Starting phenix.real_space_refine
on Wed Mar  4 18:35:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rze_24757/03_2026/7rze_24757.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rze_24757/03_2026/7rze_24757.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rze_24757/03_2026/7rze_24757.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rze_24757/03_2026/7rze_24757.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rze_24757/03_2026/7rze_24757.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rze_24757/03_2026/7rze_24757.map"
  }
  resolution = 3.3
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C   10017      2.51       5
     N    2606      2.21       5
     O    2878      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15545
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 947, 7749
          Classifications: {'peptide': 947}
          Link IDs: {'PTRANS': 51, 'TRANS': 895}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 7704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 940, 7704
          Classifications: {'peptide': 940}
          Link IDs: {'PTRANS': 49, 'TRANS': 890}
          Chain breaks: 1
    Chain: "a"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 66
          Classifications: {'peptide': 8}
          Link IDs: {'TRANS': 7}
    Chain: "b"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 26
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
  Time building chain proxies: 3.71, per 1000 atoms: 0.24
  Number of scatterers: 15545
  At special positions: 0
  Unit cell: (113.841, 124.683, 147.451, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    2878      8.00
     N    2606      7.00
     C   10017      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.30
  Conformation dependent library (CDL) restraints added in 784.6 milliseconds
  

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3620

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 12 sheets defined
      45.6% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 3.614A  pdb=" N   SER A  98 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASP A  99 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 95 through 99'
    Processing helix  chain 'A' and resid 105 through 115
      removed outlier: 3.874A  pdb=" N   PHE A 115 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 133
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 4.447A  pdb=" N   ARG A 164 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   PHE A 168 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 193
      removed outlier: 4.224A  pdb=" N   VAL A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   ASN A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   ALA A 185 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASN A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 208
      removed outlier: 3.548A  pdb=" N   THR A 208 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 233
    Processing helix  chain 'A' and resid 237 through 249
    Processing helix  chain 'A' and resid 267 through 273
      removed outlier: 3.740A  pdb=" N   LYS A 273 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 298
      removed outlier: 3.533A  pdb=" N   LEU A 298 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 339
    Processing helix  chain 'A' and resid 345 through 353
      removed outlier: 3.744A  pdb=" N   LEU A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 403
    Processing helix  chain 'A' and resid 407 through 424
      removed outlier: 3.699A  pdb=" N   PHE A 411 " --> pdb=" O   GLN A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 440
      removed outlier: 3.622A  pdb=" N   TYR A 433 " --> pdb=" O   ARG A 429 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   THR A 434 " --> pdb=" O   PRO A 430 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   SER A 435 " --> pdb=" O   ARG A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 470
      removed outlier: 3.848A  pdb=" N   ILE A 464 " --> pdb=" O   ARG A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 514
      removed outlier: 4.128A  pdb=" N   ILE A 510 " --> pdb=" O   PRO A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 615
      removed outlier: 4.030A  pdb=" N   ALA A 593 " --> pdb=" O   HIS A 589 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   TYR A 594 " --> pdb=" O   SER A 590 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   GLU A 606 " --> pdb=" O   ASP A 602 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   TYR A 607 " --> pdb=" O   SER A 603 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   ALA A 610 " --> pdb=" O   GLU A 606 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   ALA A 611 " --> pdb=" O   TYR A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 651
      removed outlier: 3.752A  pdb=" N   LEU A 641 " --> pdb=" O   LYS A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 671
      removed outlier: 3.844A  pdb=" N   GLU A 664 " --> pdb=" O   GLU A 660 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER A 669 " --> pdb=" O   ALA A 665 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASN A 671 " --> pdb=" O   MET A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 674
      No H-bonds generated for 'chain 'A' and resid 672 through 674'
    Processing helix  chain 'A' and resid 677 through 690
    Processing helix  chain 'A' and resid 696 through 701
      removed outlier: 3.703A  pdb=" N   LEU A 700 " --> pdb=" O   THR A 696 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS A 701 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 696 through 701'
    Processing helix  chain 'A' and resid 708 through 714
    Processing helix  chain 'A' and resid 715 through 720
    Processing helix  chain 'A' and resid 734 through 754
    Processing helix  chain 'A' and resid 759 through 763
      removed outlier: 3.725A  pdb=" N   LEU A 763 " --> pdb=" O   PRO A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 815
      removed outlier: 3.813A  pdb=" N   LEU A 808 " --> pdb=" O   GLU A 804 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 815 " --> pdb=" O   PHE A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 824
      removed outlier: 3.858A  pdb=" N   PHE A 820 " --> pdb=" O   SER A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 877
      removed outlier: 3.542A  pdb=" N   LEU A 859 " --> pdb=" O   PRO A 855 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET A 877 " --> pdb=" O   SER A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 893
    Processing helix  chain 'A' and resid 899 through 912
      removed outlier: 3.558A  pdb=" N   GLU A 903 " --> pdb=" O   LYS A 899 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LYS A 906 " --> pdb=" O   ALA A 902 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY A 909 " --> pdb=" O   ALA A 905 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   GLU A 910 " --> pdb=" O   LYS A 906 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 929
    Processing helix  chain 'A' and resid 932 through 944
      removed outlier: 3.501A  pdb=" N   ILE A 936 " --> pdb=" O   THR A 932 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLU A 942 " --> pdb=" O   LYS A 938 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   MET A 943 " --> pdb=" O   PHE A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1001
      removed outlier: 3.618A  pdb=" N   PHE A 998 " --> pdb=" O   ASN A 994 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY A1001 " --> pdb=" O   GLU A 997 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 99
      removed outlier: 3.768A  pdb=" N   ASP B  99 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 114
      removed outlier: 3.640A  pdb=" N   PHE B 109 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 134
    Processing helix  chain 'B' and resid 157 through 164
    Processing helix  chain 'B' and resid 166 through 171
      removed outlier: 3.851A  pdb=" N   LEU B 170 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 193
      removed outlier: 4.229A  pdb=" N   ASN B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 208
