (0.26), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 575 
 TYR   0.013   0.001   TYR A 290 
 PHE   0.012   0.001   PHE A1033 
 TRP   0.016   0.002   TRP A 452 
 HIS   0.004   0.001   HIS A 898 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9800)
  covalent geometry    : angle       0.61785 (13212)
  hydrogen bonds       : bond        0.05022 (  435)
  hydrogen bonds       : angle       4.02413 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 101
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7758 (mtt90)
REVERT: A  399 LEU cc_start: 0.7802 (tp) cc_final: 0.7410 (mm)
REVERT: A  480 TYR cc_start: 0.6872 (m-10) cc_final: 0.6455 (m-80)
REVERT: A  542 HIS cc_start: 0.6426 (p-80) cc_final: 0.6078 (p-80)
REVERT: A  578 MET cc_start: 0.4705 (ttt) cc_final: 0.4147 (mmm)
REVERT: A  690 MET cc_start: 0.5796 (mmm) cc_final: 0.5012 (ptm)
REVERT: A  793 PHE cc_start: 0.7289 (t80) cc_final: 0.6971 (t80)
REVERT: A  916 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7387 (tpp)
REVERT: A 1231 GLU cc_start: 0.7363 (mp0) cc_final: 0.6897 (mp0)
REVERT: A 1259 MET cc_start: 0.6988 (tpp) cc_final: 0.6767 (ttm)
REVERT: A 1397 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.7505 (p-80)
  outliers start: 36
  outliers final: 27
  residues processed: 126
  average time/residue: 0.0802
  time to fit residues: 14.8687
Evaluate side-chains
  128 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  146 ASN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  855 ILE
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  916 MET
Chi-restraints excluded: chain A residue  926 PHE
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1171 MET
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1412 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 116 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 110 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 71 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1243 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.162905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.121688 restraints weight = 17988.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.126655 restraints weight = 7069.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.129723 restraints weight = 3843.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.131377 restraints weight = 2649.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.132455 restraints weight = 2167.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.5466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9800  Z= 0.117
  Angle     :  0.595  12.979  13212  Z= 0.304
  Chirality :  0.042   0.215   1514
  Planarity :  0.003   0.037   1638
  Dihedral  :  4.471  18.387   1307
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.36 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.24), residues: 1178
  helix:  0.59 (0.20), residues: 699
  sheet: -0.61 (0.80), residues: 45
  loop : -2.46 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 575 
 TYR   0.012   0.001   TYR A1097 
 PHE   0.017   0.001   PHE A 411 
 TRP   0.011   0.002   TRP A 452 
 HIS   0.003   0.001   HIS A 898 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9800)
  covalent geometry    : angle       0.59506 (13212)
  hydrogen bonds       : bond        0.04591 (  435)
  hydrogen bonds       : angle       3.88069 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7853 (mtt90)
REVERT: A  399 LEU cc_start: 0.7797 (tp) cc_final: 0.7428 (mm)
REVERT: A  480 TYR cc_start: 0.6774 (m-10) cc_final: 0.6365 (m-80)
REVERT: A  542 HIS cc_start: 0.6217 (p-80) cc_final: 0.5981 (p-80)
REVERT: A  578 MET cc_start: 0.4533 (ttt) cc_final: 0.4015 (mmm)
REVERT: A  690 MET cc_start: 0.5680 (mmm) cc_final: 0.4938 (ptm)
REVERT: A  793 PHE cc_start: 0.7164 (t80) cc_final: 0.6845 (t80)
REVERT: A  916 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7332 (tpp)
REVERT: A 1335 LEU cc_start: 0.8793 (mt) cc_final: 0.8279 (tt)
REVERT: A 1397 HIS cc_start: 0.8326 (t70) cc_final: 0.7723 (p-80)
  outliers start: 29
  outliers final: 25
  residues processed: 126
  average time/residue: 0.0713
  time to fit residues: 13.2921
Evaluate side-chains
  129 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  146 ASN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  916 MET
Chi-restraints excluded: chain A residue  926 PHE
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1171 MET
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1412 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 56 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 101 optimal weight:    0.2980
