Starting phenix.real_space_refine
on Thu Feb  5 07:56:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9krn_62534/02_2026/9krn_62534_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9krn_62534/02_2026/9krn_62534.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9krn_62534/02_2026/9krn_62534_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9krn_62534/02_2026/9krn_62534_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9krn_62534/02_2026/9krn_62534.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9krn_62534/02_2026/9krn_62534.map"
  }
  resolution = 3.14
  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=  -0.002 sd=   0.091
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      37      5.16       5
     C    4981      2.51       5
     N    1271      2.21       5
     O    1344      1.98       5
     H    7806      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15439
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 15414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 947, 15414
          Classifications: {'peptide': 947}
          Link IDs: {'PTRANS': 31, 'TRANS': 915}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'P2E': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.84, per 1000 atoms: 0.18
  Number of scatterers: 15439
  At special positions: 0
  Unit cell: (81.4, 97.9, 148.5, 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      37     16.00
     O    1344      8.00
     N    1271      7.00
     C    4981      6.00
     H    7806      1.00
    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: 1.24
  Conformation dependent library (CDL) restraints added in 460.8 milliseconds
  

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1806

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 1 sheets defined
      70.5% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 38
      removed outlier: 4.010A  pdb=" N   PHE A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   LYS A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ARG A  38 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
      removed outlier: 3.672A  pdb=" N   ASP A  51 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 51'
    Processing helix  chain 'A' and resid 52 through 74
      removed outlier: 3.520A  pdb=" N   LEU A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLU A  58 " --> pdb=" O   GLN A  54 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   GLU A  59 " --> pdb=" O   HIS A  55 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LEU A  60 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP A  74 " --> pdb=" O   ARG A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 86
      removed outlier: 4.045A  pdb=" N   ILE A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 103
      removed outlier: 4.244A  pdb=" N   TYR A  92 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ILE A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 122
      removed outlier: 4.068A  pdb=" N   LYS A 115 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ILE A 116 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ASN A 118 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR A 119 " --> pdb=" O   LYS A 115 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   PHE A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU A 121 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASN A 122 " --> pdb=" O   ASN A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 141
    Processing helix  chain 'A' and resid 143 through 150
      removed outlier: 3.526A  pdb=" N   ILE A 147 " --> pdb=" O   PHE A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 178
      removed outlier: 4.107A  pdb=" N   TYR A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   TYR A 157 " --> pdb=" O   HIS A 153 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   GLY A 163 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   MET A 164 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG A 165 " --> pdb=" O   CYS A 161 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   LEU A 166 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   CYS A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 190 through 201
      removed outlier: 3.751A  pdb=" N   LEU A 198 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 209
      removed outlier: 3.750A  pdb=" N   VAL A 208 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 204 through 209'
    Processing helix  chain 'A' and resid 210 through 212
      No H-bonds generated for 'chain 'A' and resid 210 through 212'
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 4.067A  pdb=" N   ILE A 223 " --> pdb=" O   PRO A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 232
      No H-bonds generated for 'chain 'A' and resid 230 through 232'
    Processing helix  chain 'A' and resid 234 through 236
      No H-bonds generated for 'chain 'A' and resid 234 through 236'
    Processing helix  chain 'A' and resid 237 through 242
    Processing helix  chain 'A' and resid 246 through 281
      removed outlier: 3.543A  pdb=" N   CYS A 253 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   PHE A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   SER A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 262 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   ALA A 271 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ARG A 272 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR A 281 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 290