      removed outlier: 3.593A  pdb=" N   THR B 208 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 222 through 228
    Processing helix  chain 'B' and resid 228 through 233
      removed outlier: 3.579A  pdb=" N   GLN B 232 " --> pdb=" O   THR B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 249
      removed outlier: 3.589A  pdb=" N   GLU B 240 " --> pdb=" O   ASP B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 275
      removed outlier: 3.746A  pdb=" N   LYS B 273 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU B 274 " --> pdb=" O   LEU B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 339
    Processing helix  chain 'B' and resid 345 through 353
    Processing helix  chain 'B' and resid 380 through 386
      removed outlier: 4.148A  pdb=" N   LEU B 385 " --> pdb=" O   GLU B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 405
    Processing helix  chain 'B' and resid 408 through 424
    Processing helix  chain 'B' and resid 429 through 440
      removed outlier: 3.718A  pdb=" N   TYR B 433 " --> pdb=" O   ARG B 429 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   THR B 434 " --> pdb=" O   PRO B 430 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   SER B 435 " --> pdb=" O   ARG B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 471
    Processing helix  chain 'B' and resid 506 through 515
      removed outlier: 3.580A  pdb=" N   ILE B 510 " --> pdb=" O   PRO B 506 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   TRP B 513 " --> pdb=" O   VAL B 509 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ASN B 515 " --> pdb=" O   LYS B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 581 through 584
      removed outlier: 3.993A  pdb=" N   TYR B 584 " --> pdb=" O   PRO B 581 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 581 through 584'
    Processing helix  chain 'B' and resid 586 through 614
      removed outlier: 5.014A  pdb=" N   GLU B 606 " --> pdb=" O   ASP B 602 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   TYR B 607 " --> pdb=" O   SER B 603 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   ALA B 610 " --> pdb=" O   GLU B 606 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ALA B 611 " --> pdb=" O   TYR B 607 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA B 614 " --> pdb=" O   ALA B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 651
    Processing helix  chain 'B' and resid 655 through 672
    Processing helix  chain 'B' and resid 673 through 676
      removed outlier: 4.102A  pdb=" N   GLU B 676 " --> pdb=" O   PHE B 673 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 673 through 676'
    Processing helix  chain 'B' and resid 677 through 690
    Processing helix  chain 'B' and resid 696 through 705
      removed outlier: 4.426A  pdb=" N   ASP B 705 " --> pdb=" O   LYS B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 722
      removed outlier: 3.651A  pdb=" N   LEU B 712 " --> pdb=" O   THR B 708 " (cutoff:3.500A)
      Proline residue:  B 717  - end of helix
      removed outlier: 4.398A  pdb=" N   ARG B 722 " --> pdb=" O   GLN B 718 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 734 through 754
    Processing helix  chain 'B' and resid 801 through 815
      removed outlier: 3.947A  pdb=" N   MET B 806 " --> pdb=" O   THR B 802 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 815 through 823
      removed outlier: 3.560A  pdb=" N   ALA B 819 " --> pdb=" O   ILE B 815 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 855 through 876
      removed outlier: 3.781A  pdb=" N   GLU B 875 " --> pdb=" O   GLU B 871 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 878 through 894
      removed outlier: 3.627A  pdb=" N   PHE B 882 " --> pdb=" O   THR B 878 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 899 through 912
    Processing helix  chain 'B' and resid 919 through 929
    Processing helix  chain 'B' and resid 932 through 944
      removed outlier: 3.512A  pdb=" N   ILE B 936 " --> pdb=" O   THR B 932 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 994 through 1001
      removed outlier: 3.962A  pdb=" N   GLY B1001 " --> pdb=" O   GLU B 997 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50
      removed outlier: 4.073A  pdb=" N   ARG A  49 " --> pdb=" O   GLU A  68 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   LYS A  74 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   VAL A 258 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LEU A  76 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   GLY A 260 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   ILE A  78 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL A 257 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER A  87 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A  88 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER A 137 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 360
      removed outlier: 4.842A  pdb=" N   THR A 358 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   ARG A 311 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 492
    Processing sheet with id=AA4, first strand: chain 'A' and resid 557 through 558
      removed outlier: 6.359A  pdb=" N   LYS A 558 " --> pdb=" O   ALA A 727 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   LEU A 729 " --> pdb=" O   LYS A 558 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 557 through 558
      removed outlier: 6.359A  pdb=" N   LYS A 558 " --> pdb=" O   ALA A 727 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   LEU A 729 " --> pdb=" O   LYS A 558 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   HIS A 724 " --> pdb=" O   PHE A 579 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 840
      removed outlier: 4.411A  pdb=" N   ILE A 832 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLN A 851 " --> pdb=" O   ILE A 832 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A 840 " --> pdb=" O   ILE A 843 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   GLN A 844 " --> pdb=" O   THR A 797 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 69
      removed outlier: 5.981A  pdb=" N   LYS B  74 " --> pdb=" O   VAL B 256 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   VAL B 258 " --> pdb=" O   LYS B  74 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   LEU B  76 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   GLY B 260 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   ILE B  78 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ASP B  91 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASN B 148 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE B 141 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304
    Processing sheet with id=AA9, first strand: chain 'B' and resid 491 through 492
    Processing sheet with id=AB1, first strand: chain 'B' and resid 549 through 553
      removed outlier: 5.828A  pdb=" N   LEU B 550 " --> pdb=" O   PHE B 561 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   PHE B 561 " --> pdb=" O   LEU B 550 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS B 552 " --> pdb=" O   LEU B 559 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 777
      removed outlier: 6.234A  pdb=" N   PHE B 777 " --> pdb=" O   SER B 955 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   HIS B 957 " --> pdb=" O   PHE B 777 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   GLN B 781 " --> pdb=" O   LEU B 959 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 776 through 777
      removed outlier: 6.234A  pdb=" N   PHE B 777 " --> pdb=" O   SER B 955 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   HIS B 957 " --> pdb=" O   PHE B 777 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLY B 790 " --> pdb=" O   VAL B 958 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE B 848 " --> pdb=" O   ILE B 793 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   THR B 797 " --> pdb=" O   GLN B 844 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   GLN B 844 " --> pdb=" O   THR B 797 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   ILE B 832 " --> pdb=" O   GLN B 851 " (cutoff:3.500A)

    681 hydrogen bonds defined for protein.
