Starting phenix.real_space_refine
on Fri Sep 11 22:37:57 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6gtc_0061/09_2026/6gtc_0061.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6gtc_0061/09_2026/6gtc_0061.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2026/6gtc_0061.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2026/6gtc_0061.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2026/6gtc_0061.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2026/6gtc_0061.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2026/6gtc_0061.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2026/6gtc_0061.cif"
  }
  resolution = 3.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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
     P      65      5.49       5
     S      22      5.16       5
     C    7423      2.51       5
     N    1994      2.21       5
     O    2427      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11931
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 10575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1280, 10575
          Classifications: {'peptide': 1280}
          Link IDs: {'PTRANS': 27, 'TRANS': 1252}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 596
          Classifications: {'RNAv2': 28}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 8, 'rna3p': 19}
    Chain: "C"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 406
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "D"
      Number of atoms: 354
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 354
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
  Time building chain proxies: 2.57, per 1000 atoms: 0.22
  Number of scatterers: 11931
  At special positions: 0
  Unit cell: (94.016, 124.8, 110.656, 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      22     16.00
     P      65     15.00
     O    2427      8.00
     N    1994      7.00
     C    7423      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: 0.68
  Conformation dependent library (CDL) restraints added in 393.6 milliseconds
  

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2454

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 13 sheets defined
      38.0% alpha, 7.7% beta
      5 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 6
      removed outlier: 3.562A  pdb=" N   GLN A   5 " --> pdb=" O   SER A   2 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   GLU A   6 " --> pdb=" O   ILE A   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2 through 6'
    Processing helix  chain 'A' and resid 26 through 35
      removed outlier: 3.850A  pdb=" N   ASN A  30 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE A  31 " --> pdb=" O   THR A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 41
      removed outlier: 3.700A  pdb=" N   GLU A  41 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 49
    Processing helix  chain 'A' and resid 50 through 64
      removed outlier: 3.799A  pdb=" N   ASP A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LYS A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ILE A  62 " --> pdb=" O   HIS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 89
      removed outlier: 3.747A  pdb=" N   TYR A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ASP A  81 " --> pdb=" O   GLN A  77 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   VAL A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS A  87 " --> pdb=" O   TYR A  83 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 107
      removed outlier: 3.724A  pdb=" N   THR A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ILE A 105 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 3.806A  pdb=" N   LYS A 114 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 128
      removed outlier: 3.749A  pdb=" N   LEU A 127 " --> pdb=" O   ASN A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 148
      removed outlier: 4.018A  pdb=" N   LYS A 146 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 170
      removed outlier: 3.555A  pdb=" N   ALA A 165 " --> pdb=" O   ASP A 161 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.580A  pdb=" N   LEU A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 223
      removed outlier: 3.663A  pdb=" N   ALA A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS A 217 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   TYR A 218 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   LEU A 221 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS A 222 " --> pdb=" O   TYR A 218 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   ASP A 223 " --> pdb=" O   GLU A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 238
      removed outlier: 3.690A  pdb=" N   ILE A 234 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   LYS A 236 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 285
      removed outlier: 3.615A  pdb=" N   ILE A 284 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 311
      removed outlier: 3.689A  pdb=" N   TYR A 303 " --> pdb=" O   GLY A 299 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASN A 305 " --> pdb=" O   ASN A 301 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   GLN A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 311 " --> pdb=" O   TYR A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 381
      removed outlier: 3.776A  pdb=" N   LEU A 374 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 408
      removed outlier: 3.635A  pdb=" N   LEU A 402 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLN A 405 " --> pdb=" O   ASP A 401 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   VAL A 406 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASP A 408 " --> pdb=" O   GLN A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 426
      removed outlier: 3.817A  pdb=" N   LEU A 418 " --> pdb=" O   GLY A 414 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ILE A 421 " --> pdb=" O   VAL A 417 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLN A 423 " --> pdb=" O   GLU A 419 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE A 425 " --> pdb=" O   ILE A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 464
      removed outlier: 4.532A  pdb=" N   GLU A 462 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   PHE A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 467
      No H-bonds generated for 'chain 'A' and resid 465 through 467'
    Processing helix  chain 'A' and resid 475 through 483
    Processing helix  chain 'A' and resid 487 through 499
      removed outlier: 3.607A  pdb=" N   GLU A 491 " --> pdb=" O   MET A 487 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ASP A 497 " --> pdb=" O   ALA A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 522
    Processing helix  chain 'A' and resid 523 through 528
      removed outlier: 3.964A  pdb=" N   ASP A 528 " --> pdb=" O   LYS A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 565
      removed outlier: 3.851A  pdb=" N   VAL A 564 " --> pdb=" O   HIS A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 580
      removed outlier: 3.851A  pdb=" N   ASN A 580 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 674
      removed outlier: 3.632A  pdb=" N   PHE A 673 " --> pdb=" O   LEU A 669 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE A 674 " --> pdb=" O   PRO A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 683
      removed outlier: 3.773A  pdb=" N   TYR A 682 " --> pdb=" O   ILE A 679 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ASN A 683 " --> pdb=" O   LYS A 680 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 679 through 683'
    Processing helix  chain 'A' and resid 685 through 695
