Starting phenix.real_space_refine
on Fri Jul  3 12:23:48 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7s7c_24883/07_2026/7s7c_24883.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s7c_24883/07_2026/7s7c_24883.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7s7c_24883/07_2026/7s7c_24883.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7s7c_24883/07_2026/7s7c_24883.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s7c_24883/07_2026/7s7c_24883.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s7c_24883/07_2026/7s7c_24883.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s7c_24883/07_2026/7s7c_24883.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s7c_24883/07_2026/7s7c_24883.cif"
  }
  resolution = 3.62
  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=   0.001 sd=   1.065
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      34      5.49       5
     S      73      5.16       5
     C    8696      2.51       5
     N    2374      2.21       5
     O    2672      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13850
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 7376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 924, 7376
          Classifications: {'peptide': 924}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 41, 'TRANS': 882}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2666
          Classifications: {'peptide': 330}
          Link IDs: {'PTRANS': 22, 'TRANS': 307}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 644
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 5, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 574
          Inner-chain residues flagged as termini: ['pdbres="  A D  23 "']
          Classifications: {'RNA': 27}
          Modifications used: {'5*END': 2, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 8, 'rna3p': 18}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "L"
      Number of atoms: 212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 212
          Classifications: {'RNA': 10}
          Modifications used: {'5*END': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5}
          Link IDs: {'rna3p': 9}
    Chain: "E"
      Number of atoms: 1166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1166
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 12, 'TRANS': 134}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 1211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1211
          Classifications: {'peptide': 149}
          Link IDs: {'PTRANS': 7, 'TRANS': 141}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8616  SG  CYS B 229      55.471  71.347  93.313  1.00150.17           S
  ATOM   8641  SG  CYS B 232      58.103  69.641  91.184  1.00149.28           S
  ATOM   8719  SG  CYS B 242      58.999  72.151  93.729  1.00145.26           S

  Time building chain proxies: 2.66, per 1000 atoms: 0.19
  Number of scatterers: 13850
  At special positions: 0
  Unit cell: (129.8, 135.3, 154, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      73     16.00
     P      34     15.00
     O    2672      8.00
     N    2374      7.00
     C    8696      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: 1.25
  Conformation dependent library (CDL) restraints added in 513.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 900 "
        pdb="ZN    ZN B 900 " - pdb=" NE2 HIS B 237 "
        pdb="ZN    ZN B 900 " - pdb=" SG  CYS B 242 "
        pdb="ZN    ZN B 900 " - pdb=" SG  CYS B 232 "
        pdb="ZN    ZN B 900 " - pdb=" SG  CYS B 229 "
      Number of angles added : 3


  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3090

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 12 sheets defined
      46.2% alpha, 11.0% beta
      8 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 141 through 153
      removed outlier: 3.550A  pdb=" N   ASN A 153 " --> pdb=" O   GLN A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 166
      removed outlier: 3.749A  pdb=" N   GLY A 166 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 163 through 166'
    Processing helix  chain 'A' and resid 167 through 181
      removed outlier: 3.975A  pdb=" N   ALA A 171 " --> pdb=" O   LYS A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 207
    Processing helix  chain 'A' and resid 229 through 238
    Processing helix  chain 'A' and resid 240 through 245
      removed outlier: 3.752A  pdb=" N   MET A 243 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLU A 245 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 259
      removed outlier: 3.706A  pdb=" N   ARG A 258 " --> pdb=" O   HIS A 255 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASP A 259 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 273
    Processing helix  chain 'A' and resid 288 through 301
      removed outlier: 3.856A  pdb=" N   PHE A 292 " --> pdb=" O   ASN A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 356
      removed outlier: 3.540A  pdb=" N   PHE A 343 " --> pdb=" O   ARG A 339 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LEU A 356 " --> pdb=" O   ASP A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 385
    Processing helix  chain 'A' and resid 397 through 406
      removed outlier: 3.778A  pdb=" N   MET A 406 " --> pdb=" O   TYR A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 429
    Processing helix  chain 'A' and resid 432 through 437
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.550A  pdb=" N   ARG A 450 " --> pdb=" O   PRO A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 474
    Processing helix  chain 'A' and resid 483 through 488
      removed outlier: 3.910A  pdb=" N   MET A 487 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 522
    Processing helix  chain 'A' and resid 544 through 553
      removed outlier: 4.347A  pdb=" N   GLN A 550 " --> pdb=" O   THR A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 576
    Processing helix  chain 'A' and resid 580 through 587
      removed outlier: 3.745A  pdb=" N   MET A 584 " --> pdb=" O   ASN A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 596
    Processing helix  chain 'A' and resid 597 through 615
      removed outlier: 3.659A  pdb=" N   ILE A 615 " --> pdb=" O   GLN A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 645
    Processing helix  chain 'A' and resid 646 through 651
      removed outlier: 3.898A  pdb=" N   LEU A 651 " --> pdb=" O   PRO A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 708
    Processing helix  chain 'A' and resid 709 through 713
      removed outlier: 3.896A  pdb=" N   GLU A 713 " --> pdb=" O   SER A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 769
      removed outlier: 3.710A  pdb=" N   ARG A 756 " --> pdb=" O   PRO A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 807
      removed outlier: 3.787A  pdb=" N   LYS A 791 " --> pdb=" O   ASP A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 812
      removed outlier: 3.740A  pdb=" N   ASP A 812 " --> pdb=" O   PRO A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 842
      removed outlier: 3.524A  pdb=" N   TYR A 819 " --> pdb=" O   LEU A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 847 through 862
    Processing helix  chain 'A' and resid 871 through 880
      removed outlier: 4.123A  pdb=" N   GLU A 879 " --> pdb=" O   ARG A 875 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ILE A 880 " --> pdb=" O   VAL A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 895