    1965 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3294
        1.33 -     1.45: 3585
        1.45 -     1.57: 8962
        1.57 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 15928
  Sorted by residual:
  bond pdb=" N   ASP B 586 "
       pdb=" CA  ASP B 586 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 8.30e-03 1.45e+04 1.75e+01
  bond pdb=" N   VAL B 707 "
       pdb=" CA  VAL B 707 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.19e-02 7.06e+03 1.15e+01
  bond pdb=" N   VAL B1008 "
       pdb=" CA  VAL B1008 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.19e-02 7.06e+03 9.49e+00
  bond pdb=" N   VAL b   2 "
       pdb=" CA  VAL b   2 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.22e-02 6.72e+03 8.89e+00
  bond pdb=" N   VAL B 585 "
       pdb=" CA  VAL B 585 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.20e-02 6.94e+03 8.79e+00
  ... (remaining 15923 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 20598
        2.25 -     4.50: 839
        4.50 -     6.75: 84
        6.75 -     9.00: 9
        9.00 -    11.26: 3
  Bond angle restraints: 21533
  Sorted by residual:
  angle pdb=" C   LEU a  16 "
        pdb=" CA  LEU a  16 "
        pdb=" CB  LEU a  16 "
      ideal   model   delta    sigma   weight residual
     116.63  111.17    5.46 1.16e+00 7.43e-01 2.21e+01
  angle pdb=" N   GLU B 529 "
        pdb=" CA  GLU B 529 "
        pdb=" C   GLU B 529 "
      ideal   model   delta    sigma   weight residual
     112.86  107.16    5.70 1.22e+00 6.72e-01 2.18e+01
  angle pdb=" CA  GLU A 176 "
        pdb=" CB  GLU A 176 "
        pdb=" CG  GLU A 176 "
      ideal   model   delta    sigma   weight residual
     114.10  122.46   -8.36 2.00e+00 2.50e-01 1.75e+01
  angle pdb=" C   ASN B 821 "
        pdb=" N   THR B 822 "
        pdb=" CA  THR B 822 "
      ideal   model   delta    sigma   weight residual
     121.52  114.33    7.19 1.84e+00 2.95e-01 1.53e+01
  angle pdb=" CA  GLY A 775 "
        pdb=" C   GLY A 775 "
        pdb=" O   GLY A 775 "
      ideal   model   delta    sigma   weight residual
     121.47  118.04    3.43 9.00e-01 1.23e+00 1.45e+01
  ... (remaining 21528 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.53: 8764
       16.53 -    33.05: 670
       33.05 -    49.58: 172
       49.58 -    66.10: 25
       66.10 -    82.63: 16
  Dihedral angle restraints: 9647
    sinusoidal: 4049
      harmonic: 5598
  Sorted by residual:
  dihedral pdb=" CA  LYS A 511 "
           pdb=" C   LYS A 511 "
           pdb=" N   LYS A 512 "
           pdb=" CA  LYS A 512 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.70   26.30     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  ARG A 261 "
           pdb=" C   ARG A 261 "
           pdb=" N   GLU A 262 "
           pdb=" CA  GLU A 262 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.22  -24.78     0      5.00e+00 4.00e-02 2.46e+01
  dihedral pdb=" CA  GLN B 800 "
           pdb=" C   GLN B 800 "
           pdb=" N   SER B 801 "
           pdb=" CA  SER B 801 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.37   24.63     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 9644 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1482
       0.045 -    0.090: 562
       0.090 -    0.135: 204
       0.135 -    0.180: 49
       0.180 -    0.225: 19
  Chirality restraints: 2316
  Sorted by residual:
  chirality pdb=" CA  TRP A 695 "
            pdb=" N   TRP A 695 "
            pdb=" C   TRP A 695 "
            pdb=" CB  TRP A 695 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  GLN B 770 "
            pdb=" N   GLN B 770 "
            pdb=" C   GLN B 770 "
            pdb=" CB  GLN B 770 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  LYS B 364 "
            pdb=" N   LYS B 364 "
            pdb=" C   LYS B 364 "
            pdb=" CB  LYS B 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 2313 not shown)

  Planarity restraints: 2785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 224 "    0.025 2.00e-02 2.50e+03   5.01e-02 2.51e+01
        pdb=" C   TYR B 224 "   -0.087 2.00e-02 2.50e+03
        pdb=" O   TYR B 224 "    0.032 2.00e-02 2.50e+03
        pdb=" N   THR B 225 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 822 "   -0.023 2.00e-02 2.50e+03   4.52e-02 2.04e+01
        pdb=" C   THR B 822 "    0.078 2.00e-02 2.50e+03
        pdb=" O   THR B 822 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   LEU B 823 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 288 "   -0.067 5.00e-02 4.00e+02   1.03e-01 1.71e+01
        pdb=" N   PRO B 289 "    0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO B 289 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO B 289 "   -0.055 5.00e-02 4.00e+02
  ... (remaining 2782 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 211
        2.66 -     3.22: 14343
        3.22 -     3.78: 22935
        3.78 -     4.34: 32482
        4.34 -     4.90: 52838
  Nonbonded interactions: 122809
  Sorted by model distance:
  nonbonded pdb=" O   THR A  83 "
            pdb=" NH1 ARG A 261 "
     model   vdw
     2.098 3.120
  nonbonded pdb=" OG  SER B 128 "
            pdb=" OE2 GLU B 817 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OG  SER A  87 "
            pdb=" O   PHE A 151 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" OD2 ASP B  91 "
            pdb=" NE2 HIS B 442 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" O   ARG A 668 "
            pdb=" ND2 ASN A 672 "
     model   vdw
     2.200 3.120
  ... (remaining 122804 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 47 through 962 or resid 989 through 1011))
  selection = (chain 'B' and (resid 47 through 198 or resid 200 through 1011))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.380
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
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   0.051  15928  Z= 0.328
  Angle     :  0.967  11.255  21533  Z= 0.593
  Chirality :  0.057   0.225   2316
  Planarity :  0.008   0.103   2785
  Dihedral  : 13.090  82.627   6027
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  2.30 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.81 (0.16), residues: 1884
  helix: -2.70 (0.14), residues: 766
  sheet: -1.98 (0.27), residues: 323
  loop : -2.40 (0.19), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  65 
 TYR   0.031   0.002   TYR A 831 
 PHE   0.043   0.002   PHE A 168 
 TRP   0.038   0.003   TRP A 695 
 HIS   0.022   0.002   HIS A 679 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 (15928)
