Starting phenix.real_space_refine
on Wed Mar  4 14:01:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s7c_24883/03_2026/7s7c_24883.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s7c_24883/03_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s7c_24883/03_2026/7s7c_24883.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s7c_24883/03_2026/7s7c_24883.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s7c_24883/03_2026/7s7c_24883.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s7c_24883/03_2026/7s7c_24883.map"
  }
  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-5986/lib/python3.9/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: 3.38, per 1000 atoms: 0.24
  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: 1.50
  Conformation dependent library (CDL) restraints added in 533.1 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: 1.77
  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: 2.44

  Time building geometry restraints manager: 1.90 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: 8528
       31.70 -    63.41: 182
       63.41 -    95.11: 34
       95.11 -   126.81: 4
      126.81 -   158.52: 1
  Dihedral angle restraints: 8749
    sinusoidal: 3996
      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 8746 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:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.220
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
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  : 13.470 158.517   5659
  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
  covalent geometry    : bond        0.00308 (14198)
  covalent geometry    : angle       0.48838 (19330)
  hydrogen bonds       : bond        0.13809 (  568)
  hydrogen bonds       : angle       5.74366 ( 1605)
  metal coordination   : bond        0.03657 (    4)
  metal coordination   : angle       4.64024 (    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  : 0.557 
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: 0.1309
  time to fit residues: 57.8112
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  : 0.384 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4018 r_free = 0.4018 target = 0.156939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.121526 restraints weight = 17776.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.122738 restraints weight = 14964.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.123617 restraints weight = 14853.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.124541 restraints weight = 9319.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.125254 restraints weight = 8109.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.1865

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= 0.138
  Angle     :  0.610   7.360  19333  Z= 0.307
  Chirality :  0.045   0.503   2176
  Planarity :  0.004   0.046   2361
  Dihedral  : 14.109 160.358   2306
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.74 %
    Favored  : 86.20 %
  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:  1.56 (0.20), residues: 678
  sheet:  0.17 (0.48), residues: 120
  loop : -1.67 (0.22), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 312 
 TYR   0.025   0.001   TYR E 649 
 PHE   0.026   0.001   PHE C  52 
 TRP   0.009   0.001   TRP B 198 
 HIS   0.004   0.001   HIS A 645 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (14198)
  covalent geometry    : angle       0.60745 (19330)
  hydrogen bonds       : bond        0.04272 (  568)
  hydrogen bonds       : angle       4.49920 ( 1605)
  metal coordination   : bond        0.01750 (    4)
  metal coordination   : angle       4.75286 (    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
  246 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 216
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8558 (pp)
REVERT: A  202 MET cc_start: 0.6858 (mmt) cc_final: 0.6613 (mmt)
REVERT: A  207 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7285 (mm-40)
REVERT: A  212 MET cc_start: 0.7294 (mtp) cc_final: 0.6942 (ttm)
REVERT: A  333 ASP cc_start: 0.6878 (t0) cc_final: 0.6560 (t0)
REVERT: A  468 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7715 (mt-10)
REVERT: A  716 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7588 (ttpp)
REVERT: A  767 GLN cc_start: 0.7397 (tt0) cc_final: 0.6461 (tm-30)
REVERT: A 1004 LEU cc_start: 0.7795 (tp) cc_final: 0.7310 (tp)
REVERT: B   79 ARG cc_start: 0.7990 (ppt170) cc_final: 0.7011 (ppt170)
REVERT: B   97 ILE cc_start: 0.8459 (pt) cc_final: 0.8194 (mt)
REVERT: B  100 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8143 (mtp)
REVERT: B  126 GLN cc_start: 0.6436 (tm-30) cc_final: 0.5850 (tt0)
REVERT: B  313 MET cc_start: 0.5761 (tmm) cc_final: 0.5238 (tmm)
REVERT: C   25 LEU cc_start: 0.8186 (mp) cc_final: 0.7628 (tp)
REVERT: E  765 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7219 (tm-30)
REVERT: E  767 GLN cc_start: 0.7320 (tp40) cc_final: 0.6939 (tp40)
REVERT: F   87 ASP cc_start: 0.6393 (p0) cc_final: 0.6176 (p0)
REVERT: F   91 ASP cc_start: 0.6479 (m-30) cc_final: 0.6250 (m-30)
  outliers start: 30
  outliers final: 16
  residues processed: 234
  average time/residue: 0.1141
  time to fit residues: 39.6757
Evaluate side-chains
  203 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
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  311 TYR
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  678 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:    7.9990
   chunk 121 optimal weight:    0.9990
   chunk 130 optimal weight:    0.0270