      removed outlier: 3.539A  pdb=" N   LEU A 888 " --> pdb=" O   ASP A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 910
    Processing helix  chain 'A' and resid 928 through 948
      removed outlier: 3.959A  pdb=" N   LEU A 932 " --> pdb=" O   LEU A 928 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLN A 934 " --> pdb=" O   GLY A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 960
    Processing helix  chain 'A' and resid 966 through 974
    Processing helix  chain 'A' and resid 978 through 984
      removed outlier: 3.908A  pdb=" N   ILE A 982 " --> pdb=" O   THR A 978 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 1015
      removed outlier: 3.606A  pdb=" N   ILE A 993 " --> pdb=" O   PHE A 989 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLY A1015 " --> pdb=" O   ALA A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1017 through 1030
    Processing helix  chain 'A' and resid 1033 through 1037
    Processing helix  chain 'B' and resid 67 through 75
    Processing helix  chain 'B' and resid 76 through 78
      No H-bonds generated for 'chain 'B' and resid 76 through 78'
    Processing helix  chain 'B' and resid 102 through 107
    Processing helix  chain 'B' and resid 108 through 128
    Processing helix  chain 'B' and resid 156 through 166
    Processing helix  chain 'B' and resid 191 through 195
    Processing helix  chain 'B' and resid 238 through 242
    Processing helix  chain 'B' and resid 277 through 281
      removed outlier: 3.851A  pdb=" N   GLU B 280 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 300
      removed outlier: 3.628A  pdb=" N   GLY B 300 " --> pdb=" O   GLN B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 317
      removed outlier: 4.247A  pdb=" N   ARG B 312 " --> pdb=" O   PRO B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 326
      removed outlier: 4.225A  pdb=" N   GLU B 325 " --> pdb=" O   GLY B 321 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ALA B 326 " --> pdb=" O   TRP B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 403
      removed outlier: 3.505A  pdb=" N   TYR B 402 " --> pdb=" O   VAL B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 667
      removed outlier: 3.680A  pdb=" N   PHE B 666 " --> pdb=" O   ASP B 662 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA B 667 " --> pdb=" O   MET B 663 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 662 through 667'
    Processing helix  chain 'B' and resid 683 through 692
    Processing helix  chain 'B' and resid 695 through 702
    Processing helix  chain 'C' and resid 22 through 32
      removed outlier: 4.030A  pdb=" N   GLN C  32 " --> pdb=" O   GLU C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 70
    Processing helix  chain 'E' and resid 633 through 645
    Processing helix  chain 'E' and resid 646 through 651
    Processing helix  chain 'E' and resid 652 through 654
      No H-bonds generated for 'chain 'E' and resid 652 through 654'
    Processing helix  chain 'E' and resid 752 through 770
      removed outlier: 3.626A  pdb=" N   ARG E 756 " --> pdb=" O   PRO E 752 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 787 through 799
    Processing helix  chain 'F' and resid 57 through 72
    Processing helix  chain 'F' and resid 102 through 127
      removed outlier: 5.742A  pdb=" N   GLN F 110 " --> pdb=" O   LYS F 106 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   GLU F 111 " --> pdb=" O   GLN F 107 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 103
      removed outlier: 6.487A  pdb=" N   VAL A 249 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   LEU A 282 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   PHE A 251 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE A 186 " --> pdb=" O   TRP A 248 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A 185 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   MET A 227 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   PHE A 187 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 455
      removed outlier: 6.669A  pdb=" N   GLY A 453 " --> pdb=" O   PHE A 480 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   VAL A 496 " --> pdb=" O   ILE A 536 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   MET A 538 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   PHE A 498 " --> pdb=" O   MET A 538 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   LEU A 328 " --> pdb=" O   TYR B 336 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 504
    Processing sheet with id=AA4, first strand: chain 'A' and resid 667 through 673
      removed outlier: 6.591A  pdb=" N   VAL A 662 " --> pdb=" O   PHE A 669 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   TRP A 671 " --> pdb=" O   VAL A 660 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   VAL A 660 " --> pdb=" O   TRP A 671 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   VAL A 673 " --> pdb=" O   ARG A 658 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   ARG A 658 " --> pdb=" O   VAL A 673 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   LEU A 659 " --> pdb=" O   ILE A 739 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   ILE A 739 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LYS A 661 " --> pdb=" O   SER A 737 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 676 through 680
    Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100
      removed outlier: 4.615A  pdb=" N   PHE B  99 " --> pdb=" O   VAL F 169 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL F 169 " --> pdb=" O   PHE B  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100
      removed outlier: 4.615A  pdb=" N   PHE B  99 " --> pdb=" O   VAL F 169 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL F 169 " --> pdb=" O   PHE B  99 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 328
    Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 40
      removed outlier: 6.897A  pdb=" N   ASN C  56 " --> pdb=" O   ILE C  37 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   VAL C  39 " --> pdb=" O   PHE C  54 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   PHE C  54 " --> pdb=" O   VAL C  39 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 74 through 75
    Processing sheet with id=AB2, first strand: chain 'E' and resid 727 through 732
      removed outlier: 3.562A  pdb=" N   LEU E 693 " --> pdb=" O   LYS E 680 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASN E 676 " --> pdb=" O   GLU E 697 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   LEU E 699 " --> pdb=" O   VAL E 674 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL E 674 " --> pdb=" O   LEU E 699 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ASP E 668 " --> pdb=" O   ASN E 664 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ASN E 664 " --> pdb=" O   ASP E 668 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLY E 670 " --> pdb=" O   VAL E 662 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL E 662 " --> pdb=" O   GLY E 670 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LYS E 663 " --> pdb=" O   LEU E 736 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   LEU E 736 " --> pdb=" O   LYS E 663 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 78 through 79
      removed outlier: 3.546A  pdb=" N   ARG F  79 " --> pdb=" O   GLU F 148 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    544 hydrogen bonds defined for protein.