  covalent geometry    : angle       0.96667 (21533)
  hydrogen bonds       : bond        0.19690 (  681)
  hydrogen bonds       : angle       7.88446 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 265
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A  188 SER cc_start: 0.7149 (t) cc_final: 0.6903 (p)
REVERT: A  254 MET cc_start: 0.7206 (pmm) cc_final: 0.7003 (mtm)
REVERT: A  689 LEU cc_start: 0.7939 (pp) cc_final: 0.7554 (mp)
REVERT: B  254 MET cc_start: 0.4697 (mmt) cc_final: 0.4261 (mmt)
REVERT: B  556 MET cc_start: 0.8815 (tpt) cc_final: 0.8565 (tpp)
REVERT: B  870 MET cc_start: 0.8151 (mmt) cc_final: 0.7828 (mmm)
  outliers start: 5
  outliers final: 2
  residues processed: 270
  average time/residue: 0.1139
  time to fit residues: 46.5093
Evaluate side-chains
  174 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 172
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain B residue  771 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.1980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    0.0970
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    3.9990
   overall best weight:    3.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 ASN
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 502 GLN
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 796 GLN
A 821 ASN
A 914 GLN
A 988 GLN
B 146 HIS
B 680 GLN
B 724 HIS
** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.164366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.136532 restraints weight = 20446.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.88
r_work: 0.3331 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  15928  Z= 0.259
  Angle     :  0.782   9.196  21533  Z= 0.409
  Chirality :  0.052   0.198   2316
  Planarity :  0.006   0.065   2785
  Dihedral  :  5.664  47.552   2064
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  8.98 %
    Favored  : 89.25 %
  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: -2.16 (0.17), residues: 1884
  helix: -0.81 (0.17), residues: 793
  sheet: -1.32 (0.26), residues: 343
  loop : -2.05 (0.20), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 200 
 TYR   0.030   0.003   TYR A 779 
 PHE   0.029   0.003   PHE A 168 
 TRP   0.028   0.002   TRP A 776 
 HIS   0.013   0.002   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00627 (15928)
  covalent geometry    : angle       0.78209 (21533)
  hydrogen bonds       : bond        0.06257 (  681)
  hydrogen bonds       : angle       5.55982 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 197
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A  123 LYS cc_start: 0.7156 (mmtt) cc_final: 0.6811 (ttpt)
REVERT: A  188 SER cc_start: 0.7347 (t) cc_final: 0.7021 (m)
REVERT: A  254 MET cc_start: 0.7423 (pmm) cc_final: 0.7110 (mtm)
REVERT: A  529 GLU cc_start: 0.7828 (mp0) cc_final: 0.7440 (tm-30)
REVERT: A  541 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8294 (mt-10)
REVERT: B   94 ILE cc_start: 0.7057 (mm) cc_final: 0.6626 (mt)
REVERT: B  324 LYS cc_start: 0.7326 (mtmm) cc_final: 0.6812 (ptmt)
REVERT: B  465 GLU cc_start: 0.6604 (tp30) cc_final: 0.6253 (mm-30)
REVERT: B  872 LYS cc_start: 0.7511 (mttp) cc_final: 0.7186 (tppt)
  outliers start: 30
  outliers final: 20
  residues processed: 219
  average time/residue: 0.1190
  time to fit residues: 39.9859
Evaluate side-chains
  186 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  371 MET
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain A residue  793 ILE
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  923 THR
Chi-restraints excluded: chain A residue  991 VAL
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  746 GLU
Chi-restraints excluded: chain B residue  771 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 102 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0870
   chunk 101 optimal weight:    7.9990
   chunk 127 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 179 optimal weight:    1.9990
   chunk 153 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 10 optimal weight:    8.9990
   chunk 183 optimal weight:    7.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 GLN
A 340 HIS
A 502 GLN
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 GLN
A 821 ASN
A 828 GLN
B 680 GLN
B 681 HIS
B 762 GLN
B 805 ASN
B 828 GLN
** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.163186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.133809 restraints weight = 20769.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.95
r_work: 0.3377 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  15928  Z= 0.111
  Angle     :  0.564   7.720  21533  Z= 0.292
  Chirality :  0.043   0.150   2316
  Planarity :  0.004   0.051   2785
  Dihedral  :  4.961  46.091   2064
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.75 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.18), residues: 1884
  helix:  0.10 (0.18), residues: 802
  sheet: -0.93 (0.26), residues: 344
  loop : -1.71 (0.21), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 368 
 TYR   0.016   0.001   TYR A 779 
 PHE   0.018   0.001   PHE A 168 
 TRP   0.014   0.001   TRP A 776 
 HIS   0.007   0.001   HIS A 957 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (15928)
  covalent geometry    : angle       0.56363 (21533)
  hydrogen bonds       : bond        0.04462 (  681)
  hydrogen bonds       : angle       4.92816 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 194
  time to evaluate  : 0.551 
Fit side-chains
REVERT: A  123 LYS cc_start: 0.7060 (mmtt) cc_final: 0.6778 (tttt)
REVERT: A  254 MET cc_start: 0.7421 (pmm) cc_final: 0.7052 (mtm)
REVERT: A  529 GLU cc_start: 0.7749 (mp0) cc_final: 0.7487 (tm-30)
REVERT: A  541 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8384 (mt-10)
REVERT: A  779 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.6620 (p90)
REVERT: B  113 MET cc_start: 0.6564 (tpp) cc_final: 0.6112 (mmm)
REVERT: B  290 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6804 (pm20)
REVERT: B  324 LYS cc_start: 0.7466 (mtmm) cc_final: 0.7039 (ptmt)
REVERT: B  465 GLU cc_start: 0.6667 (tp30) cc_final: 0.6363 (mm-30)
REVERT: B  743 GLN cc_start: 0.8370 (tp40) cc_final: 0.8054 (tt0)
  outliers start: 31
  outliers final: 17
  residues processed: 213
  average time/residue: 0.1149
  time to fit residues: 37.3238
Evaluate side-chains
  189 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  371 MET
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  877 MET
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue 1009 LYS
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  771 LEU