      removed outlier: 3.714A  pdb=" N   MET A 288 " --> pdb=" O   ARG A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 326
      removed outlier: 3.701A  pdb=" N   SER A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LEU A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   ARG A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   SER A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 342
      removed outlier: 3.964A  pdb=" N   ILE A 331 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   VAL A 332 " --> pdb=" O   SER A 328 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A 333 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL A 334 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 390
      removed outlier: 4.170A  pdb=" N   VAL A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   PHE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   VAL A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   THR A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      Proline residue:  A 370  - end of helix
      removed outlier: 3.918A  pdb=" N   ILE A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLU A 374 " --> pdb=" O   PRO A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 706
      removed outlier: 4.133A  pdb=" N   TYR A 704 " --> pdb=" O   ALA A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 744
      removed outlier: 3.809A  pdb=" N   PHE A 714 " --> pdb=" O   HIS A 710 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ILE A 718 " --> pdb=" O   PHE A 714 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A 719 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA A 723 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ALA A 724 " --> pdb=" O   LEU A 720 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLN A 725 " --> pdb=" O   ASN A 721 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   VAL A 726 " --> pdb=" O   THR A 722 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LEU A 735 " --> pdb=" O   GLN A 731 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A 736 " --> pdb=" O   ASP A 732 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   MET A 744 " --> pdb=" O   ASN A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 806
      removed outlier: 4.122A  pdb=" N   TYR A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   TYR A 768 " --> pdb=" O   TYR A 764 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER A 769 " --> pdb=" O   LEU A 765 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR A 775 " --> pdb=" O   LEU A 771 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL A 776 " --> pdb=" O   THR A 772 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ARG A 782 " --> pdb=" O   PHE A 778 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER A 783 " --> pdb=" O   GLY A 779 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU A 784 " --> pdb=" O   ILE A 780 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER A 793 " --> pdb=" O   VAL A 789 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   SER A 794 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASN A 799 " --> pdb=" O   GLN A 795 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS A 800 " --> pdb=" O   THR A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 816
      removed outlier: 3.697A  pdb=" N   ARG A 815 " --> pdb=" O   LEU A 811 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ASN A 816 " --> pdb=" O   PHE A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 835
      removed outlier: 3.731A  pdb=" N   ILE A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ILE A 829 " --> pdb=" O   PHE A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 861
      removed outlier: 3.908A  pdb=" N   VAL A 850 " --> pdb=" O   THR A 846 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A 851 " --> pdb=" O   LEU A 847 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL A 860 " --> pdb=" O   VAL A 856 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE A 861 " --> pdb=" O   ALA A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 865
      removed outlier: 3.673A  pdb=" N   ALA A 865 " --> pdb=" O   PRO A 862 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 862 through 865'
    Processing helix  chain 'A' and resid 867 through 887
      removed outlier: 3.906A  pdb=" N   ILE A 874 " --> pdb=" O   PRO A 870 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   PHE A 875 " --> pdb=" O   LEU A 871 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ILE A 876 " --> pdb=" O   GLY A 872 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   PHE A 877 " --> pdb=" O   ILE A 873 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ARG A 880 " --> pdb=" O   ILE A 876 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ARG A 887 " --> pdb=" O   LEU A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 888 through 910
      Proline residue:  A 899  - end of helix
      removed outlier: 3.611A  pdb=" N   GLN A 909 " --> pdb=" O   SER A 905 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY A 910 " --> pdb=" O   SER A 906 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 916
    Processing helix  chain 'A' and resid 921 through 970