    1557 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      24 hydrogen bonds
      48 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 2.40

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 4229
        1.33 -     1.45: 1916
        1.45 -     1.57: 7867
        1.57 -     1.69: 68
        1.69 -     1.81: 118
  Bond restraints: 14198
  Sorted by residual:
  bond pdb=" C5    G D   8 "
       pdb=" C6    G D   8 "
    ideal  model  delta    sigma   weight residual
    1.419  1.403  0.016 2.00e-02 2.50e+03 6.07e-01
  bond pdb=" N7    G D   6 "
       pdb=" C5    G D   6 "
    ideal  model  delta    sigma   weight residual
    1.388  1.374  0.014 2.00e-02 2.50e+03 4.83e-01
  bond pdb=" C6    G D   8 "
       pdb=" O6    G D   8 "
    ideal  model  delta    sigma   weight residual
    1.237  1.223  0.014 2.00e-02 2.50e+03 4.68e-01
  bond pdb=" C   ILE B 660 "
       pdb=" O   ILE B 660 "
    ideal  model  delta    sigma   weight residual
    1.247  1.239  0.008 1.23e-02 6.61e+03 4.51e-01
  bond pdb=" C1'   A D  23 "
       pdb=" N9    A D  23 "
    ideal  model  delta    sigma   weight residual
    1.478  1.465  0.013 2.00e-02 2.50e+03 4.51e-01
  ... (remaining 14193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 18676
        1.08 -     2.16: 515
        2.16 -     3.25: 71
        3.25 -     4.33: 62
        4.33 -     5.41: 6
  Bond angle restraints: 19330
  Sorted by residual:
  angle pdb=" C   LYS F 160 "
        pdb=" N   ASN F 161 "
        pdb=" CA  ASN F 161 "
      ideal   model   delta    sigma   weight residual
     121.54  126.73   -5.19 1.91e+00 2.74e-01 7.38e+00
  angle pdb=" C3'   A D  23 "
        pdb=" C2'   A D  23 "
        pdb=" O2'   A D  23 "
      ideal   model   delta    sigma   weight residual
     109.80  114.71   -4.91 2.00e+00 2.50e-01 6.03e+00
  angle pdb=" C3'   U D  18 "
        pdb=" O3'   U D  18 "
        pdb=" P     U D  19 "
      ideal   model   delta    sigma   weight residual
     120.20  123.16   -2.96 1.50e+00 4.44e-01 3.88e+00
  angle pdb=" O3'   A D  23 "
        pdb=" C3'   A D  23 "
        pdb=" C2'   A D  23 "
      ideal   model   delta    sigma   weight residual
     113.80  109.98    3.82 2.00e+00 2.50e-01 3.65e+00
  angle pdb=" O2'   A D  23 "
        pdb=" C2'   A D  23 "
        pdb=" C1'   A D  23 "
      ideal   model   delta    sigma   weight residual
     108.20  111.84   -3.64 2.00e+00 2.50e-01 3.32e+00
  ... (remaining 19325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.70: 8477
       31.70 -    63.41: 143
       63.41 -    95.11: 12
       95.11 -   126.81: 4
      126.81 -   158.52: 1
  Dihedral angle restraints: 8637
    sinusoidal: 3884
      harmonic: 4753
  Sorted by residual:
  dihedral pdb=" C4'   A D  23 "
           pdb=" C3'   A D  23 "
           pdb=" C2'   A D  23 "
           pdb=" C1'   A D  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -35.91   72.26     1      3.10e+00 1.04e-01 6.95e+02
  dihedral pdb=" O4'   A D  23 "
           pdb=" C4'   A D  23 "
           pdb=" C3'   A D  23 "
           pdb=" C2'   A D  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.15   25.29  -60.43     1      4.00e+00 6.25e-02 3.04e+02
  dihedral pdb=" O4'   A D  23 "
           pdb=" C2'   A D  23 "
           pdb=" C1'   A D  23 "
           pdb=" C3'   A D  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -94.41  -35.07  -59.33     3      3.80e+00 6.93e-02 1.48e+02
  ... (remaining 8634 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1879
       0.054 -    0.109: 242
       0.109 -    0.163: 53
       0.163 -    0.218: 0
       0.218 -    0.272: 2
  Chirality restraints: 2176
  Sorted by residual:
  chirality pdb=" C2'   A D  23 "
            pdb=" C3'   A D  23 "
            pdb=" O2'   A D  23 "
            pdb=" C1'   A D  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.52   -0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" C3'   A D  23 "
            pdb=" C4'   A D  23 "
            pdb=" O3'   A D  23 "
            pdb=" C2'   A D  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.72    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE C  41 "
            pdb=" N   ILE C  41 "
            pdb=" C   ILE C  41 "
            pdb=" CB  ILE C  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.50e-01
  ... (remaining 2173 not shown)

  Planarity restraints: 2361
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D   9 "   -0.006 2.00e-02 2.50e+03   1.01e-02 2.29e+00
        pdb=" N1    C D   9 "    0.009 2.00e-02 2.50e+03
        pdb=" C2    C D   9 "   -0.022 2.00e-02 2.50e+03
        pdb=" O2    C D   9 "    0.013 2.00e-02 2.50e+03
        pdb=" N3    C D   9 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    C D   9 "   -0.010 2.00e-02 2.50e+03
        pdb=" N4    C D   9 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    C D   9 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    C D   9 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 655 "   -0.024 5.00e-02 4.00e+02   3.67e-02 2.16e+00
        pdb=" N   PRO A 656 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 656 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 656 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  26 "    0.020 2.00e-02 2.50e+03   8.44e-03 1.96e+00
        pdb=" N9    A D  26 "   -0.017 2.00e-02 2.50e+03
        pdb=" C8    A D  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A D  26 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A D  26 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  26 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A D  26 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    A D  26 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A D  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  26 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 2358 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 186
        2.60 -     3.17: 12485
        3.17 -     3.75: 20322
        3.75 -     4.32: 27806
        4.32 -     4.90: 47166
  Nonbonded interactions: 107965
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 393 "
            pdb=" OG1 THR A 499 "
     model   vdw
     2.019 3.040
  nonbonded pdb=" OG  SER B 234 "
            pdb="ZN    ZN B 900 "
     model   vdw
     2.066 2.230
  nonbonded pdb=" OG  SER B 695 "
            pdb=" OD1 ASN B 698 "
     model   vdw
     2.079 3.040
  nonbonded pdb=" NZ  LYS A 192 "
            pdb=" OD2 ASP A 215 "
     model   vdw
     2.110 3.120
  nonbonded pdb=" NE2 GLN B 272 "
            pdb=" O   ALA B 276 "
     model   vdw
     2.144 3.120
  ... (remaining 107960 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.070
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
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      :  0.003   0.058  14202  Z= 0.135
  Angle     :  0.492   6.558  19333  Z= 0.252
  Chirality :  0.040   0.272   2176
  Planarity :  0.003   0.037   2361
  Dihedral  : 12.150 158.517   5547
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.93 %
    Favored  : 91.97 %
  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: -0.49 (0.22), residues: 1599
  helix:  1.39 (0.21), residues: 677
  sheet: -0.07 (0.49), residues: 125
  loop : -2.01 (0.22), residues: 797

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1005 
 TYR   0.009   0.001   TYR A 612 
 PHE   0.011   0.001   PHE C  13 
 TRP   0.009   0.001   TRP F 198 
 HIS   0.002   0.001   HIS B 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.13 (14198)
  covalent geometry    : angle       0.48838 /  0.25 (19330)
  hydrogen bonds       : bond        0.13809 / 10.12 (  568)
  hydrogen bonds       : angle       5.74366 /  4.10 ( 1605)
  metal coordination   : bond        0.03657 /  1.82 (    4)
  metal coordination   : angle       4.64024 /  2.63 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 294
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8233 (pp)
REVERT: A  202 MET cc_start: 0.6643 (mmt) cc_final: 0.6441 (mmt)