      removed outlier: 4.812A  pdb=" N   ILE A 691 " --> pdb=" O   ASP A 687 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ARG A 692 " --> pdb=" O   ILE A 688 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN A 693 " --> pdb=" O   LEU A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 718
      removed outlier: 3.964A  pdb=" N   ARG A 718 " --> pdb=" O   GLU A 715 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 715 through 718'
    Processing helix  chain 'A' and resid 719 through 729
    Processing helix  chain 'A' and resid 743 through 747
      removed outlier: 3.792A  pdb=" N   TYR A 747 " --> pdb=" O   THR A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 758
      removed outlier: 3.663A  pdb=" N   ARG A 755 " --> pdb=" O   ASP A 751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 775
      removed outlier: 3.917A  pdb=" N   ILE A 774 " --> pdb=" O   SER A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 802 through 807
    Processing helix  chain 'A' and resid 808 through 811
    Processing helix  chain 'A' and resid 813 through 819
      removed outlier: 4.266A  pdb=" N   ASP A 819 " --> pdb=" O   ARG A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 870 through 874
    Processing helix  chain 'A' and resid 895 through 902
      removed outlier: 3.574A  pdb=" N   ASN A 901 " --> pdb=" O   ASN A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 911
      removed outlier: 4.129A  pdb=" N   GLU A 906 " --> pdb=" O   LEU A 903 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA A 908 " --> pdb=" O   LYS A 905 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   ASN A 909 " --> pdb=" O   GLU A 906 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL A 911 " --> pdb=" O   ALA A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 959
    Processing helix  chain 'A' and resid 970 through 994
      removed outlier: 3.790A  pdb=" N   ILE A 974 " --> pdb=" O   ASP A 970 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LYS A 978 " --> pdb=" O   ILE A 974 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   MET A 980 " --> pdb=" O   ASN A 976 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL A 989 " --> pdb=" O   LEU A 985 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   HIS A 990 " --> pdb=" O   SER A 986 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLU A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 999
    Processing helix  chain 'A' and resid 1021 through 1026
      removed outlier: 3.785A  pdb=" N   GLN A1025 " --> pdb=" O   LYS A1021 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LYS A1026 " --> pdb=" O   GLN A1022 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1021 through 1026'
    Processing helix  chain 'A' and resid 1064 through 1068
      removed outlier: 3.713A  pdb=" N   GLY A1068 " --> pdb=" O   LYS A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1103 through 1112
      removed outlier: 3.914A  pdb=" N   GLU A1107 " --> pdb=" O   SER A1103 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   PHE A1108 " --> pdb=" O   LYS A1104 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE A1112 " --> pdb=" O   PHE A1108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1133
      removed outlier: 3.688A  pdb=" N   ASN A1132 " --> pdb=" O   ASP A1129 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE A1133 " --> pdb=" O   TYR A1130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1129 through 1133'
    Processing helix  chain 'A' and resid 1169 through 1180
    Processing helix  chain 'A' and resid 1191 through 1198
      removed outlier: 3.530A  pdb=" N   ILE A1195 " --> pdb=" O   ILE A1191 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU A1198 " --> pdb=" O   ALA A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1200 through 1212
      removed outlier: 3.853A  pdb=" N   PHE A1204 " --> pdb=" O   ASP A1200 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   THR A1208 " --> pdb=" O   PHE A1204 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   SER A1209 " --> pdb=" O   ALA A1205 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A1210 " --> pdb=" O   LYS A1206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1242 through 1246
      removed outlier: 3.790A  pdb=" N   ALA A1246 " --> pdb=" O   SER A1243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1256 through 1275
      removed outlier: 3.779A  pdb=" N   HIS A1261 " --> pdb=" O   ASN A1257 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   ILE A1262 " --> pdb=" O   GLY A1258 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   MET A1268 " --> pdb=" O   LEU A1264 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LEU A1269 " --> pdb=" O   LYS A1265 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU A1270 " --> pdb=" O   GLY A1266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1287 through 1295
      removed outlier: 3.691A  pdb=" N   GLU A1293 " --> pdb=" O   GLU A1289 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 595 through 597
      removed outlier: 3.567A  pdb=" N   LYS A 877 " --> pdb=" O   ARG A 833 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   PHE A 878 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLU A  20 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE A 788 " --> pdb=" O   TYR A 628 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   TYR A 628 " --> pdb=" O   ILE A 788 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 595 through 597
      removed outlier: 3.567A  pdb=" N   LYS A 877 " --> pdb=" O   ARG A 833 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244
      removed outlier: 3.912A  pdb=" N   PHE A 244 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   ARG A 256 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 290
      removed outlier: 4.037A  pdb=" N   LYS A 288 " --> pdb=" O   ARG A 297 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ARG A 297 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   VAL A 290 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   THR A 295 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 394
    Processing sheet with id=AA6, first strand: chain 'A' and resid 657 through 661
      removed outlier: 3.621A  pdb=" N   THR A 765 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 841 through 843
    Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 929
      removed outlier: 7.211A  pdb=" N   LEU A 928 " --> pdb=" O   ILE A 936 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 943 through 944
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1003 through 1006
      removed outlier: 6.788A  pdb=" N   VAL A1003 " --> pdb=" O   TYR A1075 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   VAL A1077 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   PHE A1005 " --> pdb=" O   VAL A1077 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1114 through 1117
      removed outlier: 3.700A  pdb=" N   LYS A1114 " --> pdb=" O   SER A1127 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1150 through 1153
      removed outlier: 3.758A  pdb=" N   ARG A1150 " --> pdb=" O   VAL A1168 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   VAL A1168 " --> pdb=" O   ARG A1150 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ILE A1152 " --> pdb=" O   ARG A1166 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   ARG A1166 " --> pdb=" O   ILE A1152 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1219 through 1220
      removed outlier: 4.334A  pdb=" N   ASN A1219 " --> pdb=" O   TYR A1228 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR A1228 " --> pdb=" O   ASN A1219 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    231 hydrogen bonds defined for protein.