      removed outlier: 3.605A  pdb=" N   LEU A 933 " --> pdb=" O   ALA A 929 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   HIS A 934 " --> pdb=" O   HIS A 930 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 940 " --> pdb=" O   GLU A 936 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   PHE A 941 " --> pdb=" O   ALA A 937 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU A 942 " --> pdb=" O   TRP A 938 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   THR A 943 " --> pdb=" O   PHE A 939 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   PHE A 948 " --> pdb=" O   THR A 944 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA A 949 " --> pdb=" O   SER A 945 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   VAL A 950 " --> pdb=" O   ARG A 946 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ARG A 951 " --> pdb=" O   TRP A 947 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE A 955 " --> pdb=" O   ARG A 951 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   VAL A 960 " --> pdb=" O   CYS A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 987
      removed outlier: 3.776A  pdb=" N   VAL A 979 " --> pdb=" O   ASP A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 1014
      removed outlier: 3.747A  pdb=" N   TRP A 995 " --> pdb=" O   GLY A 991 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   SER A1000 " --> pdb=" O   CYS A 996 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   ALA A1001 " --> pdb=" O   VAL A 997 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLU A1002 " --> pdb=" O   ARG A 998 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ILE A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   SER A1009 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   VAL A1010 " --> pdb=" O   MET A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1089
      removed outlier: 4.192A  pdb=" N   LEU A1088 " --> pdb=" O   LEU A1084 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A1089 " --> pdb=" O   ILE A1085 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1084 through 1089'
    Processing helix  chain 'A' and resid 1109 through 1115
      removed outlier: 3.555A  pdb=" N   LEU A1113 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1142 through 1153
    Processing helix  chain 'A' and resid 1156 through 1161
    Processing helix  chain 'A' and resid 1178 through 1194
    Processing helix  chain 'A' and resid 1209 through 1222
      removed outlier: 4.377A  pdb=" N   GLU A1213 " --> pdb=" O   PRO A1209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1262
      removed outlier: 3.670A  pdb=" N   LEU A1261 " --> pdb=" O   GLU A1257 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A1262 " --> pdb=" O   PRO A1258 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1257 through 1262'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1117 through 1120
      removed outlier: 6.718A  pdb=" N   SER A1118 " --> pdb=" O   ILE A1199 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU A1229 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL A1071 " --> pdb=" O   THR A1230 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1137 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: 2.99

  Time building geometry restraints manager: 1.75 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7793
        1.03 -     1.23: 14
        1.23 -     1.42: 3228
        1.42 -     1.62: 4513
        1.62 -     1.81: 62
  Bond restraints: 15610
  Sorted by residual:
  bond pdb=" C8  P2E A1401 "
       pdb=" C9  P2E A1401 "
    ideal  model  delta    sigma   weight residual
    1.515  1.378  0.137 2.00e-02 2.50e+03 4.71e+01
  bond pdb=" C10 P2E A1401 "
       pdb=" C9  P2E A1401 "
    ideal  model  delta    sigma   weight residual
    1.512  1.645 -0.133 2.00e-02 2.50e+03 4.45e+01
  bond pdb=" C11 P2E A1401 "
       pdb=" C12 P2E A1401 "
    ideal  model  delta    sigma   weight residual
    1.529  1.605 -0.076 2.00e-02 2.50e+03 1.46e+01
  bond pdb=" C12 P2E A1401 "
       pdb=" C13 P2E A1401 "
    ideal  model  delta    sigma   weight residual
    1.491  1.417  0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C6  P2E A1401 "
       pdb=" C7  P2E A1401 "
    ideal  model  delta    sigma   weight residual
    1.499  1.570 -0.071 2.00e-02 2.50e+03 1.26e+01
  ... (remaining 15605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 28034
        1.81 -     3.61: 206
        3.61 -     5.42: 23
        5.42 -     7.22: 5
        7.22 -     9.03: 2
  Bond angle restraints: 28270
  Sorted by residual:
  angle pdb=" N   ILE A 864 "
        pdb=" CA  ILE A 864 "
        pdb=" C   ILE A 864 "
      ideal   model   delta    sigma   weight residual
     111.91  108.81    3.10 8.90e-01 1.26e+00 1.21e+01
  angle pdb=" N   GLY A 234 "
        pdb=" CA  GLY A 234 "
        pdb=" C   GLY A 234 "
      ideal   model   delta    sigma   weight residual
     111.56  114.90   -3.34 1.01e+00 9.80e-01 1.10e+01
  angle pdb=" C10 P2E A1401 "
        pdb=" C11 P2E A1401 "
        pdb=" O4  P2E A1401 "
      ideal   model   delta    sigma   weight residual
     115.13  106.10    9.03 3.00e+00 1.11e-01 9.05e+00
  angle pdb=" N   ILE A1159 "
        pdb=" CA  ILE A1159 "
        pdb=" C   ILE A1159 "
      ideal   model   delta    sigma   weight residual
     113.16  109.12    4.04 1.49e+00 4.50e-01 7.35e+00
  angle pdb=" C4  P2E A1401 "
        pdb=" C5  P2E A1401 "
        pdb=" C6  P2E A1401 "
      ideal   model   delta    sigma   weight residual
     127.52  120.10    7.42 3.00e+00 1.11e-01 6.11e+00
  ... (remaining 28265 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 6599
       17.39 -    34.79: 512
       34.79 -    52.18: 125
       52.18 -    69.57: 43
       69.57 -    86.97: 14
  Dihedral angle restraints: 7293
    sinusoidal: 3950
      harmonic: 3343