Chi-restraints excluded: chain B residue  874 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 143 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   chunk 71 optimal weight:    0.7980
   chunk 28 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 132 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
A 190 HIS
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 GLN
A 800 GLN
A 821 ASN
B 190 HIS
B 718 GLN
B 762 GLN
** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 952 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.164381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.137610 restraints weight = 20488.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.88
r_work: 0.3337 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15928  Z= 0.162
  Angle     :  0.612   7.800  21533  Z= 0.315
  Chirality :  0.045   0.260   2316
  Planarity :  0.005   0.049   2785
  Dihedral  :  4.810  30.011   2062
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 10.93 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.19), residues: 1884
  helix:  0.44 (0.18), residues: 808
  sheet: -0.63 (0.26), residues: 348
  loop : -1.57 (0.21), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 200 
 TYR   0.021   0.002   TYR A 779 
 PHE   0.019   0.002   PHE A 168 
 TRP   0.020   0.001   TRP A 776 
 HIS   0.008   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (15928)
  covalent geometry    : angle       0.61205 (21533)
  hydrogen bonds       : bond        0.04893 (  681)
  hydrogen bonds       : angle       4.78171 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 184
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
REVERT: A  541 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8324 (mt-10)
REVERT: A  577 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8088 (tt0)
REVERT: A  618 TYR cc_start: 0.8935 (p90) cc_final: 0.8667 (p90)
REVERT: A  779 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.6952 (p90)
REVERT: A  800 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8246 (mm-40)
REVERT: A  851 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8461 (tt0)
REVERT: B  267 LEU cc_start: 0.3196 (OUTLIER) cc_final: 0.2971 (mt)
REVERT: B  290 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6719 (pm20)
REVERT: B  324 LYS cc_start: 0.7388 (mtmm) cc_final: 0.7029 (ptmt)
REVERT: B  465 GLU cc_start: 0.6469 (tp30) cc_final: 0.5894 (mm-30)
REVERT: B  779 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.6273 (p90)
  outliers start: 55
  outliers final: 29
  residues processed: 225
  average time/residue: 0.1048
  time to fit residues: 36.8397
Evaluate side-chains
  201 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 166
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  554 THR
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  793 ILE
Chi-restraints excluded: chain A residue  800 GLN
Chi-restraints excluded: chain A residue  816 SER
Chi-restraints excluded: chain A residue  846 LEU
Chi-restraints excluded: chain A residue  851 GLN
Chi-restraints excluded: chain A residue  877 MET
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  923 THR
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  991 VAL
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  363 GLN
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  627 MET
Chi-restraints excluded: chain B residue  771 LEU
Chi-restraints excluded: chain B residue  779 TYR
Chi-restraints excluded: chain B residue  874 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 168 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 131 optimal weight:    0.5980
   chunk 138 optimal weight:    4.9990
   chunk 185 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 GLN
A 821 ASN
** B 851 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.165629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.139086 restraints weight = 20380.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.82
r_work: 0.3348 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15928  Z= 0.119
  Angle     :  0.553   8.033  21533  Z= 0.285
  Chirality :  0.043   0.178   2316
  Planarity :  0.004   0.042   2785
  Dihedral  :  4.602  26.888   2062
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.11 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.19), residues: 1884
  helix:  0.75 (0.18), residues: 808
  sheet: -0.40 (0.26), residues: 351
  loop : -1.48 (0.21), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 200 
 TYR   0.017   0.001   TYR A 779 
 PHE   0.014   0.001   PHE B 109 
 TRP   0.012   0.001   TRP A 776 
 HIS   0.010   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (15928)
  covalent geometry    : angle       0.55319 (21533)
  hydrogen bonds       : bond        0.04233 (  681)
  hydrogen bonds       : angle       4.59003 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 182
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 LYS cc_start: 0.7983 (mttm) cc_final: 0.7097 (mmmt)
REVERT: A   80 ASP cc_start: 0.6761 (t0) cc_final: 0.6461 (t0)
REVERT: A  541 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8292 (mt-10)
REVERT: A  577 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8020 (tt0)
REVERT: A  779 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7104 (p90)
REVERT: A  851 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8412 (tt0)
REVERT: B  290 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6746 (pm20)
REVERT: B  324 LYS cc_start: 0.7299 (mtmm) cc_final: 0.6919 (ptmt)
REVERT: B  465 GLU cc_start: 0.6367 (tp30) cc_final: 0.5882 (mm-30)
REVERT: B  688 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8599 (mt)
REVERT: B  779 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.6264 (p90)
REVERT: B  874 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7418 (mt)
  outliers start: 42
  outliers final: 22
  residues processed: 212
  average time/residue: 0.1091
  time to fit residues: 36.4239
Evaluate side-chains
  198 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 170
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  793 ILE
Chi-restraints excluded: chain A residue  851 GLN
Chi-restraints excluded: chain A residue  877 MET
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1009 LYS
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  619 ASP
Chi-restraints excluded: chain B residue  627 MET
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  733 ILE
Chi-restraints excluded: chain B residue  771 LEU
Chi-restraints excluded: chain B residue  779 TYR