   chunk 68 optimal weight:    9.9990
   chunk 134 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 156 optimal weight:    0.4980
   chunk 106 optimal weight:    3.9990
   chunk 131 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.6040

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3991 r_free = 0.3991 target = 0.154202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.118808 restraints weight = 18222.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.117540 restraints weight = 15978.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.119562 restraints weight = 15332.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.120330 restraints weight = 10330.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.120814 restraints weight = 9513.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14202  Z= 0.120
  Angle     :  0.572   6.415  19333  Z= 0.286
  Chirality :  0.042   0.212   2176
  Planarity :  0.004   0.046   2361
  Dihedral  : 13.962 162.987   2293
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.63 %
    Favored  : 84.49 %
  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: -0.09 (0.21), residues: 1599
  helix:  1.59 (0.20), residues: 675
  sheet:  0.07 (0.47), residues: 123
  loop : -1.62 (0.22), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1032 
 TYR   0.026   0.001   TYR E 649 
 PHE   0.019   0.001   PHE A 893 
 TRP   0.014   0.001   TRP A 973 
 HIS   0.003   0.001   HIS A 594 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (14198)
  covalent geometry    : angle       0.57026 (19330)
  hydrogen bonds       : bond        0.03811 (  568)
  hydrogen bonds       : angle       4.27166 ( 1605)
  metal coordination   : bond        0.00973 (    4)
  metal coordination   : angle       3.23629 (    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
  233 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 191
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8505 (pp)
REVERT: A  207 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7301 (mm-40)
REVERT: A  212 MET cc_start: 0.7173 (mtp) cc_final: 0.6778 (mtm)
REVERT: A  408 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8102 (ttmt)
REVERT: A  468 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7617 (mt-10)
REVERT: A  693 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5604 (mm)
REVERT: A  767 GLN cc_start: 0.7373 (tt0) cc_final: 0.6469 (tm-30)
REVERT: A  891 MET cc_start: 0.7431 (mtp) cc_final: 0.6987 (ttm)
REVERT: A 1004 LEU cc_start: 0.7840 (tp) cc_final: 0.7339 (tp)
REVERT: B   97 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8219 (mt)
REVERT: B  100 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8053 (mtp)
REVERT: B  120 VAL cc_start: 0.6991 (t) cc_final: 0.6724 (t)
REVERT: B  126 GLN cc_start: 0.6232 (tm-30) cc_final: 0.5712 (tt0)
REVERT: B  313 MET cc_start: 0.5844 (tmm) cc_final: 0.5348 (tmm)
REVERT: B  663 MET cc_start: 0.6894 (mmm) cc_final: 0.6273 (mtm)
REVERT: B  676 GLU cc_start: 0.7505 (tp30) cc_final: 0.7006 (pm20)
REVERT: C   25 LEU cc_start: 0.8212 (mp) cc_final: 0.7626 (tp)
REVERT: C   54 PHE cc_start: 0.5758 (m-80) cc_final: 0.5270 (m-80)
REVERT: E  765 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7258 (tm-30)
REVERT: E  788 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7256 (mm-40)
  outliers start: 42
  outliers final: 25
  residues processed: 220
  average time/residue: 0.1090
  time to fit residues: 36.4117
Evaluate side-chains
  198 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 168
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
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  207 GLN
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  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  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  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:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 12 optimal weight:    0.3980
   chunk 66 optimal weight:    6.9990
   chunk 155 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
C  59 HIS
** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.154519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.119083 restraints weight = 18015.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.118422 restraints weight = 15693.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.120328 restraints weight = 15705.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.121101 restraints weight = 10261.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.121855 restraints weight = 9242.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14202  Z= 0.142
  Angle     :  0.576   8.863  19333  Z= 0.289
  Chirality :  0.043   0.199   2176
  Planarity :  0.004   0.052   2361
  Dihedral  : 13.953 162.559   2293
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 13.59 %
    Favored  : 83.18 %
  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:  1.59 (0.20), residues: 663
  sheet:  0.05 (0.51), residues: 111
  loop : -1.56 (0.21), residues: 825

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 C  13 
 TRP   0.028   0.002   TRP A 973 
 HIS   0.005   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (14198)
  covalent geometry    : angle       0.57502 (19330)
  hydrogen bonds       : bond        0.03941 (  568)
  hydrogen bonds       : angle       4.25955 ( 1605)
  metal coordination   : bond        0.01070 (    4)
  metal coordination   : angle       2.79111 (    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
  226 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 179