  Sorted by residual:
  dihedral pdb=" CA  TRP A1035 "
           pdb=" C   TRP A1035 "
           pdb=" N   PRO A1036 "
           pdb=" CA  PRO A1036 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.77   20.23     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  PRO A1036 "
           pdb=" C   PRO A1036 "
           pdb=" N   HIS A1037 "
           pdb=" CA  HIS A1037 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.65  -18.35     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  PRO A1209 "
           pdb=" C   PRO A1209 "
           pdb=" N   ARG A1210 "
           pdb=" CA  ARG A1210 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.83  -18.17     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 7290 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1139
       0.071 -    0.142: 91
       0.142 -    0.213: 2
       0.213 -    0.283: 0
       0.283 -    0.354: 2
  Chirality restraints: 1234
  Sorted by residual:
  chirality pdb=" C15 P2E A1401 "
            pdb=" C14 P2E A1401 "
            pdb=" C16 P2E A1401 "
            pdb=" O5  P2E A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.23    2.58   -0.35 2.00e-01 2.50e+01 3.14e+00
  chirality pdb=" C11 P2E A1401 "
            pdb=" C10 P2E A1401 "
            pdb=" C12 P2E A1401 "
            pdb=" O4  P2E A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.83   -0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" C8  P2E A1401 "
            pdb=" C12 P2E A1401 "
            pdb=" C7  P2E A1401 "
            pdb=" C9  P2E A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.74    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1231 not shown)

  Planarity restraints: 2221
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 365 "   -0.008 2.00e-02 2.50e+03   1.69e-02 2.85e+00
        pdb=" C   VAL A 365 "    0.029 2.00e-02 2.50e+03
        pdb=" O   VAL A 365 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   THR A 366 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 218 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A 219 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 219 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 219 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1208 "   -0.021 5.00e-02 4.00e+02   3.25e-02 1.68e+00
        pdb=" N   PRO A1209 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A1209 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A1209 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 2218 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 1186
        2.22 -     2.82: 33447
        2.82 -     3.41: 36564
        3.41 -     4.01: 47633
        4.01 -     4.60: 75864
  Nonbonded interactions: 194694
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 892 "
            pdb=" HG1 THR A 896 "
     model   vdw
     1.629 2.450
  nonbonded pdb=" O   TYR A1016 "
            pdb=" HG1 THR A1017 "
     model   vdw
     1.645 2.450
  nonbonded pdb=" HD1 HIS A  35 "
            pdb=" OE1 GLU A 884 "
     model   vdw
     1.661 2.450
  nonbonded pdb=" OE1 GLU A1020 "
            pdb=" H   GLU A1020 "
     model   vdw
     1.682 2.450
  nonbonded pdb=" O   ARG A1234 "
            pdb=" HG1 THR A1237 "
     model   vdw
     1.685 2.450
  ... (remaining 194689 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  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:             0.090
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.950
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
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   0.137   7804  Z= 0.231
  Angle     :  0.605   9.027  10585  Z= 0.350
  Chirality :  0.041   0.354   1234
  Planarity :  0.003   0.034   1308
  Dihedral  : 14.548  86.967   2857
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.88 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.13 (0.23), residues: 941
  helix: -1.96 (0.18), residues: 610
  sheet: -3.17 (0.82), residues: 31
  loop : -4.13 (0.28), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1251 
 TYR   0.013   0.001   TYR A 728 
 PHE   0.013   0.001   PHE A 352 
 TRP   0.016   0.001   TRP A 763 
 HIS   0.009   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 7804)
  covalent geometry    : angle       0.60485 (10585)
  hydrogen bonds       : bond        0.16068 (  379)
  hydrogen bonds       : angle       5.55505 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.8290 (tt0) cc_final: 0.8079 (tt0)
REVERT: A   92 TYR cc_start: 0.6227 (t80) cc_final: 0.5502 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 115
  average time/residue: 0.2551
  time to fit residues: 37.5205
Evaluate side-chains
  85 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0170
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7620

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

Flipped N/Q/H residues before XYZ refinement:
A 816 ASN
A1233 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.186307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.138724 restraints weight = 26545.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.39
r_work: 0.3511 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7804  Z= 0.129
  Angle     :  0.536   6.114  10585  Z= 0.286
  Chirality :  0.038   0.140   1234
  Planarity :  0.004   0.044   1308
  Dihedral  :  7.876  62.983   1054
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  8.75 %
    Favored  : 90.77 %
  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 are not related in a simple way.