Chi-restraints excluded: chain B residue  874 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 150 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 144 optimal weight:    4.9990
   chunk 11 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 59 optimal weight:    0.9990
   chunk 134 optimal weight:    9.9990
   chunk 148 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 312 ASN
A 752 HIS
A 762 GLN
A 800 GLN
A 821 ASN
B 680 GLN
** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.154198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.125625 restraints weight = 20789.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.87
r_work: 0.3256 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  15928  Z= 0.233
  Angle     :  0.684   8.803  21533  Z= 0.351
  Chirality :  0.048   0.214   2316
  Planarity :  0.005   0.049   2785
  Dihedral  :  4.997  31.735   2062
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 12.82 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.19), residues: 1884
  helix:  0.70 (0.18), residues: 802
  sheet: -0.37 (0.27), residues: 349
  loop : -1.66 (0.21), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 200 
 TYR   0.025   0.002   TYR A 779 
 PHE   0.024   0.002   PHE B 109 
 TRP   0.020   0.001   TRP A 776 
 HIS   0.009   0.002   HIS A 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 (15928)
  covalent geometry    : angle       0.68429 (21533)
  hydrogen bonds       : bond        0.05517 (  681)
  hydrogen bonds       : angle       4.81975 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 179
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
REVERT: A  268 THR cc_start: 0.6410 (OUTLIER) cc_final: 0.6099 (m)
REVERT: A  541 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8400 (mt-10)
REVERT: A  577 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8080 (tt0)
REVERT: A  597 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8437 (mt)
REVERT: A  618 TYR cc_start: 0.8920 (p90) cc_final: 0.8559 (p90)
REVERT: A  779 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.6621 (p90)
REVERT: A  780 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8035 (pt0)
REVERT: A  851 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8471 (tt0)
REVERT: B  290 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6935 (pm20)
REVERT: B  465 GLU cc_start: 0.6676 (tp30) cc_final: 0.6198 (mm-30)
REVERT: B  483 LYS cc_start: 0.8442 (tptm) cc_final: 0.7886 (tptm)
REVERT: B  688 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8688 (mt)
REVERT: B  770 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8456 (mt0)
REVERT: B  779 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7026 (p90)
  outliers start: 64
  outliers final: 38
  residues processed: 227
  average time/residue: 0.1117
  time to fit residues: 39.5330
Evaluate side-chains
  213 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 166
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  793 ILE
Chi-restraints excluded: chain A residue  800 GLN
Chi-restraints excluded: chain A residue  816 SER
Chi-restraints excluded: chain A residue  846 LEU
Chi-restraints excluded: chain A residue  851 GLN
Chi-restraints excluded: chain A residue  877 MET
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  923 THR
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  991 VAL
Chi-restraints excluded: chain A residue 1009 LYS
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  363 GLN
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  619 ASP
Chi-restraints excluded: chain B residue  627 MET
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  764 VAL
Chi-restraints excluded: chain B residue  770 GLN
Chi-restraints excluded: chain B residue  771 LEU
Chi-restraints excluded: chain B residue  779 TYR
Chi-restraints excluded: chain B residue  874 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 145 optimal weight:    5.9990
   chunk 164 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 104 optimal weight:    4.9990
   chunk 165 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 144 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 148 optimal weight:    0.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 HIS
A 638 GLN
** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 800 GLN
A 821 ASN
B 680 GLN
B 851 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.156270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.128507 restraints weight = 20568.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.72
r_work: 0.3313 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15928  Z= 0.134
  Angle     :  0.587   8.706  21533  Z= 0.302
  Chirality :  0.043   0.165   2316
  Planarity :  0.004   0.040   2785
  Dihedral  :  4.728  27.628   2062
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.71 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.19), residues: 1884
  helix:  0.97 (0.18), residues: 802
  sheet: -0.29 (0.27), residues: 343
  loop : -1.53 (0.21), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 368 
 TYR   0.018   0.001   TYR A 779 
 PHE   0.017   0.001   PHE B 169 
 TRP   0.011   0.001   TRP A 776 
 HIS   0.005   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (15928)
  covalent geometry    : angle       0.58680 (21533)
  hydrogen bonds       : bond        0.04445 (  681)
  hydrogen bonds       : angle       4.61504 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 176
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
REVERT: A  541 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8353 (mt-10)
REVERT: A  577 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8025 (tt0)
REVERT: A  779 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.6978 (p90)
REVERT: A  800 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8300 (mm-40)
REVERT: A  801 SER cc_start: 0.8072 (m) cc_final: 0.7699 (t)
REVERT: A  851 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8416 (tt0)
REVERT: B  254 MET cc_start: 0.4205 (mmt) cc_final: 0.3725 (mmt)
REVERT: B  290 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6925 (pm20)
REVERT: B  465 GLU cc_start: 0.6560 (tp30) cc_final: 0.6019 (mm-30)
REVERT: B  483 LYS cc_start: 0.8418 (tptm) cc_final: 0.7826 (tptm)
REVERT: B  511 LYS cc_start: 0.6079 (tmtt) cc_final: 0.5671 (tmmt)
REVERT: B  688 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8663 (mt)
REVERT: B  779 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.6721 (p90)
  outliers start: 49
  outliers final: 29
  residues processed: 209
  average time/residue: 0.1073
  time to fit residues: 35.6408