    639 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      11 hydrogen bonds
      18 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3054
        1.33 -     1.45: 2553
        1.45 -     1.57: 6533
        1.57 -     1.69: 127
        1.69 -     1.81: 35
  Bond restraints: 12302
  Sorted by residual:
  bond pdb=" C   VAL A 576 "
       pdb=" N   PRO A 577 "
    ideal  model  delta    sigma   weight residual
    1.331  1.400 -0.068 7.90e-03 1.60e+04 7.51e+01
  bond pdb=" C3'  DG C  -7 "
       pdb=" O3'  DG C  -7 "
    ideal  model  delta    sigma   weight residual
    1.435  1.485 -0.050 1.30e-02 5.92e+03 1.46e+01
  bond pdb=" C3'  DG C  -7 "
       pdb=" C2'  DG C  -7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.46e+01
  bond pdb=" C   VAL A1168 "
       pdb=" N   TYR A1169 "
    ideal  model  delta    sigma   weight residual
    1.331  1.403 -0.072 2.07e-02 2.33e+03 1.22e+01
  bond pdb=" C3'  DA C   3 "
       pdb=" C2'  DA C   3 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.00e+01
  ... (remaining 12297 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 16557
        3.20 -     6.39: 222
        6.39 -     9.59: 36
        9.59 -    12.78: 6
       12.78 -    15.98: 1
  Bond angle restraints: 16822
  Sorted by residual:
  angle pdb=" N   ILE A 105 "
        pdb=" CA  ILE A 105 "
        pdb=" C   ILE A 105 "
      ideal   model   delta    sigma   weight residual
     113.53  107.60    5.93 9.80e-01 1.04e+00 3.66e+01
  angle pdb=" N   VAL A 523 "
        pdb=" CA  VAL A 523 "
        pdb=" C   VAL A 523 "
      ideal   model   delta    sigma   weight residual
     112.96  107.00    5.96 1.00e+00 1.00e+00 3.55e+01
  angle pdb=" N   ILE A  65 "
        pdb=" CA  ILE A  65 "
        pdb=" C   ILE A  65 "
      ideal   model   delta    sigma   weight residual
     113.71  108.22    5.49 9.50e-01 1.11e+00 3.34e+01
  angle pdb=" C   LYS A 869 "
        pdb=" N   ASP A 870 "
        pdb=" CA  ASP A 870 "
      ideal   model   delta    sigma   weight residual
     121.54  131.17   -9.63 1.91e+00 2.74e-01 2.54e+01
  angle pdb=" N   ILE A 913 "
        pdb=" CA  ILE A 913 "
        pdb=" C   ILE A 913 "
      ideal   model   delta    sigma   weight residual
     108.93  115.48   -6.55 1.35e+00 5.49e-01 2.36e+01
  ... (remaining 16817 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.06: 6736
       25.06 -    50.11: 447
       50.11 -    75.17: 112
       75.17 -   100.23: 9
      100.23 -   125.28: 1
  Dihedral angle restraints: 7305
    sinusoidal: 3508
      harmonic: 3797
  Sorted by residual:
  dihedral pdb=" C4'   A B -18 "
           pdb=" C3'   A B -18 "
           pdb=" C2'   A B -18 "
           pdb=" C1'   A B -18 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -35.94   72.29     1      3.10e+00 1.04e-01 6.95e+02
  dihedral pdb=" C4'   U B  -7 "
           pdb=" C3'   U B  -7 "
           pdb=" C2'   U B  -7 "
           pdb=" C1'   U B  -7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -35.22   71.57     1      3.10e+00 1.04e-01 6.83e+02
  dihedral pdb=" C4'   U B -10 "
           pdb=" C3'   U B -10 "
           pdb=" C2'   U B -10 "
           pdb=" C1'   U B -10 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -35.13   71.47     1      3.10e+00 1.04e-01 6.82e+02
  ... (remaining 7302 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1690
       0.105 -    0.210: 90
       0.210 -    0.315: 46
       0.315 -    0.420: 1
       0.420 -    0.525: 1
  Chirality restraints: 1828
  Sorted by residual:
  chirality pdb=" CB  ILE A1002 "
            pdb=" CA  ILE A1002 "
            pdb=" CG1 ILE A1002 "
            pdb=" CG2 ILE A1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.12    0.52 2.00e-01 2.50e+01 6.88e+00
  chirality pdb=" CB  ILE A1074 "
            pdb=" CA  ILE A1074 "
            pdb=" CG1 ILE A1074 "
            pdb=" CG2 ILE A1074 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.41 2.00e-01 2.50e+01 4.22e+00
  chirality pdb=" C2'   G B   0 "
            pdb=" C3'   G B   0 "
            pdb=" O2'   G B   0 "
            pdb=" C1'   G B   0 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.50   -0.29 2.00e-01 2.50e+01 2.14e+00
  ... (remaining 1825 not shown)

  Planarity restraints: 1925
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 614 "    0.060 5.00e-02 4.00e+02   9.01e-02 1.30e+01
        pdb=" N   PRO A 615 "   -0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO A 615 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 615 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 669 "   -0.054 5.00e-02 4.00e+02   8.24e-02 1.09e+01
        pdb=" N   PRO A 670 "    0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 670 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 670 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 272 "    0.016 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" C   TYR A 272 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   TYR A 272 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 273 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1922 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3158
        2.80 -     3.32: 10135
        3.32 -     3.85: 19859
        3.85 -     4.37: 23088
        4.37 -     4.90: 37513
  Nonbonded interactions: 93753
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 825 "
            pdb=" OG1 THR A 885 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OH  TYR A  83 "
            pdb=" O   PRO A 209 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   PHE A 941 "
            pdb=" OH  TYR A 984 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OH  TYR A 392 "
            pdb=" OD1 ASP A 556 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   LEU A 418 "
            pdb=" OG1 THR A 422 "
     model   vdw
     2.316 3.040
  ... (remaining 93748 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.780