  whole: -2.71 (0.26), residues: 941
  helix: -0.79 (0.21), residues: 618
  sheet: -2.75 (0.79), residues: 31
  loop : -3.83 (0.29), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 815 
 TYR   0.009   0.001   TYR A  92 
 PHE   0.015   0.001   PHE A 336 
 TRP   0.012   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7804)
  covalent geometry    : angle       0.53568 (10585)
  hydrogen bonds       : bond        0.06034 (  379)
  hydrogen bonds       : angle       4.16787 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.8224 (ttp) cc_final: 0.7873 (tpt)
REVERT: A  267 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7988 (t)
  outliers start: 4
  outliers final: 3
  residues processed: 88
  average time/residue: 0.1816
  time to fit residues: 21.9789
Evaluate side-chains
  84 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  823 ASN
Chi-restraints excluded: chain A residue 1200 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 76 optimal weight:    8.9990
   chunk 24 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.182535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133241 restraints weight = 27035.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.42
r_work: 0.3433 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7804  Z= 0.141
  Angle     :  0.523   5.788  10585  Z= 0.280
  Chirality :  0.038   0.140   1234
  Planarity :  0.004   0.043   1308
  Dihedral  :  6.852  56.653   1053
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.07 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.11 (0.27), residues: 941
  helix: -0.33 (0.21), residues: 626
  sheet: -2.34 (0.82), residues: 31
  loop : -3.69 (0.29), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 815 
 TYR   0.021   0.001   TYR A  92 
 PHE   0.015   0.001   PHE A 258 
 TRP   0.011   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7804)
  covalent geometry    : angle       0.52271 (10585)
  hydrogen bonds       : bond        0.06363 (  379)
  hydrogen bonds       : angle       4.00460 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6685 (pp)
REVERT: A  267 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8027 (t)
REVERT: A  284 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.7910 (ttm110)
  outliers start: 9
  outliers final: 6
  residues processed: 93
  average time/residue: 0.2085
  time to fit residues: 25.6790
Evaluate side-chains
  89 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue 1169 GLU
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.182504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.133125 restraints weight = 26873.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.39
r_work: 0.3427 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7804  Z= 0.127
  Angle     :  0.509   5.591  10585  Z= 0.272
  Chirality :  0.038   0.137   1234
  Planarity :  0.004   0.044   1308
  Dihedral  :  6.351  53.707   1053
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 11.27 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.27), residues: 941
  helix: -0.08 (0.22), residues: 624
  sheet: -1.96 (0.83), residues: 31
  loop : -3.40 (0.31), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1114 
 TYR   0.021   0.001   TYR A  92 
 PHE   0.014   0.001   PHE A 336 
 TRP   0.009   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7804)
  covalent geometry    : angle       0.50855 (10585)
  hydrogen bonds       : bond        0.05968 (  379)
  hydrogen bonds       : angle       3.87939 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6673 (pp)
REVERT: A  262 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7495 (mtt180)
REVERT: A  267 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7928 (t)
REVERT: A  771 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7907 (mm)
REVERT: A  897 ARG cc_start: 0.8363 (ttp-170) cc_final: 0.7934 (ttm-80)
REVERT: A 1123 GLU cc_start: 0.8266 (pp20) cc_final: 0.7705 (pp20)
  outliers start: 10
  outliers final: 6
  residues processed: 87
  average time/residue: 0.1853
  time to fit residues: 21.7721
Evaluate side-chains
  87 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue 1169 GLU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0020
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.9994

-------------------------------------------------------------------------------
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 = 0.4199 r_free = 0.4199 target = 0.181083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.131385 restraints weight = 27043.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.36
r_work: 0.3391 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7804  Z= 0.135
  Angle     :  0.511   5.556  10585  Z= 0.274
  Chirality :  0.038   0.135   1234
  Planarity :  0.003   0.044   1308
  Dihedral  :  5.835  49.032   1053
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.99 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.28), residues: 941
  helix:  0.05 (0.22), residues: 627
  sheet: -1.74 (0.83), residues: 31
  loop : -3.23 (0.32), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1114 