REVERT: A  207 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7473 (mm-40)
REVERT: A  648 LYS cc_start: 0.7189 (ptmt) cc_final: 0.6876 (ttpt)
REVERT: A  679 LYS cc_start: 0.7521 (tttt) cc_final: 0.7288 (tttm)
REVERT: A  767 GLN cc_start: 0.7096 (tt0) cc_final: 0.6198 (tm-30)
REVERT: A  915 GLN cc_start: 0.7463 (mt0) cc_final: 0.7050 (mt0)
REVERT: A  973 TRP cc_start: 0.7695 (t-100) cc_final: 0.7357 (t-100)
REVERT: A  986 THR cc_start: 0.9196 (t) cc_final: 0.8878 (m)
REVERT: B   97 ILE cc_start: 0.8412 (pt) cc_final: 0.8201 (mt)
REVERT: B  271 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7362 (mp10)
REVERT: B  671 THR cc_start: 0.8029 (m) cc_final: 0.7779 (p)
REVERT: E  642 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7559 (tm-30)
REVERT: F  152 LYS cc_start: 0.6845 (mmtp) cc_final: 0.6624 (mmtt)
  outliers start: 16
  outliers final: 9
  residues processed: 309
  average time/residue: 0.1315
  time to fit residues: 58.1094
Evaluate side-chains
  202 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 190
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  530 ASP
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1034 ILE
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  271 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.0570
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    0.8980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 ASN
B 191 ASN
B 391 GLN
B 698 ASN
F 177 ASN
** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.156768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.121323 restraints weight = 17823.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.123013 restraints weight = 15114.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.123534 restraints weight = 14900.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.124704 restraints weight = 9367.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.125094 restraints weight = 7946.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14202  Z= 0.134
  Angle     :  0.611   7.677  19333  Z= 0.308
  Chirality :  0.045   0.547   2176
  Planarity :  0.004   0.046   2361
  Dihedral  : 10.712 160.563   2194
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.67 %
    Favored  : 86.41 %
  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: -0.13 (0.22), residues: 1599
  helix:  1.59 (0.20), residues: 676
  sheet:  0.18 (0.48), residues: 120
  loop : -1.70 (0.22), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 312 
 TYR   0.025   0.001   TYR E 649 
 PHE   0.025   0.001   PHE C  52 
 TRP   0.008   0.001   TRP B 198 
 HIS   0.004   0.001   HIS A 645 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.13 (14198)
  covalent geometry    : angle       0.60785 /  0.31 (19330)
  hydrogen bonds       : bond        0.04396 /  2.96 (  568)
  hydrogen bonds       : angle       4.54159 /  3.25 ( 1605)
  metal coordination   : bond        0.01579 /  0.79 (    4)
  metal coordination   : angle       4.92700 /  2.66 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 210
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8563 (pp)
REVERT: A  202 MET cc_start: 0.6866 (mmt) cc_final: 0.6615 (mmt)
REVERT: A  212 MET cc_start: 0.7297 (mtp) cc_final: 0.6951 (ttm)
REVERT: A  333 ASP cc_start: 0.6781 (t0) cc_final: 0.6560 (t0)
REVERT: A  716 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7591 (ttpp)
REVERT: A  767 GLN cc_start: 0.7407 (tt0) cc_final: 0.6470 (tm-30)
REVERT: A 1004 LEU cc_start: 0.7808 (tp) cc_final: 0.7341 (tp)
REVERT: B   79 ARG cc_start: 0.7992 (ppt170) cc_final: 0.7015 (ppt170)
REVERT: B   97 ILE cc_start: 0.8469 (pt) cc_final: 0.8218 (mt)
REVERT: B  100 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8181 (mtp)
REVERT: B  126 GLN cc_start: 0.6477 (tm-30) cc_final: 0.5840 (tt0)
REVERT: B  313 MET cc_start: 0.5755 (tmm) cc_final: 0.5216 (tmm)
REVERT: C   25 LEU cc_start: 0.8176 (mp) cc_final: 0.7617 (tp)
REVERT: E  765 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7283 (tm-30)
REVERT: E  767 GLN cc_start: 0.7316 (tp40) cc_final: 0.6942 (tp40)
REVERT: E  788 GLN cc_start: 0.7444 (tp40) cc_final: 0.6986 (mm-40)
REVERT: F   87 ASP cc_start: 0.6378 (p0) cc_final: 0.6112 (p0)
REVERT: F   91 ASP cc_start: 0.6464 (m-30) cc_final: 0.6212 (m-30)
  outliers start: 28
  outliers final: 15
  residues processed: 226
  average time/residue: 0.1157
  time to fit residues: 39.2098
Evaluate side-chains
  199 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  978 THR
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain B residue   88 THR
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain E residue  662 VAL
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain F residue  102 ASN
Chi-restraints excluded: chain F residue  176 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 121 optimal weight:    8.9990
   chunk 130 optimal weight:    0.0870
   chunk 68 optimal weight:   10.0000
   chunk 134 optimal weight:   10.0000
   chunk 54 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 156 optimal weight:    0.3980
   chunk 106 optimal weight:    0.0970
   chunk 131 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 ASN
B 189 ASN
B 699 GLN
C  16 ASN
E 664 ASN
F 127 GLN
** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 193 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.157507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.121746 restraints weight = 18026.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.123211 restraints weight = 14999.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.123160 restraints weight = 16548.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.124658 restraints weight = 10231.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.125249 restraints weight = 8348.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14202  Z= 0.122
  Angle     :  0.572   6.416  19333  Z= 0.286
  Chirality :  0.043   0.210   2176
  Planarity :  0.004   0.047   2361
  Dihedral  : 10.442 162.914   2178
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 12.29 %
    Favored  : 84.90 %
  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: -0.08 (0.21), residues: 1599
  helix:  1.59 (0.20), residues: 675
  sheet:  0.18 (0.49), residues: 116
  loop : -1.62 (0.22), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 751 
 TYR   0.026   0.001   TYR E 649 
 PHE   0.020   0.001   PHE A 893 
 TRP   0.015   0.001   TRP A 973 
 HIS   0.003   0.001   HIS A 594 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 (14198)
  covalent geometry    : angle       0.57024 /  0.29 (19330)
  hydrogen bonds       : bond        0.03858 /  2.57 (  568)
  hydrogen bonds       : angle       4.27547 /  3.05 ( 1605)
  metal coordination   : bond        0.00934 /  0.47 (    4)
  metal coordination   : angle       3.18875 /  1.72 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 194
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8508 (pp)
REVERT: A  202 MET cc_start: 0.6784 (mmt) cc_final: 0.6566 (mmt)
REVERT: A  212 MET cc_start: 0.7260 (mtp) cc_final: 0.6842 (mtm)
REVERT: A  408 LYS cc_start: 0.8357 (ttmt) cc_final: 0.8104 (ttmt)
REVERT: A  468 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7550 (mt-10)
REVERT: A  693 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5573 (mm)
REVERT: A  767 GLN cc_start: 0.7368 (tt0) cc_final: 0.6450 (tm-30)
REVERT: B   79 ARG cc_start: 0.7954 (ppt170) cc_final: 0.6970 (ppt170)
REVERT: B   97 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8236 (mt)
REVERT: B  100 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8067 (mtp)
REVERT: B  126 GLN cc_start: 0.6220 (tm-30) cc_final: 0.5710 (tt0)
REVERT: B  313 MET cc_start: 0.5865 (tmm) cc_final: 0.5367 (tmm)
REVERT: B  676 GLU cc_start: 0.7518 (tp30) cc_final: 0.6983 (pm20)
REVERT: C   25 LEU cc_start: 0.8224 (mp) cc_final: 0.7637 (tp)
REVERT: C   54 PHE cc_start: 0.5832 (m-80) cc_final: 0.5307 (m-80)
REVERT: E  765 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7286 (tm-30)