Evaluate side-chains
  202 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 167
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  325 TYR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  793 ILE
Chi-restraints excluded: chain A residue  800 GLN
Chi-restraints excluded: chain A residue  816 SER
Chi-restraints excluded: chain A residue  846 LEU
Chi-restraints excluded: chain A residue  851 GLN
Chi-restraints excluded: chain A residue  877 MET
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1009 LYS
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  363 GLN
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  619 ASP
Chi-restraints excluded: chain B residue  627 MET
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  771 LEU
Chi-restraints excluded: chain B residue  779 TYR
Chi-restraints excluded: chain B residue  874 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 127 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 161 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 GLN
A 800 GLN
A 821 ASN
B 680 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.156567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.128751 restraints weight = 20761.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.75
r_work: 0.3315 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15928  Z= 0.128
  Angle     :  0.577   9.208  21533  Z= 0.295
  Chirality :  0.043   0.199   2316
  Planarity :  0.004   0.033   2785
  Dihedral  :  4.602  26.171   2062
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 14.59 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.19), residues: 1884
  helix:  1.10 (0.19), residues: 803
  sheet: -0.19 (0.27), residues: 343
  loop : -1.44 (0.21), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 200 
 TYR   0.017   0.001   TYR A 779 
 PHE   0.011   0.001   PHE A 567 
 TRP   0.012   0.001   TRP A 776 
 HIS   0.005   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (15928)
  covalent geometry    : angle       0.57653 (21533)
  hydrogen bonds       : bond        0.04283 (  681)
  hydrogen bonds       : angle       4.52999 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 177
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.5639 (mtp180) cc_final: 0.5158 (mmp-170)
REVERT: A  268 THR cc_start: 0.6421 (OUTLIER) cc_final: 0.5973 (m)
REVERT: A  448 GLU cc_start: 0.7715 (pm20) cc_final: 0.7306 (pt0)
REVERT: A  541 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8357 (mt-10)
REVERT: A  577 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8015 (tt0)
REVERT: A  779 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7108 (p90)
REVERT: A  780 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7981 (pt0)
REVERT: A  801 SER cc_start: 0.8121 (m) cc_final: 0.7771 (t)
REVERT: A  851 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8435 (tt0)
REVERT: B  290 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7001 (pm20)
REVERT: B  465 GLU cc_start: 0.6577 (tp30) cc_final: 0.6020 (mm-30)
REVERT: B  483 LYS cc_start: 0.8441 (tptm) cc_final: 0.7859 (tptm)
REVERT: B  688 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8680 (mt)
REVERT: B  779 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6684 (p90)
REVERT: B  874 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7609 (mt)
  outliers start: 53
  outliers final: 36
  residues processed: 211
  average time/residue: 0.1153
  time to fit residues: 38.4105
Evaluate side-chains
  218 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 174
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  793 ILE
Chi-restraints excluded: chain A residue  800 GLN
Chi-restraints excluded: chain A residue  816 SER
Chi-restraints excluded: chain A residue  846 LEU
Chi-restraints excluded: chain A residue  851 GLN
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  923 THR
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  991 VAL
Chi-restraints excluded: chain A residue 1009 LYS
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  363 GLN
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  517 ASP
Chi-restraints excluded: chain B residue  619 ASP
Chi-restraints excluded: chain B residue  627 MET
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  771 LEU
Chi-restraints excluded: chain B residue  779 TYR
Chi-restraints excluded: chain B residue  874 ILE
Chi-restraints excluded: chain B residue  996 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   chunk 154 optimal weight:    0.8980
   chunk 187 optimal weight:    0.9980
   chunk 110 optimal weight:    0.0370
   chunk 68 optimal weight:    1.9990
   chunk 142 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 120 optimal weight:    0.9980
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 800 GLN
A 821 ASN
B 762 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.158879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.131377 restraints weight = 20577.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.74
r_work: 0.3345 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  15928  Z= 0.105
  Angle     :  0.548   9.306  21533  Z= 0.280
  Chirality :  0.042   0.163   2316
  Planarity :  0.004   0.032   2785
  Dihedral  :  4.412  22.266   2062
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.18 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.19), residues: 1884
  helix:  1.27 (0.19), residues: 803
  sheet: -0.07 (0.27), residues: 351
  loop : -1.31 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 368 
 TYR   0.014   0.001   TYR B 326 
 PHE   0.010   0.001   PHE A 866 
 TRP   0.008   0.001   TRP A 776 
 HIS   0.008   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (15928)
  covalent geometry    : angle       0.54825 (21533)
  hydrogen bonds       : bond        0.03823 (  681)
  hydrogen bonds       : angle       4.40173 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 182
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.5658 (mtp180) cc_final: 0.5179 (mmp-170)
REVERT: A  448 GLU cc_start: 0.7719 (pm20) cc_final: 0.7337 (pt0)
REVERT: A  541 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8335 (mt-10)
REVERT: A  577 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8002 (tt0)
REVERT: A  779 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7316 (p90)
REVERT: A  801 SER cc_start: 0.8146 (m) cc_final: 0.7852 (t)
REVERT: B  254 MET cc_start: 0.4173 (mmt) cc_final: 0.3673 (mmt)
REVERT: B  290 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7045 (pm20)
REVERT: B  465 GLU cc_start: 0.6574 (tp30) cc_final: 0.6020 (mm-30)