  Find NCS groups from input model:        0.040
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
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   0.072  12302  Z= 0.290
  Angle     :  0.994  15.978  16822  Z= 0.557
  Chirality :  0.067   0.525   1828
  Planarity :  0.006   0.090   1925
  Dihedral  : 16.671 125.283   4851
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.73 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.69 (0.16), residues: 1272
  helix: -4.79 (0.08), residues: 474
  sheet: -2.79 (0.51), residues: 95
  loop : -3.23 (0.18), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 833 
 TYR   0.021   0.002   TYR A 272 
 PHE   0.027   0.002   PHE A 258 
 TRP   0.036   0.003   TRP A 971 
 HIS   0.008   0.002   HIS A 544 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00462 /  0.29 (12302)
  covalent geometry    : angle       0.99377 /  0.56 (16822)
  hydrogen bonds       : bond        0.34175 / 21.81 (  235)
  hydrogen bonds       : angle      11.30654 /  7.66 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 259
  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  688 ILE cc_start: 0.7326 (mp) cc_final: 0.6581 (mm)
REVERT: A  920 GLU cc_start: 0.4849 (mt-10) cc_final: 0.4202 (mt-10)
REVERT: A 1027 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8049 (tt)
  outliers start: 10
  outliers final: 0
  residues processed: 268
  average time/residue: 0.1158
  time to fit residues: 43.2894
Evaluate side-chains
  149 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1027 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    0.0070
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.6602

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  58 HIS
A  77 GLN
A  78 ASN
A 126 ASN
** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 395 ASN
A 538 HIS
A 580 ASN
A 588 GLN
A 612 ASN
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 790 ASN
A 843 HIS
** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 853 ASN
** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 912 HIS
** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.177946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.146078 restraints weight = 16517.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.145325 restraints weight = 17859.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.148011 restraints weight = 16689.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.147888 restraints weight = 12146.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.148124 restraints weight = 12083.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12302  Z= 0.194
  Angle     :  0.976  22.879  16822  Z= 0.463
  Chirality :  0.079   1.126   1828
  Planarity :  0.005   0.072   1925
  Dihedral  : 18.276 135.374   2113
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 12.63 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.04 (0.18), residues: 1272
  helix: -3.89 (0.13), residues: 501
  sheet: -2.74 (0.48), residues: 108
  loop : -3.01 (0.20), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 918 
 TYR   0.018   0.002   TYR A  11 
 PHE   0.020   0.002   PHE A 888 
 TRP   0.016   0.002   TRP A 971 
 HIS   0.008   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.19 (12302)
  covalent geometry    : angle       0.97558 /  0.46 (16822)
  hydrogen bonds       : bond        0.06403 /  3.99 (  235)
  hydrogen bonds       : angle       6.97670 /  4.56 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 157
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.6577 (mtmt) cc_final: 0.6366 (mtmt)
REVERT: A  294 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7925 (t0)
REVERT: A  388 LEU cc_start: 0.8444 (tp) cc_final: 0.8044 (tp)
REVERT: A  688 ILE cc_start: 0.7525 (mp) cc_final: 0.6843 (mm)
REVERT: A 1217 MET cc_start: 0.5391 (mmp) cc_final: 0.5061 (mmt)
REVERT: A 1221 LYS cc_start: 0.5920 (tptp) cc_final: 0.5545 (tptp)
  outliers start: 33
  outliers final: 14
  residues processed: 183
  average time/residue: 0.1021
  time to fit residues: 26.7732
Evaluate side-chains
  153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1207 LEU
Chi-restraints excluded: chain A residue 1214 ILE
Chi-restraints excluded: chain A residue 1230 ILE
Chi-restraints excluded: chain A residue 1295 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 69 optimal weight:    9.9990
   chunk 120 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 86 optimal weight:    0.7980
   chunk 96 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 24 optimal weight:    8.9990
   chunk 121 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 538 HIS
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 790 ASN
A 851 ASN
** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.175227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.144344 restraints weight = 16700.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.143408 restraints weight = 19392.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.145916 restraints weight = 17876.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.145747 restraints weight = 13142.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.145901 restraints weight = 12494.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  12302  Z= 0.187
  Angle     :  0.841  20.089  16822  Z= 0.407
  Chirality :  0.060   0.555   1828
  Planarity :  0.005   0.072   1925
  Dihedral  : 18.654 146.924   2111
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.00 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -4.58 (0.19), residues: 1272
  helix: -3.31 (0.17), residues: 508
  sheet: -2.63 (0.48), residues: 108
  loop : -2.89 (0.21), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1166 
 TYR   0.023   0.002   TYR A  47 
 PHE   0.027   0.002   PHE A 182 
 TRP   0.009   0.002   TRP A1163 
 HIS   0.005   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.19 (12302)