REVERT: E  788 GLN cc_start: 0.7512 (tp40) cc_final: 0.7180 (mm-40)
REVERT: F  152 LYS cc_start: 0.6406 (mmtt) cc_final: 0.6170 (mmtt)
  outliers start: 41
  outliers final: 26
  residues processed: 223
  average time/residue: 0.1125
  time to fit residues: 37.8591
Evaluate side-chains
  199 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 169
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  530 ASP
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  978 THR
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain B residue   88 THR
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain E residue  662 VAL
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain E residue  780 ILE
Chi-restraints excluded: chain F residue  102 ASN
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  176 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 11 optimal weight:    0.4980
   chunk 62 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 112 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 155 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  59 HIS
** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.155781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.119703 restraints weight = 18069.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.121083 restraints weight = 14641.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.121394 restraints weight = 14663.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.122369 restraints weight = 9270.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.125752 restraints weight = 7990.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14202  Z= 0.146
  Angle     :  0.585   8.733  19333  Z= 0.293
  Chirality :  0.043   0.199   2176
  Planarity :  0.004   0.053   2361
  Dihedral  : 10.450 163.001   2178
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.21 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.21), residues: 1599
  helix:  1.55 (0.20), residues: 663
  sheet:  0.04 (0.51), residues: 111
  loop : -1.57 (0.21), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  72 
 TYR   0.023   0.001   TYR E 649 
 PHE   0.022   0.002   PHE A 893 
 TRP   0.026   0.002   TRP A 973 
 HIS   0.005   0.001   HIS C  59 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 (14198)
  covalent geometry    : angle       0.58426 /  0.29 (19330)
  hydrogen bonds       : bond        0.03982 /  2.63 (  568)
  hydrogen bonds       : angle       4.27656 /  3.06 ( 1605)
  metal coordination   : bond        0.00958 /  0.48 (    4)
  metal coordination   : angle       2.82469 /  1.51 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 176
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8507 (pp)
REVERT: A  202 MET cc_start: 0.6891 (mmt) cc_final: 0.6662 (mmt)
REVERT: A  212 MET cc_start: 0.7338 (mtp) cc_final: 0.6850 (mtm)
REVERT: A  408 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8187 (ttmt)
REVERT: A  468 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7681 (mt-10)
REVERT: A  651 LEU cc_start: 0.8388 (mt) cc_final: 0.8039 (mt)
REVERT: A  693 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.5489 (mm)
REVERT: A  716 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7607 (ttpp)
REVERT: A  767 GLN cc_start: 0.7332 (tt0) cc_final: 0.6398 (tm-30)
REVERT: B   79 ARG cc_start: 0.7972 (ppt170) cc_final: 0.6940 (ppt170)
REVERT: B   97 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8287 (mt)
REVERT: B  126 GLN cc_start: 0.6106 (tm-30) cc_final: 0.5668 (tt0)
REVERT: B  130 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6145 (p0)
REVERT: B  313 MET cc_start: 0.5911 (tmm) cc_final: 0.5362 (tmm)
REVERT: B  676 GLU cc_start: 0.7272 (tp30) cc_final: 0.6860 (pm20)
REVERT: C   25 LEU cc_start: 0.8294 (mp) cc_final: 0.7747 (tp)
REVERT: C   54 PHE cc_start: 0.5848 (m-80) cc_final: 0.5341 (m-80)
REVERT: E  639 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7038 (tm-30)
REVERT: E  765 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7313 (tm-30)
REVERT: E  788 GLN cc_start: 0.7538 (tp40) cc_final: 0.7183 (mm-40)
  outliers start: 47
  outliers final: 31
  residues processed: 208
  average time/residue: 0.1083
  time to fit residues: 33.8772
Evaluate side-chains
  199 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 163
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  443 HIS
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  530 ASP
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  978 THR
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1034 ILE
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  671 THR
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain E residue  662 VAL
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain E residue  780 ILE
Chi-restraints excluded: chain F residue  102 ASN
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  176 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0770
   chunk 143 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 107 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 144 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 155 optimal weight:    2.9990
   chunk 134 optimal weight:   10.0000
   overall best weight:    1.3944

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 700 GLN
C  56 ASN
C  59 HIS
** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.150562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.115449 restraints weight = 18249.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.114706 restraints weight = 17115.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.116168 restraints weight = 16547.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.117004 restraints weight = 11009.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.117460 restraints weight = 10091.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14202  Z= 0.173
  Angle     :  0.606   9.287  19333  Z= 0.303
  Chirality :  0.043   0.191   2176
  Planarity :  0.005   0.056   2361
  Dihedral  : 10.464 162.209   2178
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 14.96 %
    Favored  : 81.40 %
  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: -0.28 (0.21), residues: 1599
  helix:  1.40 (0.20), residues: 666
  sheet: -0.03 (0.50), residues: 116
  loop : -1.64 (0.21), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  72 
 TYR   0.024   0.001   TYR E 649 
 PHE   0.014   0.002   PHE A 893 
 TRP   0.019   0.002   TRP A 973 
 HIS   0.003   0.001   HIS E 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.17 (14198)
  covalent geometry    : angle       0.60528 /  0.30 (19330)
  hydrogen bonds       : bond        0.04205 /  2.77 (  568)
  hydrogen bonds       : angle       4.37387 /  3.15 ( 1605)
  metal coordination   : bond        0.01015 /  0.51 (    4)
  metal coordination   : angle       2.56709 /  1.39 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 174
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8492 (pp)
REVERT: A  202 MET cc_start: 0.6853 (mmt) cc_final: 0.6646 (mmt)
REVERT: A  212 MET cc_start: 0.7367 (mtp) cc_final: 0.6908 (mtm)
REVERT: A  254 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7784 (pp)
REVERT: A  306 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8138 (m)
REVERT: A  408 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8204 (ttmm)
REVERT: A  468 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: A  679 LYS cc_start: 0.8096 (tttm) cc_final: 0.7692 (mmtt)
REVERT: A  693 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5198 (mm)
REVERT: A  716 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7477 (ttpt)
REVERT: A  767 GLN cc_start: 0.7427 (tt0) cc_final: 0.6503 (tm-30)
REVERT: B   79 ARG cc_start: 0.7988 (ppt170) cc_final: 0.6973 (ppt170)
REVERT: B   97 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8262 (mt)
REVERT: B  126 GLN cc_start: 0.6124 (tm-30) cc_final: 0.5558 (tt0)
REVERT: B  130 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6262 (p0)