REVERT: B  483 LYS cc_start: 0.8445 (tptm) cc_final: 0.7872 (tptm)
REVERT: B  671 ASN cc_start: 0.8102 (p0) cc_final: 0.7818 (m110)
REVERT: B  688 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8661 (mt)
REVERT: B  779 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.6486 (p90)
REVERT: B  874 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7423 (mt)
  outliers start: 43
  outliers final: 31
  residues processed: 208
  average time/residue: 0.1073
  time to fit residues: 35.0525
Evaluate side-chains
  205 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 169
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  325 TYR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  793 ILE
Chi-restraints excluded: chain A residue  800 GLN
Chi-restraints excluded: chain A residue  816 SER
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  923 THR
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  991 VAL
Chi-restraints excluded: chain A residue 1009 LYS
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  363 GLN
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  517 ASP
Chi-restraints excluded: chain B residue  619 ASP
Chi-restraints excluded: chain B residue  627 MET
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  779 TYR
Chi-restraints excluded: chain B residue  874 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 177 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 140 optimal weight:    1.9990
   chunk 155 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 154 optimal weight:    0.0070
   chunk 127 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.9804

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

Flipped N/Q/H residues before XYZ refinement:
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 800 GLN
A 821 ASN
B 475 ASN
B 680 GLN
B 762 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.156857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.128956 restraints weight = 20727.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.75
r_work: 0.3445 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15928  Z= 0.112
  Angle     :  0.552   9.681  21533  Z= 0.281
  Chirality :  0.042   0.152   2316
  Planarity :  0.004   0.045   2785
  Dihedral  :  4.334  17.555   2060
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.71 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.19), residues: 1884
  helix:  1.34 (0.19), residues: 804
  sheet: -0.06 (0.27), residues: 343
  loop : -1.25 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 368 
 TYR   0.014   0.001   TYR A 779 
 PHE   0.010   0.001   PHE A 866 
 TRP   0.011   0.001   TRP A 776 
 HIS   0.006   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (15928)
  covalent geometry    : angle       0.55198 (21533)
  hydrogen bonds       : bond        0.03865 (  681)
  hydrogen bonds       : angle       4.37175 ( 1965)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 171
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.5792 (mtp180) cc_final: 0.5322 (mmp-170)
REVERT: A  268 THR cc_start: 0.6468 (OUTLIER) cc_final: 0.6032 (m)
REVERT: A  448 GLU cc_start: 0.7746 (pm20) cc_final: 0.7355 (pt0)
REVERT: A  503 GLU cc_start: 0.4462 (tt0) cc_final: 0.3701 (mm-30)
REVERT: A  541 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8358 (mt-10)
REVERT: A  577 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8003 (tt0)
REVERT: A  779 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7294 (p90)
REVERT: A  800 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8087 (mm-40)
REVERT: A  801 SER cc_start: 0.8203 (m) cc_final: 0.7933 (t)
REVERT: B  290 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7023 (pm20)
REVERT: B  465 GLU cc_start: 0.6625 (tp30) cc_final: 0.6060 (mm-30)
REVERT: B  483 LYS cc_start: 0.8458 (tptm) cc_final: 0.7901 (tptm)
REVERT: B  671 ASN cc_start: 0.8099 (p0) cc_final: 0.7859 (m110)
REVERT: B  688 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8690 (mt)
REVERT: B  779 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.6561 (p90)
REVERT: B  874 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7445 (mt)
  outliers start: 42
  outliers final: 29
  residues processed: 196
  average time/residue: 0.1087
  time to fit residues: 33.6147
Evaluate side-chains
  204 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  793 ILE
Chi-restraints excluded: chain A residue  800 GLN
Chi-restraints excluded: chain A residue  816 SER
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  923 THR
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  991 VAL
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  363 GLN
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  517 ASP
Chi-restraints excluded: chain B residue  619 ASP
Chi-restraints excluded: chain B residue  627 MET
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  779 TYR
Chi-restraints excluded: chain B residue  874 ILE
Chi-restraints excluded: chain B residue  996 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 142 optimal weight:    0.8980
   chunk 165 optimal weight:    3.9990
   chunk 153 optimal weight:    0.5980
   chunk 146 optimal weight:    0.6980
   chunk 180 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 108 optimal weight:    8.9990
   chunk 84 optimal weight:    0.0980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 800 GLN
A 821 ASN
B 680 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.157951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.130072 restraints weight = 20589.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.76
r_work: 0.3450 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  15928  Z= 0.102
  Angle     :  0.539   9.526  21533  Z= 0.274
  Chirality :  0.042   0.153   2316
  Planarity :  0.004   0.043   2785
  Dihedral  :  4.253  18.062   2060
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.95 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.19), residues: 1884
  helix:  1.46 (0.19), residues: 802
  sheet:  0.07 (0.28), residues: 340
  loop : -1.18 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 368 
 TYR   0.014   0.001   TYR B 326 
 PHE   0.010   0.001   PHE A 866 
 TRP   0.009   0.001   TRP A 776 
 HIS   0.005   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (15928)
  covalent geometry    : angle       0.53889 (21533)
  hydrogen bonds       : bond        0.03644 (  681)
  hydrogen bonds       : angle       4.30926 ( 1965)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3807.43 seconds
wall clock time: 65 minutes 51.51 seconds (3951.51 seconds total)