  covalent geometry    : angle       0.84080 /  0.41 (16822)
  hydrogen bonds       : bond        0.05587 /  3.69 (  235)
  hydrogen bonds       : angle       6.27769 /  4.09 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 145
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.6384 (mtmt) cc_final: 0.6108 (ttmt)
REVERT: A  162 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7228 (pp)
REVERT: A  294 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7860 (t0)
REVERT: A  311 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6494 (mp)
REVERT: A  388 LEU cc_start: 0.8415 (tp) cc_final: 0.7941 (tp)
REVERT: A  581 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8752 (ttmm)
REVERT: A  646 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6413 (mt)
REVERT: A  688 ILE cc_start: 0.7521 (mp) cc_final: 0.6736 (mm)
REVERT: A  785 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7099 (tt)
  outliers start: 40
  outliers final: 22
  residues processed: 172
  average time/residue: 0.1035
  time to fit residues: 25.8570
Evaluate side-chains
  158 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  851 ASN
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1207 LEU
Chi-restraints excluded: chain A residue 1214 ILE
Chi-restraints excluded: chain A residue 1230 ILE
Chi-restraints excluded: chain A residue 1237 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 42 optimal weight:    0.0010
   chunk 109 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 62 optimal weight:    0.3980
   chunk 49 optimal weight:    4.9990
   chunk 116 optimal weight:    0.0270
   chunk 118 optimal weight:    6.9990
   chunk 6 optimal weight:    0.2980
   chunk 21 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.3446

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 ASN
A 538 HIS
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 851 ASN
** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.179362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.148651 restraints weight = 16400.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.147269 restraints weight = 18680.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.148596 restraints weight = 17315.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.148817 restraints weight = 13528.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.149154 restraints weight = 12069.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12302  Z= 0.128
  Angle     :  0.759  14.359  16822  Z= 0.371
  Chirality :  0.054   0.412   1828
  Planarity :  0.004   0.067   1925
  Dihedral  : 18.700 145.145   2111
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.03 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -4.20 (0.20), residues: 1272
  helix: -2.97 (0.18), residues: 519
  sheet: -2.40 (0.52), residues: 97
  loop : -2.68 (0.21), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1166 
 TYR   0.021   0.001   TYR A  47 
 PHE   0.028   0.001   PHE A 941 
 TRP   0.012   0.001   TRP A 609 
 HIS   0.006   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.13 (12302)
  covalent geometry    : angle       0.75862 /  0.37 (16822)
  hydrogen bonds       : bond        0.04986 /  3.46 (  235)
  hydrogen bonds       : angle       5.84711 /  3.78 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7827 (t0)
REVERT: A  311 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6571 (mp)
REVERT: A  388 LEU cc_start: 0.8392 (tp) cc_final: 0.7889 (tp)
REVERT: A  688 ILE cc_start: 0.7568 (mp) cc_final: 0.7337 (mt)
REVERT: A 1023 VAL cc_start: 0.8545 (t) cc_final: 0.8286 (t)
  outliers start: 39
  outliers final: 16
  residues processed: 178
  average time/residue: 0.0968
  time to fit residues: 25.3326
Evaluate side-chains
  152 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  882 CYS
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain A residue 1035 LEU
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1226 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 131 optimal weight:   30.0000
   chunk 96 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 120 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 887 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 = 0.4251 r_free = 0.4251 target = 0.178330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.146754 restraints weight = 16405.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.145801 restraints weight = 19501.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.149162 restraints weight = 17642.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.148690 restraints weight = 12049.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.149032 restraints weight = 11913.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12302  Z= 0.139
  Angle     :  0.751  12.845  16822  Z= 0.365
  Chirality :  0.054   0.520   1828
  Planarity :  0.004   0.067   1925
  Dihedral  : 18.769 145.816   2111
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.46 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.81 (0.21), residues: 1272
  helix: -2.62 (0.19), residues: 514
  sheet: -2.12 (0.55), residues: 97
  loop : -2.51 (0.21), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 202 
 TYR   0.022   0.001   TYR A  47 
 PHE   0.025   0.001   PHE A 941 
 TRP   0.010   0.001   TRP A1163 
 HIS   0.012   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 (12302)
  covalent geometry    : angle       0.75053 /  0.37 (16822)
  hydrogen bonds       : bond        0.04851 /  3.34 (  235)
  hydrogen bonds       : angle       5.61384 /  3.64 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 138
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7808 (t0)
REVERT: A  311 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6541 (mp)
REVERT: A  345 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.5836 (t0)