REVERT: B  313 MET cc_start: 0.5963 (tmm) cc_final: 0.5723 (tmm)
REVERT: B  676 GLU cc_start: 0.7370 (tp30) cc_final: 0.6873 (mp0)
REVERT: B  684 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6574 (tpp)
REVERT: C   25 LEU cc_start: 0.8245 (mp) cc_final: 0.7803 (tp)
REVERT: E  639 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6975 (tm-30)
REVERT: E  765 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7349 (tm-30)
REVERT: E  788 GLN cc_start: 0.7590 (tp40) cc_final: 0.7240 (mm-40)
  outliers start: 53
  outliers final: 34
  residues processed: 210
  average time/residue: 0.1139
  time to fit residues: 36.3191
Evaluate side-chains
  201 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 159
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  530 ASP
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  978 THR
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1034 ILE
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  671 THR
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain B residue  700 GLN
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 HIS
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain E residue  662 VAL
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain E residue  780 ILE
Chi-restraints excluded: chain F residue  102 ASN
Chi-restraints excluded: chain F residue  176 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 121 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 123 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 69 optimal weight:    8.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 GLN
B 700 GLN
C  59 HIS
E 786 GLN
** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.151846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.116471 restraints weight = 18104.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.115877 restraints weight = 15715.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.117747 restraints weight = 15200.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.118233 restraints weight = 9687.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.118914 restraints weight = 8965.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14202  Z= 0.183
  Angle     :  0.612   7.544  19333  Z= 0.307
  Chirality :  0.043   0.210   2176
  Planarity :  0.005   0.058   2361
  Dihedral  : 10.480 163.713   2178
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 15.37 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.21), residues: 1599
  helix:  1.31 (0.20), residues: 671
  sheet:  0.17 (0.51), residues: 113
  loop : -1.69 (0.21), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  72 
 TYR   0.026   0.001   TYR E 649 
 PHE   0.015   0.002   PHE C  54 
 TRP   0.017   0.002   TRP A 973 
 HIS   0.011   0.001   HIS C  59 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.18 (14198)
  covalent geometry    : angle       0.61089 /  0.31 (19330)
  hydrogen bonds       : bond        0.04253 /  2.80 (  568)
  hydrogen bonds       : angle       4.40460 /  3.17 ( 1605)
  metal coordination   : bond        0.01256 /  0.63 (    4)
  metal coordination   : angle       2.61171 /  1.42 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 168
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8476 (pp)
REVERT: A  202 MET cc_start: 0.6849 (mmt) cc_final: 0.6630 (mmt)
REVERT: A  212 MET cc_start: 0.7387 (mtp) cc_final: 0.7068 (ttm)
REVERT: A  254 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7791 (pp)
REVERT: A  306 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8131 (m)
REVERT: A  408 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8134 (ttmm)
REVERT: A  679 LYS cc_start: 0.8132 (tttm) cc_final: 0.7685 (mmtt)
REVERT: A  693 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5363 (mm)
REVERT: A  716 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7472 (ttpt)
REVERT: A  767 GLN cc_start: 0.7448 (tt0) cc_final: 0.6487 (tm-30)
REVERT: B   79 ARG cc_start: 0.7957 (ppt170) cc_final: 0.6922 (ppt170)
REVERT: B   97 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8321 (mt)
REVERT: B  126 GLN cc_start: 0.6111 (tm-30) cc_final: 0.5719 (tt0)
REVERT: B  130 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6413 (p0)
REVERT: B  313 MET cc_start: 0.6006 (tmm) cc_final: 0.5748 (tmm)
REVERT: B  676 GLU cc_start: 0.7272 (tp30) cc_final: 0.6721 (pm20)
REVERT: C   25 LEU cc_start: 0.8281 (mp) cc_final: 0.7847 (tp)
REVERT: C   56 ASN cc_start: 0.7762 (m-40) cc_final: 0.7419 (p0)
REVERT: E  639 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6890 (tm-30)
REVERT: E  765 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7384 (tm-30)
REVERT: E  788 GLN cc_start: 0.7595 (tp40) cc_final: 0.7262 (mm-40)
  outliers start: 51
  outliers final: 35
  residues processed: 201
  average time/residue: 0.1091
  time to fit residues: 33.5686
Evaluate side-chains
  203 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 161
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  530 ASP
Chi-restraints excluded: chain A residue  543 MET
Chi-restraints excluded: chain A residue  566 THR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  978 THR
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1034 ILE
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  671 THR
Chi-restraints excluded: chain B residue  700 GLN
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   11 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain E residue  662 VAL
Chi-restraints excluded: chain E residue  735 LEU
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain F residue  102 ASN
Chi-restraints excluded: chain F residue  176 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 130 optimal weight:    0.7980
   chunk 128 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 160 optimal weight:    0.3980
   chunk 91 optimal weight:    0.2980
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 150 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 109 HIS
B 700 GLN
C  59 HIS
** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.154422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.118345 restraints weight = 18019.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.118430 restraints weight = 15363.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.121094 restraints weight = 12880.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.121305 restraints weight = 8808.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.121875 restraints weight = 8858.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14202  Z= 0.117
  Angle     :  0.550   7.273  19333  Z= 0.277
  Chirality :  0.041   0.205   2176
  Planarity :  0.004   0.057   2361
  Dihedral  : 10.318 163.388   2178
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.27 %
    Favored  : 80.92 %
  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 (0.21), residues: 1599
  helix:  1.50 (0.20), residues: 677
  sheet:  0.02 (0.50), residues: 116
  loop : -1.64 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  72 
 TYR   0.024   0.001   TYR E 649 
 PHE   0.023   0.001   PHE C  13 
 TRP   0.015   0.001   TRP A 973 
 HIS   0.003   0.001   HIS E 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 (14198)
  covalent geometry    : angle       0.54950 /  0.28 (19330)
  hydrogen bonds       : bond        0.03603 /  2.38 (  568)
  hydrogen bonds       : angle       4.18603 /  3.00 ( 1605)
  metal coordination   : bond        0.00811 /  0.41 (    4)
  metal coordination   : angle       2.42164 /  1.30 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 175
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8453 (pp)
REVERT: A  181 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7692 (mm-30)
REVERT: A  202 MET cc_start: 0.6854 (mmt) cc_final: 0.6613 (mmt)
REVERT: A  212 MET cc_start: 0.7228 (mtp) cc_final: 0.6927 (ttm)
REVERT: A  306 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.7969 (m)
REVERT: A  408 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8134 (ttmm)
REVERT: A  693 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5587 (mm)