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8518 (pp)
REVERT: A  207 GLN cc_start: 0.7598 (mp10) cc_final: 0.7316 (mm-40)
REVERT: A  212 MET cc_start: 0.7219 (mtp) cc_final: 0.6753 (mtm)
REVERT: A  693 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5416 (mm)
REVERT: A  716 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7616 (ttpp)
REVERT: A  767 GLN cc_start: 0.7380 (tt0) cc_final: 0.6457 (tm-30)
REVERT: B   72 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7426 (ttt-90)
REVERT: B   79 ARG cc_start: 0.7973 (ppt170) cc_final: 0.6970 (ppt170)
REVERT: B   97 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8232 (mt)
REVERT: B  100 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8314 (mtp)
REVERT: B  126 GLN cc_start: 0.6034 (tm-30) cc_final: 0.5614 (tt0)
REVERT: B  130 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6146 (p0)
REVERT: B  313 MET cc_start: 0.5909 (tmm) cc_final: 0.5387 (tmm)
REVERT: B  676 GLU cc_start: 0.7349 (tp30) cc_final: 0.6883 (pm20)
REVERT: B  701 LYS cc_start: 0.7084 (ptpt) cc_final: 0.6728 (mtmt)
REVERT: C   25 LEU cc_start: 0.8261 (mp) cc_final: 0.7729 (tp)
REVERT: C   54 PHE cc_start: 0.5734 (m-80) cc_final: 0.5267 (m-80)
REVERT: E  639 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6952 (tm-30)
REVERT: E  765 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7290 (tm-30)
REVERT: E  788 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7246 (mm-40)
  outliers start: 47
  outliers final: 29
  residues processed: 211
  average time/residue: 0.1123
  time to fit residues: 35.7313
Evaluate side-chains
  204 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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  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  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  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   72 ARG
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  130 ASP
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  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:    0.5980
   chunk 143 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 107 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 144 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 155 optimal weight:    2.9990
   chunk 134 optimal weight:    9.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 ASN
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 HIS
** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.150495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.115050 restraints weight = 18270.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.113704 restraints weight = 16893.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115771 restraints weight = 15205.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.116182 restraints weight = 10830.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.116636 restraints weight = 10424.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  14202  Z= 0.200
  Angle     :  0.631   9.398  19333  Z= 0.317
  Chirality :  0.045   0.205   2176
  Planarity :  0.005   0.059   2361
  Dihedral  : 14.007 163.967   2290
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.24 %
    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: -0.38 (0.21), residues: 1599
  helix:  1.27 (0.20), residues: 666
  sheet:  0.08 (0.49), residues: 121
  loop : -1.69 (0.21), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 312 
 TYR   0.026   0.002   TYR E 649 
 PHE   0.023   0.002   PHE A 893 
 TRP   0.021   0.002   TRP A 973 
 HIS   0.003   0.001   HIS E 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (14198)
  covalent geometry    : angle       0.62997 (19330)
  hydrogen bonds       : bond        0.04521 (  568)
  hydrogen bonds       : angle       4.49100 ( 1605)
  metal coordination   : bond        0.01163 (    4)
  metal coordination   : angle       2.67375 (    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
  228 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 175
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8472 (pp)
REVERT: A  207 GLN cc_start: 0.7613 (mp10) cc_final: 0.7372 (mm-40)
REVERT: A  212 MET cc_start: 0.7367 (mtp) cc_final: 0.7050 (ttm)
REVERT: A  254 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7817 (pp)
REVERT: A  306 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8182 (m)
REVERT: A  679 LYS cc_start: 0.8096 (tttm) cc_final: 0.7714 (mmtt)
REVERT: A  693 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5180 (mm)
REVERT: A  716 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7498 (ttpt)
REVERT: A  767 GLN cc_start: 0.7477 (tt0) cc_final: 0.6530 (tm-30)
REVERT: B   79 ARG cc_start: 0.7966 (ppt170) cc_final: 0.6866 (ppt170)
REVERT: B   97 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8281 (mt)
REVERT: B  126 GLN cc_start: 0.6038 (tm-30) cc_final: 0.5486 (tt0)
REVERT: B  313 MET cc_start: 0.6035 (tmm) cc_final: 0.5771 (tmm)
REVERT: B  328 LEU cc_start: 0.7850 (mt) cc_final: 0.7339 (tt)
REVERT: B  676 GLU cc_start: 0.7407 (tp30) cc_final: 0.6830 (pm20)
REVERT: C   25 LEU cc_start: 0.8275 (mp) cc_final: 0.7832 (tp)
REVERT: E  639 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6937 (tm-30)
REVERT: E  765 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7388 (tm-30)
REVERT: E  788 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7304 (mm-40)
  outliers start: 53
  outliers final: 32
  residues processed: 209
  average time/residue: 0.1085
  time to fit residues: 34.5859
Evaluate side-chains
  198 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 160