REVERT: A  388 LEU cc_start: 0.8427 (tp) cc_final: 0.7943 (tp)
REVERT: A  646 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6712 (mt)
REVERT: A  688 ILE cc_start: 0.7539 (mp) cc_final: 0.7313 (mt)
REVERT: A  689 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7501 (tp)
REVERT: A  785 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7003 (tt)
REVERT: A  789 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7225 (p90)
REVERT: A  949 MET cc_start: 0.6718 (mmm) cc_final: 0.6308 (ttt)
  outliers start: 39
  outliers final: 22
  residues processed: 163
  average time/residue: 0.1065
  time to fit residues: 25.2883
Evaluate side-chains
  157 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  882 CYS
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1214 ILE
Chi-restraints excluded: chain A residue 1217 MET
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1237 ASN
Chi-restraints excluded: chain A residue 1267 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 127 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 11 optimal weight:    0.2980
   chunk 60 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0370
   chunk 107 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.5058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 HIS
A 731 HIS
** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.180264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.148118 restraints weight = 16419.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.148332 restraints weight = 18252.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.149485 restraints weight = 17598.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.149950 restraints weight = 13740.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.149885 restraints weight = 13690.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12302  Z= 0.122
  Angle     :  0.705  12.217  16822  Z= 0.346
  Chirality :  0.052   0.488   1828
  Planarity :  0.004   0.064   1925
  Dihedral  : 18.779 145.629   2111
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.98 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.49 (0.21), residues: 1272
  helix: -2.35 (0.20), residues: 513
  sheet: -1.73 (0.58), residues: 95
  loop : -2.37 (0.22), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1150 
 TYR   0.017   0.001   TYR A  47 
 PHE   0.020   0.001   PHE A1294 
 TRP   0.011   0.001   TRP A1163 
 HIS   0.010   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 (12302)
  covalent geometry    : angle       0.70516 /  0.35 (16822)
  hydrogen bonds       : bond        0.04956 /  3.47 (  235)
  hydrogen bonds       : angle       5.33321 /  3.46 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 132
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6989 (tt0)
REVERT: A  294 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7692 (t0)
REVERT: A  311 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6598 (mp)
REVERT: A  345 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.5687 (t0)
REVERT: A  388 LEU cc_start: 0.8445 (tp) cc_final: 0.7988 (tp)
REVERT: A  688 ILE cc_start: 0.7580 (mp) cc_final: 0.7332 (mt)
REVERT: A  689 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7543 (tp)
REVERT: A  789 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.7297 (p90)
REVERT: A  949 MET cc_start: 0.6785 (mmm) cc_final: 0.6260 (ttt)
REVERT: A  964 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.5454 (pmt100)
REVERT: A 1066 LYS cc_start: 0.7364 (mtpm) cc_final: 0.6640 (mptt)
  outliers start: 38
  outliers final: 20
  residues processed: 156
  average time/residue: 0.0951
  time to fit residues: 21.8390
Evaluate side-chains
  156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  882 CYS
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  964 ARG
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1214 ILE
Chi-restraints excluded: chain A residue 1217 MET
Chi-restraints excluded: chain A residue 1237 ASN
Chi-restraints excluded: chain A residue 1262 ILE
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1295 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   chunk 116 optimal weight:    6.9990
   chunk 125 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 130 optimal weight:   30.0000
   chunk 66 optimal weight:    0.0050
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.7398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 856 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 = 0.4225 r_free = 0.4225 target = 0.176028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.144275 restraints weight = 16665.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.143029 restraints weight = 19377.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145805 restraints weight = 17776.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.145559 restraints weight = 13022.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145837 restraints weight = 12636.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  12302  Z= 0.166
  Angle     :  0.728  12.114  16822  Z= 0.356
  Chirality :  0.054   0.500   1828
  Planarity :  0.004   0.064   1925
  Dihedral  : 18.801 149.865   2111
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.98 %
    Favored  : 80.33 %
  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: -3.35 (0.22), residues: 1272
  helix: -2.21 (0.21), residues: 517
  sheet: -1.71 (0.58), residues: 95
  loop : -2.29 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 202 
 TYR   0.021   0.002   TYR A  11 
 PHE   0.018   0.002   PHE A 407 
 TRP   0.009   0.002   TRP A1163 
 HIS   0.010   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.17 (12302)
  covalent geometry    : angle       0.72836 /  0.36 (16822)
  hydrogen bonds       : bond        0.04595 /  3.19 (  235)
  hydrogen bonds       : angle       5.21746 /  3.40 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 138