 TYR   0.016   0.001   TYR A  92 
 PHE   0.014   0.001   PHE A 336 
 TRP   0.007   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7804)
  covalent geometry    : angle       0.51053 (10585)
  hydrogen bonds       : bond        0.06118 (  379)
  hydrogen bonds       : angle       3.85431 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7871 (t)
REVERT: A  771 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7991 (mm)
REVERT: A 1123 GLU cc_start: 0.8359 (pp20) cc_final: 0.7781 (pp20)
  outliers start: 14
  outliers final: 9
  residues processed: 90
  average time/residue: 0.2041
  time to fit residues: 25.0757
Evaluate side-chains
  87 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue 1169 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 58 optimal weight:    0.0870
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7758

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.182145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.132538 restraints weight = 26819.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.37
r_work: 0.3416 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7804  Z= 0.116
  Angle     :  0.490   5.420  10585  Z= 0.263
  Chirality :  0.037   0.133   1234
  Planarity :  0.003   0.044   1308
  Dihedral  :  5.410  43.860   1053
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.31 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.28), residues: 941
  helix:  0.26 (0.22), residues: 626
  sheet: -1.49 (0.81), residues: 31
  loop : -3.11 (0.32), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 262 
 TYR   0.011   0.001   TYR A  92 
 PHE   0.014   0.001   PHE A 258 
 TRP   0.007   0.001   TRP A 711 
 HIS   0.002   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7804)
  covalent geometry    : angle       0.48983 (10585)
  hydrogen bonds       : bond        0.05704 (  379)
  hydrogen bonds       : angle       3.71093 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7840 (t)
REVERT: A  771 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7948 (mm)
REVERT: A  897 ARG cc_start: 0.8314 (ttp-170) cc_final: 0.7918 (ttm-80)
REVERT: A 1123 GLU cc_start: 0.8355 (pp20) cc_final: 0.7758 (pp20)
REVERT: A 1131 MET cc_start: 0.7541 (tpp) cc_final: 0.7304 (tpp)
  outliers start: 13
  outliers final: 8
  residues processed: 86
  average time/residue: 0.1825
  time to fit residues: 21.4718
Evaluate side-chains
  85 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue 1169 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 78 optimal weight:    0.4980
   chunk 85 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.179581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.129712 restraints weight = 26971.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.33
r_work: 0.3386 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7804  Z= 0.156
  Angle     :  0.523   5.453  10585  Z= 0.283
  Chirality :  0.039   0.132   1234
  Planarity :  0.004   0.044   1308
  Dihedral  :  5.378  45.892   1053
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.67 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.28), residues: 941
  helix:  0.22 (0.22), residues: 626
  sheet: -1.37 (0.81), residues: 31
  loop : -3.12 (0.32), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 262 
 TYR   0.009   0.001   TYR A 728 
 PHE   0.015   0.001   PHE A 352 
 TRP   0.007   0.001   TRP A 711 
 HIS   0.002   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7804)
  covalent geometry    : angle       0.52316 (10585)
  hydrogen bonds       : bond        0.06415 (  379)
  hydrogen bonds       : angle       3.89040 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7876 (t)
REVERT: A  771 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7982 (mm)
REVERT: A  897 ARG cc_start: 0.8349 (ttp-170) cc_final: 0.7954 (ttm-80)
REVERT: A 1131 MET cc_start: 0.7571 (tpp) cc_final: 0.7344 (tpp)
  outliers start: 14
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1991
  time to fit residues: 23.3258
Evaluate side-chains
  87 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue 1169 GLU
Chi-restraints excluded: chain A residue 1197 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 93 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 88 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.179638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.129886 restraints weight = 27100.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.34
r_work: 0.3386 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7804  Z= 0.145
  Angle     :  0.514   5.405  10585  Z= 0.278
  Chirality :  0.038   0.131   1234
  Planarity :  0.004   0.053   1308
  Dihedral  :  5.315  46.653   1053
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.15 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.28), residues: 941
  helix:  0.28 (0.22), residues: 626
  sheet: -1.20 (0.82), residues: 31
  loop : -3.03 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 262 
 TYR   0.009   0.001   TYR A 728 
 PHE   0.017   0.001   PHE A 258 
 TRP   0.008   0.001   TRP A 711 