REVERT: A  716 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7430 (ttpt)
REVERT: A  767 GLN cc_start: 0.7323 (tt0) cc_final: 0.6397 (tm-30)
REVERT: B   79 ARG cc_start: 0.7825 (ppt170) cc_final: 0.6915 (ppt170)
REVERT: B   97 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8246 (mt)
REVERT: B  126 GLN cc_start: 0.6150 (tm-30) cc_final: 0.5648 (tt0)
REVERT: B  130 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6162 (p0)
REVERT: B  313 MET cc_start: 0.5978 (tmm) cc_final: 0.5773 (tmm)
REVERT: B  676 GLU cc_start: 0.7217 (tp30) cc_final: 0.6834 (pm20)
REVERT: B  701 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6681 (mttp)
REVERT: C   25 LEU cc_start: 0.8171 (mp) cc_final: 0.7765 (tp)
REVERT: C   56 ASN cc_start: 0.7590 (m-40) cc_final: 0.7357 (p0)
REVERT: E  765 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7337 (tm-30)
REVERT: E  788 GLN cc_start: 0.7593 (tp40) cc_final: 0.7255 (mm-40)
REVERT: F  101 ASN cc_start: 0.8014 (t0) cc_final: 0.7700 (t0)
  outliers start: 41
  outliers final: 27
  residues processed: 206
  average time/residue: 0.1050
  time to fit residues: 33.1242
Evaluate side-chains
  198 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  530 ASP
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  978 THR
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  671 THR
Chi-restraints excluded: chain B residue  700 GLN
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   11 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain E residue  662 VAL
Chi-restraints excluded: chain E residue  735 LEU
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain E residue  780 ILE
Chi-restraints excluded: chain F residue  176 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 134 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 138 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 153 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0570
   chunk 9 optimal weight:    0.9980
   chunk 146 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0980
   overall best weight:    0.5298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 700 GLN
C  59 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.154614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.118723 restraints weight = 17884.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.117201 restraints weight = 15297.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.118930 restraints weight = 16660.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.120159 restraints weight = 10433.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.122547 restraints weight = 9186.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14202  Z= 0.110
  Angle     :  0.557   9.016  19333  Z= 0.278
  Chirality :  0.041   0.198   2176
  Planarity :  0.004   0.054   2361
  Dihedral  : 10.207 162.356   2178
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.54 %
    Favored  : 80.71 %
  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: -0.11 (0.21), residues: 1599
  helix:  1.56 (0.20), residues: 677
  sheet: -0.00 (0.50), residues: 114
  loop : -1.59 (0.21), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  72 
 TYR   0.024   0.001   TYR E 649 
 PHE   0.020   0.001   PHE C  54 
 TRP   0.033   0.002   TRP A 973 
 HIS   0.003   0.001   HIS A 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 (14198)
  covalent geometry    : angle       0.55612 /  0.28 (19330)
  hydrogen bonds       : bond        0.03429 /  2.26 (  568)
  hydrogen bonds       : angle       4.08679 /  2.92 ( 1605)
  metal coordination   : bond        0.00695 /  0.35 (    4)
  metal coordination   : angle       2.24387 /  1.22 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 172
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8439 (pp)
REVERT: A  181 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7660 (mm-30)
REVERT: A  202 MET cc_start: 0.6863 (mmt) cc_final: 0.6621 (mmt)
REVERT: A  212 MET cc_start: 0.7230 (mtp) cc_final: 0.6931 (ttm)
REVERT: A  254 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7726 (pp)
REVERT: A  306 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8259 (p)
REVERT: A  408 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8140 (ttmm)
REVERT: A  679 LYS cc_start: 0.8091 (tttm) cc_final: 0.7611 (tptp)
REVERT: A  693 LEU cc_start: 0.5523 (OUTLIER) cc_final: 0.5289 (mm)
REVERT: A  716 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7372 (ttpt)
REVERT: A  767 GLN cc_start: 0.7274 (tt0) cc_final: 0.6366 (tm-30)
REVERT: B   79 ARG cc_start: 0.7774 (ppt170) cc_final: 0.6814 (ppt170)
REVERT: B   97 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8215 (mt)
REVERT: B  126 GLN cc_start: 0.6012 (tm-30) cc_final: 0.5631 (tt0)
REVERT: B  130 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6193 (p0)
REVERT: B  676 GLU cc_start: 0.7252 (tp30) cc_final: 0.6856 (pm20)
REVERT: C   25 LEU cc_start: 0.8213 (mp) cc_final: 0.7799 (tp)
REVERT: C   56 ASN cc_start: 0.7603 (m-40) cc_final: 0.7349 (p0)
REVERT: E  765 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7354 (tm-30)
REVERT: E  788 GLN cc_start: 0.7588 (tp40) cc_final: 0.7300 (mm-40)
REVERT: F  101 ASN cc_start: 0.8108 (t0) cc_final: 0.7777 (t0)
  outliers start: 40
  outliers final: 27
  residues processed: 200
  average time/residue: 0.1012
  time to fit residues: 30.9174
Evaluate side-chains
  197 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 162
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  530 ASP
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  978 THR
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  671 THR
Chi-restraints excluded: chain B residue  700 GLN
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain E residue  662 VAL
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain E residue  780 ILE
Chi-restraints excluded: chain F residue  176 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 114 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0870
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 138 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.3564

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 109 HIS
B 275 HIS
C  59 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.153476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.117553 restraints weight = 18148.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.117342 restraints weight = 15646.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.118773 restraints weight = 15462.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.119606 restraints weight = 9736.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.120170 restraints weight = 8710.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14202  Z= 0.170
  Angle     :  0.604  11.980  19333  Z= 0.302
  Chirality :  0.043   0.197   2176
  Planarity :  0.004   0.057   2361
  Dihedral  : 10.248 161.511   2178
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.27 %
    Favored  : 80.71 %
  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: -0.27 (0.21), residues: 1599
  helix:  1.38 (0.20), residues: 674
  sheet: -0.04 (0.50), residues: 114
  loop : -1.62 (0.21), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  72 
 TYR   0.024   0.001   TYR E 649 
 PHE   0.021   0.002   PHE C  54 
 TRP   0.028   0.002   TRP A 973 
 HIS   0.003   0.001   HIS E 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.17 (14198)
  covalent geometry    : angle       0.60356 /  0.30 (19330)
  hydrogen bonds       : bond        0.03964 /  2.60 (  568)
  hydrogen bonds       : angle       4.24916 /  3.06 ( 1605)
  metal coordination   : bond        0.00600 /  0.30 (    4)
  metal coordination   : angle       2.20337 /  1.21 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 174
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8466 (pp)
REVERT: A  181 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7753 (mm-30)
REVERT: A  202 MET cc_start: 0.6849 (mmt) cc_final: 0.6638 (mmt)