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6992 (tt0)
REVERT: A  294 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7788 (t0)
REVERT: A  311 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6610 (mp)
REVERT: A  345 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.5945 (t0)
REVERT: A  388 LEU cc_start: 0.8478 (tp) cc_final: 0.8009 (tp)
REVERT: A  688 ILE cc_start: 0.7603 (mp) cc_final: 0.7384 (mt)
REVERT: A  689 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7522 (tp)
REVERT: A  785 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6975 (tt)
REVERT: A  789 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7276 (p90)
REVERT: A  949 MET cc_start: 0.6779 (mmm) cc_final: 0.6416 (ttt)
REVERT: A  964 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5518 (pmt100)
REVERT: A 1066 LYS cc_start: 0.7255 (mtpm) cc_final: 0.6608 (mptt)
  outliers start: 43
  outliers final: 26
  residues processed: 165
  average time/residue: 0.0980
  time to fit residues: 23.4995
Evaluate side-chains
  164 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   47 TYR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  882 CYS
Chi-restraints excluded: chain A residue  890 SER
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  964 ARG
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain A residue 1052 LEU
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1230 ILE
Chi-restraints excluded: chain A residue 1237 ASN
Chi-restraints excluded: chain A residue 1267 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 78 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 132 optimal weight:   40.0000
   chunk 79 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 124 optimal weight:    0.0870
   chunk 80 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 130 optimal weight:   30.0000
   overall best weight:    0.8960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1000 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 = 0.4251 r_free = 0.4251 target = 0.178523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.147642 restraints weight = 16323.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.147048 restraints weight = 20736.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.150780 restraints weight = 16642.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.150561 restraints weight = 11672.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.150424 restraints weight = 11956.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12302  Z= 0.127
  Angle     :  0.717  23.610  16822  Z= 0.345
  Chirality :  0.052   0.489   1828
  Planarity :  0.004   0.066   1925
  Dihedral  : 18.781 149.946   2111
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 16.84 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.22), residues: 1272
  helix: -2.07 (0.21), residues: 510
  sheet: -1.52 (0.59), residues: 95
  loop : -2.18 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 202 
 TYR   0.021   0.001   TYR A  11 
 PHE   0.018   0.001   PHE A 888 
 TRP   0.012   0.001   TRP A1163 
 HIS   0.010   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.13 (12302)
  covalent geometry    : angle       0.71728 /  0.34 (16822)
  hydrogen bonds       : bond        0.04666 /  3.27 (  235)
  hydrogen bonds       : angle       5.10432 /  3.34 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6954 (tt0)
REVERT: A  294 ASN cc_start: 0.7966 (t0) cc_final: 0.7739 (t0)
REVERT: A  311 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6576 (mp)
REVERT: A  345 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.5815 (t0)
REVERT: A  388 LEU cc_start: 0.8427 (tp) cc_final: 0.7974 (tp)
REVERT: A  570 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.6196 (m-80)
REVERT: A  688 ILE cc_start: 0.7545 (mp) cc_final: 0.7334 (mt)
REVERT: A  689 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7531 (tp)
REVERT: A  785 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7011 (tt)
REVERT: A  789 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.7212 (p90)
REVERT: A  964 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.5492 (pmt100)
REVERT: A 1066 LYS cc_start: 0.7203 (mtpm) cc_final: 0.6581 (mptt)
  outliers start: 37
  outliers final: 24
  residues processed: 153
  average time/residue: 0.0928
  time to fit residues: 20.8038
Evaluate side-chains
  153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   47 TYR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  570 PHE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  882 CYS
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  964 ARG
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain A residue 1052 LEU
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1230 ILE
Chi-restraints excluded: chain A residue 1237 ASN
Chi-restraints excluded: chain A residue 1267 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0170
   chunk 28 optimal weight:    0.7980
   chunk 29 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 856 ASN
** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.179928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.150019 restraints weight = 16397.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.148477 restraints weight = 15855.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.149220 restraints weight = 15510.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.149540 restraints weight = 13680.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.149795 restraints weight = 12167.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12302  Z= 0.121
  Angle     :  0.696  20.363  16822  Z= 0.338
  Chirality :  0.051   0.483   1828
  Planarity :  0.004   0.062   1925
  Dihedral  : 18.764 149.968   2111
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.35 %
    Favored  : 79.47 %
  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 are not related in a simple way.