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
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  472 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  530 ASP
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  302 THR
Chi-restraints excluded: chain B residue  671 THR
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   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 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:   10.0000
   chunk 121 optimal weight:    0.0570
   chunk 49 optimal weight:    4.9990
   chunk 123 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0970
   chunk 39 optimal weight:    0.4980
   chunk 82 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 73 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
B 394 GLN
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4008 r_free = 0.4008 target = 0.156249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.119982 restraints weight = 17811.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.120238 restraints weight = 15025.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.121626 restraints weight = 15153.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.122447 restraints weight = 9768.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.123498 restraints weight = 8760.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14202  Z= 0.106
  Angle     :  0.542   6.793  19333  Z= 0.273
  Chirality :  0.041   0.205   2176
  Planarity :  0.004   0.054   2361
  Dihedral  : 13.845 164.151   2290
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.99 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.21), residues: 1599
  helix:  1.56 (0.20), residues: 677
  sheet:  0.18 (0.51), residues: 111
  loop : -1.59 (0.22), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  72 
 TYR   0.023   0.001   TYR E 649 
 PHE   0.017   0.001   PHE C  52 
 TRP   0.017   0.001   TRP A 973 
 HIS   0.027   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (14198)
  covalent geometry    : angle       0.54144 (19330)
  hydrogen bonds       : bond        0.03472 (  568)
  hydrogen bonds       : angle       4.13644 ( 1605)
  metal coordination   : bond        0.00830 (    4)
  metal coordination   : angle       2.39448 (    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
  213 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 178
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8450 (pp)
REVERT: A  181 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7642 (mm-30)
REVERT: A  207 GLN cc_start: 0.7581 (mp10) cc_final: 0.7283 (mm-40)
REVERT: A  212 MET cc_start: 0.7188 (mtp) cc_final: 0.6877 (ttm)
REVERT: A  306 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.7942 (m)
REVERT: A  679 LYS cc_start: 0.8055 (tttm) cc_final: 0.7641 (mmtt)
REVERT: A  693 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5250 (mm)
REVERT: A  716 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7429 (ttpt)
REVERT: A  767 GLN cc_start: 0.7317 (tt0) cc_final: 0.6424 (tm-30)
REVERT: A 1004 LEU cc_start: 0.7689 (tp) cc_final: 0.7223 (tp)
REVERT: B   72 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7336 (ttt-90)
REVERT: B   79 ARG cc_start: 0.7811 (ppt170) cc_final: 0.6893 (ppt170)
REVERT: B   97 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8209 (mt)
REVERT: B  126 GLN cc_start: 0.5946 (tm-30) cc_final: 0.5567 (tt0)
REVERT: B  130 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6195 (p0)
REVERT: B  676 GLU cc_start: 0.7230 (tp30) cc_final: 0.6823 (pm20)
REVERT: C   25 LEU cc_start: 0.8156 (mp) cc_final: 0.7716 (tp)
REVERT: C   56 ASN cc_start: 0.7636 (m110) cc_final: 0.7364 (p0)
REVERT: E  765 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7305 (tm-30)
REVERT: E  788 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7312 (mm-40)
REVERT: F  101 ASN cc_start: 0.8011 (t0) cc_final: 0.7700 (t0)
  outliers start: 35
  outliers final: 18
  residues processed: 204
  average time/residue: 0.1050
  time to fit residues: 32.8047
Evaluate side-chains
  193 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
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  275 ASP
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  311 TYR
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  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 B residue   72 ARG
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 E residue  662 VAL
Chi-restraints excluded: chain E residue  746 ILE
Chi-restraints excluded: chain E residue  774 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 130 optimal weight:    0.8980
   chunk 128 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 160 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 150 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 112 optimal weight:    0.0010
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
B 109 HIS
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.156181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.120402 restraints weight = 17887.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.119080 restraints weight = 15200.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.120874 restraints weight = 16311.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122054 restraints weight = 10215.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.124233 restraints weight = 9021.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.2935

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= 0.117
  Angle     :  0.556   7.614  19333  Z= 0.278
  Chirality :  0.042   0.199   2176