   chunk 36 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 894 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.160229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.118884 restraints weight = 17954.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.123729 restraints weight = 7104.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.126747 restraints weight = 3877.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.128486 restraints weight = 2689.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.129270 restraints weight = 2190.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.5585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9800  Z= 0.141
  Angle     :  0.618  13.230  13212  Z= 0.319
  Chirality :  0.043   0.223   1514
  Planarity :  0.004   0.040   1638
  Dihedral  :  4.523  18.444   1307
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.83 %
    Favored  : 81.47 %
  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: -0.84 (0.24), residues: 1178
  helix:  0.55 (0.20), residues: 696
  sheet: -0.45 (0.83), residues: 45
  loop : -2.44 (0.27), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 575 
 TYR   0.015   0.001   TYR A 290 
 PHE   0.012   0.001   PHE A 401 
 TRP   0.013   0.002   TRP A 452 
 HIS   0.004   0.001   HIS A 898 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9800)
  covalent geometry    : angle       0.61772 (13212)
  hydrogen bonds       : bond        0.04987 (  435)
  hydrogen bonds       : angle       3.97145 ( 1272)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 LEU cc_start: 0.7828 (tp) cc_final: 0.7434 (mm)
REVERT: A  480 TYR cc_start: 0.6830 (m-10) cc_final: 0.6427 (m-80)
REVERT: A  542 HIS cc_start: 0.6324 (p-80) cc_final: 0.6081 (p-80)
REVERT: A  578 MET cc_start: 0.4647 (ttt) cc_final: 0.4059 (mmm)
REVERT: A  690 MET cc_start: 0.5723 (mmm) cc_final: 0.4899 (ptm)
REVERT: A  793 PHE cc_start: 0.7289 (t80) cc_final: 0.6896 (t80)
REVERT: A  916 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7359 (tpp)
REVERT: A 1267 GLU cc_start: 0.8776 (tp30) cc_final: 0.8413 (tp30)
REVERT: A 1310 LYS cc_start: 0.7038 (mttm) cc_final: 0.6785 (mttp)
REVERT: A 1397 HIS cc_start: 0.8419 (t70) cc_final: 0.7627 (p-80)
  outliers start: 29
  outliers final: 27
  residues processed: 120
  average time/residue: 0.0756
  time to fit residues: 13.4417
Evaluate side-chains
  126 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  146 ASN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  916 MET
Chi-restraints excluded: chain A residue  926 PHE
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1171 MET
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1412 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0070
   chunk 114 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 103 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.163530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.123277 restraints weight = 17940.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.128332 restraints weight = 6920.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.131432 restraints weight = 3710.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.133250 restraints weight = 2527.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.134027 restraints weight = 2040.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.4248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.5657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9800  Z= 0.111
  Angle     :  0.583  13.306  13212  Z= 0.297
  Chirality :  0.041   0.237   1514
  Planarity :  0.003   0.037   1638
  Dihedral  :  4.280  18.128   1307
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.01 %
    Favored  : 81.47 %
  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: -0.61 (0.25), residues: 1178
  helix:  0.74 (0.20), residues: 698
  sheet: -0.36 (0.84), residues: 45
  loop : -2.36 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 575 
 TYR   0.011   0.001   TYR A1097 
 PHE   0.010   0.001   PHE A1033 
 TRP   0.011   0.001   TRP A 452 
 HIS   0.002   0.001   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 9800)
  covalent geometry    : angle       0.58275 (13212)
  hydrogen bonds       : bond        0.04276 (  435)
  hydrogen bonds       : angle       3.75586 ( 1272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1824.28 seconds
wall clock time: 32 minutes 7.14 seconds (1927.14 seconds total)