  whole: -3.01 (0.22), residues: 1272
  helix: -1.92 (0.22), residues: 510
  sheet: -1.37 (0.60), residues: 95
  loop : -2.15 (0.23), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 948 
 TYR   0.020   0.001   TYR A  11 
 PHE   0.021   0.001   PHE A1128 
 TRP   0.013   0.001   TRP A1163 
 HIS   0.010   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 (12302)
  covalent geometry    : angle       0.69630 /  0.34 (16822)
  hydrogen bonds       : bond        0.04763 /  3.35 (  235)
  hydrogen bonds       : angle       4.97562 /  3.28 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 130
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 ASN cc_start: 0.7997 (t0) cc_final: 0.7774 (t0)
REVERT: A  311 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6617 (mp)
REVERT: A  345 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.5806 (t0)
REVERT: A  388 LEU cc_start: 0.8423 (tp) cc_final: 0.7928 (tp)
REVERT: A  401 ASP cc_start: 0.6773 (t70) cc_final: 0.6508 (m-30)
REVERT: A  570 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.6116 (m-80)
REVERT: A  688 ILE cc_start: 0.7524 (mp) cc_final: 0.7315 (mt)
REVERT: A  689 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7457 (mt)
REVERT: A  785 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6911 (tt)
REVERT: A  789 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.7160 (p90)
REVERT: A  964 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.5514 (ppt170)
REVERT: A 1066 LYS cc_start: 0.7211 (mtpm) cc_final: 0.6610 (mptt)
  outliers start: 37
  outliers final: 24
  residues processed: 155
  average time/residue: 0.0981
  time to fit residues: 22.2849
Evaluate side-chains
  154 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   47 TYR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  570 PHE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  882 CYS
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  964 ARG
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain A residue 1052 LEU
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1230 ILE
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 128 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    2.3188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1000 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 = 0.4219 r_free = 0.4219 target = 0.175334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.144232 restraints weight = 16896.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.143515 restraints weight = 18926.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.144510 restraints weight = 17188.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.144704 restraints weight = 14194.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.145100 restraints weight = 13802.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12302  Z= 0.192
  Angle     :  0.760  20.220  16822  Z= 0.369
  Chirality :  0.054   0.457   1828
  Planarity :  0.004   0.064   1925
  Dihedral  : 18.773 152.538   2111
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.53 %
    Favored  : 79.21 %
  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: -3.00 (0.22), residues: 1272
  helix: -1.93 (0.22), residues: 509
  sheet: -1.51 (0.59), residues: 95
  loop : -2.10 (0.23), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  18 
 TYR   0.023   0.002   TYR A  11 
 PHE   0.020   0.002   PHE A1128 
 TRP   0.016   0.002   TRP A 609 
 HIS   0.010   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.19 (12302)
  covalent geometry    : angle       0.76001 /  0.37 (16822)
  hydrogen bonds       : bond        0.04574 /  3.17 (  235)
  hydrogen bonds       : angle       5.00485 /  3.31 (  657)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 125
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.7273 (t80) cc_final: 0.7014 (t80)
REVERT: A  294 ASN cc_start: 0.8047 (t0) cc_final: 0.7819 (t0)
REVERT: A  311 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6591 (mp)
REVERT: A  345 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.5887 (t0)
REVERT: A  388 LEU cc_start: 0.8528 (tp) cc_final: 0.8046 (tp)
REVERT: A  401 ASP cc_start: 0.6919 (t70) cc_final: 0.6629 (m-30)
REVERT: A  689 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7442 (mt)
REVERT: A  785 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6936 (tt)
REVERT: A  789 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.7258 (p90)
REVERT: A  964 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.5518 (ppt170)
REVERT: A 1066 LYS cc_start: 0.7359 (mtpm) cc_final: 0.6744 (mptt)
  outliers start: 38
  outliers final: 29
  residues processed: 150
  average time/residue: 0.0969
  time to fit residues: 21.6036
Evaluate side-chains
  158 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   47 TYR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  882 CYS
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  964 ARG
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain A residue 1052 LEU
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1230 ILE
Chi-restraints excluded: chain A residue 1237 ASN
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 128 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0670
   chunk 111 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 115 optimal weight:    8.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.6122

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1000 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 = 0.4226 r_free = 0.4226 target = 0.175948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.144869 restraints weight = 16704.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.144929 restraints weight = 21778.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.145933 restraints weight = 18612.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.146267 restraints weight = 15286.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.147009 restraints weight = 13976.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12302  Z= 0.156
  Angle     :  0.734  20.128  16822  Z= 0.356
  Chirality :  0.053   0.450   1828
  Planarity :  0.004   0.067   1925
  Dihedral  : 18.802 152.392   2111
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.13 %
    Favored  : 78.87 %
  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: -2.97 (0.22), residues: 1272
  helix: -1.83 (0.22), residues: 515
  sheet: -1.52 (0.55), residues: 109
  loop : -2.15 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 202 
 TYR   0.022   0.001   TYR A  11 
 PHE   0.029   0.002   PHE A 710 
 TRP   0.013   0.002   TRP A1163 
 HIS   0.011   0.001   HIS A 990 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 (12302)
  covalent geometry    : angle       0.73423 /  0.36 (16822)
  hydrogen bonds       : bond        0.04424 /  3.08 (  235)
  hydrogen bonds       : angle       4.96690 /  3.27 (  657)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1745.20 seconds
wall clock time: 31 minutes 29.07 seconds (1889.07 seconds total)