REVERT: A  212 MET cc_start: 0.7262 (mtp) cc_final: 0.6976 (ttm)
REVERT: A  254 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7790 (pp)
REVERT: A  306 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8368 (p)
REVERT: A  408 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8151 (ttmm)
REVERT: A  679 LYS cc_start: 0.8033 (tttm) cc_final: 0.7559 (tptp)
REVERT: A  693 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5529 (mm)
REVERT: A  716 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7351 (ttpt)
REVERT: A  767 GLN cc_start: 0.7370 (tt0) cc_final: 0.6418 (tm-30)
REVERT: B   79 ARG cc_start: 0.7893 (ppt170) cc_final: 0.6866 (ppt170)
REVERT: B   97 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8244 (mt)
REVERT: B  126 GLN cc_start: 0.6081 (tm-30) cc_final: 0.5674 (tt0)
REVERT: B  130 ASP cc_start: 0.6559 (OUTLIER) cc_final: 0.6082 (p0)
REVERT: B  188 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5856 (tm)
REVERT: B  313 MET cc_start: 0.5750 (tmm) cc_final: 0.5399 (tmm)
REVERT: B  676 GLU cc_start: 0.7221 (tp30) cc_final: 0.6734 (mp0)
REVERT: C   25 LEU cc_start: 0.8226 (mp) cc_final: 0.7803 (tp)
REVERT: E  765 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7373 (tm-30)
REVERT: E  788 GLN cc_start: 0.7618 (tp40) cc_final: 0.7321 (mm-40)
REVERT: F  101 ASN cc_start: 0.8085 (t0) cc_final: 0.7764 (t0)
  outliers start: 44
  outliers final: 25
  residues processed: 208
  average time/residue: 0.1036
  time to fit residues: 32.9986
Evaluate side-chains
  202 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 168
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  530 ASP
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  978 THR
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  671 THR
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain E residue  662 VAL
Chi-restraints excluded: chain E residue  735 LEU
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain F residue  176 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0980
   chunk 35 optimal weight:    0.5980
   chunk 145 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 119 optimal weight:    0.9980
   chunk 113 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN
C  59 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.154648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.118551 restraints weight = 18041.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.117256 restraints weight = 15412.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.118984 restraints weight = 16523.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.120163 restraints weight = 10446.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.122624 restraints weight = 9220.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14202  Z= 0.118
  Angle     :  0.566   8.367  19333  Z= 0.284
  Chirality :  0.042   0.197   2176
  Planarity :  0.004   0.056   2361
  Dihedral  : 10.172 162.049   2178
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.88 %
    Favored  : 80.37 %
  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: -0.16 (0.21), residues: 1599
  helix:  1.48 (0.20), residues: 678
  sheet: -0.03 (0.50), residues: 116
  loop : -1.58 (0.22), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  72 
 TYR   0.023   0.001   TYR E 649 
 PHE   0.022   0.001   PHE C  54 
 TRP   0.031   0.002   TRP A 973 
 HIS   0.003   0.001   HIS E 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 (14198)
  covalent geometry    : angle       0.56568 /  0.28 (19330)
  hydrogen bonds       : bond        0.03480 /  2.29 (  568)
  hydrogen bonds       : angle       4.09008 /  2.92 ( 1605)
  metal coordination   : bond        0.00686 /  0.34 (    4)
  metal coordination   : angle       2.06558 /  1.13 (    3)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 169
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8442 (pp)
REVERT: A  181 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7716 (mm-30)
REVERT: A  202 MET cc_start: 0.6836 (mmt) cc_final: 0.6579 (mmt)
REVERT: A  212 MET cc_start: 0.7240 (mtp) cc_final: 0.6957 (ttm)
REVERT: A  254 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7757 (pp)
REVERT: A  306 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8255 (p)
REVERT: A  408 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8147 (ttmm)
REVERT: A  679 LYS cc_start: 0.8060 (tttm) cc_final: 0.7473 (tptp)
REVERT: A  693 LEU cc_start: 0.5831 (OUTLIER) cc_final: 0.5569 (mm)
REVERT: A  716 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7388 (ttpt)
REVERT: A  767 GLN cc_start: 0.7301 (tt0) cc_final: 0.6390 (tm-30)
REVERT: B   79 ARG cc_start: 0.7753 (ppt170) cc_final: 0.6803 (ppt170)
REVERT: B   97 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8241 (mt)
REVERT: B  126 GLN cc_start: 0.6033 (tm-30) cc_final: 0.5648 (tt0)
REVERT: B  130 ASP cc_start: 0.6530 (OUTLIER) cc_final: 0.6042 (p0)
REVERT: B  188 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5827 (tm)
REVERT: B  313 MET cc_start: 0.5650 (tmm) cc_final: 0.5280 (tmm)
REVERT: B  676 GLU cc_start: 0.7232 (tp30) cc_final: 0.6835 (pm20)
REVERT: B  700 GLN cc_start: 0.6246 (pp30) cc_final: 0.6042 (pp30)
REVERT: C   25 LEU cc_start: 0.8301 (mp) cc_final: 0.7860 (tp)
REVERT: E  765 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7356 (tm-30)
REVERT: E  788 GLN cc_start: 0.7565 (tp40) cc_final: 0.7253 (mm-40)
REVERT: F  101 ASN cc_start: 0.8075 (t0) cc_final: 0.7739 (t0)
  outliers start: 40
  outliers final: 26
  residues processed: 200
  average time/residue: 0.1040
  time to fit residues: 31.9989
Evaluate side-chains
  199 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 164
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  530 ASP
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  978 THR
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  671 THR
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain E residue  662 VAL
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain E residue  780 ILE
Chi-restraints excluded: chain F residue  176 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 160 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 141 optimal weight:    0.0030
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.6592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN
C  59 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.158280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.122567 restraints weight = 17799.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.121137 restraints weight = 15178.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.123022 restraints weight = 16183.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.124034 restraints weight = 10422.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.124851 restraints weight = 9327.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14202  Z= 0.121
  Angle     :  0.580  10.261  19333  Z= 0.292
  Chirality :  0.042   0.196   2176
  Planarity :  0.004   0.054   2361
  Dihedral  : 10.122 161.825   2178
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.16 %
    Favored  : 80.10 %
  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: -0.16 (0.21), residues: 1599
  helix:  1.46 (0.20), residues: 679
  sheet: -0.04 (0.49), residues: 114
  loop : -1.56 (0.22), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  72 
 TYR   0.024   0.001   TYR E 649 
 PHE   0.023   0.001   PHE C  54 
 TRP   0.029   0.002   TRP A 973 
 HIS   0.002   0.001   HIS E 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 (14198)
  covalent geometry    : angle       0.57957 /  0.29 (19330)
  hydrogen bonds       : bond        0.03528 /  2.31 (  568)
  hydrogen bonds       : angle       4.06371 /  2.88 ( 1605)
  metal coordination   : bond        0.00683 /  0.34 (    4)
  metal coordination   : angle       1.97711 /  1.09 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3534.24 seconds
wall clock time: 61 minutes 23.01 seconds (3683.01 seconds total)