 HIS   0.002   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7804)
  covalent geometry    : angle       0.51409 (10585)
  hydrogen bonds       : bond        0.06304 (  379)
  hydrogen bonds       : angle       3.85801 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.8418 (ttp) cc_final: 0.8024 (tpt)
REVERT: A  267 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7905 (t)
REVERT: A  771 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7987 (mm)
  outliers start: 13
  outliers final: 9
  residues processed: 83
  average time/residue: 0.2318
  time to fit residues: 26.0606
Evaluate side-chains
  83 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue 1169 GLU
Chi-restraints excluded: chain A residue 1197 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.179219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.129920 restraints weight = 26981.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.27
r_work: 0.3388 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7804  Z= 0.145
  Angle     :  0.518   5.476  10585  Z= 0.279
  Chirality :  0.038   0.132   1234
  Planarity :  0.004   0.044   1308
  Dihedral  :  5.302  45.920   1053
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.39 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.28), residues: 941
  helix:  0.32 (0.22), residues: 626
  sheet: -0.96 (0.81), residues: 31
  loop : -3.01 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1114 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.016   0.001   PHE A 258 
 TRP   0.007   0.001   TRP A 711 
 HIS   0.002   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7804)
  covalent geometry    : angle       0.51775 (10585)
  hydrogen bonds       : bond        0.06320 (  379)
  hydrogen bonds       : angle       3.88606 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.8415 (ttp) cc_final: 0.8010 (tpt)
REVERT: A  262 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7609 (mtt-85)
REVERT: A  267 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7876 (t)
REVERT: A  771 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7973 (mm)
  outliers start: 15
  outliers final: 10
  residues processed: 84
  average time/residue: 0.2260
  time to fit residues: 25.4681
Evaluate side-chains
  82 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  978 GLN
Chi-restraints excluded: chain A residue 1169 GLU
Chi-restraints excluded: chain A residue 1197 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.178166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.129495 restraints weight = 27128.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.42
r_work: 0.3375 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7804  Z= 0.164
  Angle     :  0.534   5.395  10585  Z= 0.288
  Chirality :  0.039   0.135   1234
  Planarity :  0.004   0.044   1308
  Dihedral  :  5.408  49.118   1053
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.23 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.28), residues: 941
  helix:  0.24 (0.21), residues: 626
  sheet: -0.87 (0.81), residues: 31
  loop : -3.02 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1114 
 TYR   0.009   0.001   TYR A 728 
 PHE   0.016   0.001   PHE A 352 
 TRP   0.008   0.001   TRP A 711 
 HIS   0.002   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 7804)
  covalent geometry    : angle       0.53360 (10585)
  hydrogen bonds       : bond        0.06707 (  379)
  hydrogen bonds       : angle       3.97042 ( 1137)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7893 (t)
REVERT: A  771 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8000 (mm)
  outliers start: 12
  outliers final: 10
  residues processed: 83
  average time/residue: 0.2150
  time to fit residues: 23.9009
Evaluate side-chains
  85 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  978 GLN
Chi-restraints excluded: chain A residue 1169 GLU
Chi-restraints excluded: chain A residue 1197 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.179805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.130682 restraints weight = 27151.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.30
r_work: 0.3397 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7804  Z= 0.126
  Angle     :  0.504   5.326  10585  Z= 0.270
  Chirality :  0.038   0.132   1234
  Planarity :  0.003   0.043   1308
  Dihedral  :  5.334  52.298   1053
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.47 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.28), residues: 941
  helix:  0.43 (0.22), residues: 626
  sheet: -0.64 (0.83), residues: 31
  loop : -2.95 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 262 
 TYR   0.008   0.001   TYR A 728 
 PHE   0.014   0.001   PHE A 258 
 TRP   0.008   0.001   TRP A 711 
 HIS   0.003   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7804)
  covalent geometry    : angle       0.50367 (10585)
  hydrogen bonds       : bond        0.05993 (  379)
  hydrogen bonds       : angle       3.80643 ( 1137)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4257.60 seconds
wall clock time: 72 minutes 40.03 seconds (4360.03 seconds total)