  Planarity :  0.004   0.052   2361
  Dihedral  : 13.765 162.989   2290
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.79 %
    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: -0.03 (0.21), residues: 1599
  helix:  1.63 (0.20), residues: 670
  sheet:  0.03 (0.50), residues: 114
  loop : -1.53 (0.22), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  72 
 TYR   0.025   0.001   TYR E 649 
 PHE   0.024   0.001   PHE C  13 
 TRP   0.029   0.002   TRP A 973 
 HIS   0.002   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (14198)
  covalent geometry    : angle       0.55523 (19330)
  hydrogen bonds       : bond        0.03491 (  568)
  hydrogen bonds       : angle       4.08194 ( 1605)
  metal coordination   : bond        0.00704 (    4)
  metal coordination   : angle       2.21201 (    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
  211 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 170
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8436 (pp)
REVERT: A  207 GLN cc_start: 0.7617 (mp10) cc_final: 0.7338 (mm-40)
REVERT: A  212 MET cc_start: 0.7243 (mtp) cc_final: 0.6934 (ttm)
REVERT: A  254 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7730 (pp)
REVERT: A  306 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8266 (p)
REVERT: A  693 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5539 (mm)
REVERT: A  716 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7416 (ttpt)
REVERT: A  767 GLN cc_start: 0.7327 (tt0) cc_final: 0.6395 (tm-30)
REVERT: A  916 GLU cc_start: 0.5677 (mp0) cc_final: 0.5467 (mp0)
REVERT: B   72 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7406 (ttt-90)
REVERT: B   79 ARG cc_start: 0.7797 (ppt170) cc_final: 0.6812 (ppt170)
REVERT: B   97 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8232 (mt)
REVERT: B  126 GLN cc_start: 0.6054 (tm-30) cc_final: 0.5628 (tt0)
REVERT: B  130 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6203 (p0)
REVERT: B  313 MET cc_start: 0.5699 (tmm) cc_final: 0.5296 (tmm)
REVERT: B  676 GLU cc_start: 0.7253 (tp30) cc_final: 0.6836 (pm20)
REVERT: B  701 LYS cc_start: 0.7349 (mtpt) cc_final: 0.6504 (mttp)
REVERT: C   25 LEU cc_start: 0.8175 (mp) cc_final: 0.7739 (tp)
REVERT: E  757 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7215 (mm110)
REVERT: E  765 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7333 (tm-30)
REVERT: E  788 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7335 (mm-40)
REVERT: F  101 ASN cc_start: 0.8067 (t0) cc_final: 0.7726 (t0)
  outliers start: 41
  outliers final: 25
  residues processed: 202
  average time/residue: 0.1083
  time to fit residues: 33.4768
Evaluate side-chains
  196 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 162
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
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  202 MET
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  441 VAL
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  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   72 ARG
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   40 LYS
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  757 GLN
Chi-restraints excluded: chain E residue  774 ILE
Chi-restraints excluded: chain E residue  780 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 134 optimal weight:   10.9990
   chunk 80 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 138 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 153 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 146 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0010
   overall best weight:    1.5994

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

Flipped N/Q/H residues before XYZ refinement:
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 275 HIS
C  56 ASN
C  59 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.152401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.116457 restraints weight = 18004.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.115587 restraints weight = 15812.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.117453 restraints weight = 15833.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.118163 restraints weight = 10168.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.118823 restraints weight = 9254.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  14202  Z= 0.193
  Angle     :  0.629   7.950  19333  Z= 0.317
  Chirality :  0.044   0.198   2176
  Planarity :  0.005   0.056   2361
  Dihedral  : 13.857 161.835   2290
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.20 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.21), residues: 1599
  helix:  1.33 (0.20), residues: 665
  sheet: -0.05 (0.48), residues: 126
  loop : -1.67 (0.21), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 751 
 TYR   0.026   0.002   TYR E 649 
 PHE   0.023   0.002   PHE C  13 
 TRP   0.023   0.002   TRP A 973 
 HIS   0.003   0.001   HIS E 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (14198)
  covalent geometry    : angle       0.62834 (19330)
  hydrogen bonds       : bond        0.04250 (  568)
  hydrogen bonds       : angle       4.35120 ( 1605)
  metal coordination   : bond        0.00661 (    4)
  metal coordination   : angle       2.32502 (    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
  219 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 173
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8498 (pp)
REVERT: A  181 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7798 (mm-30)
REVERT: A  207 GLN cc_start: 0.7621 (mp10) cc_final: 0.7413 (mm-40)
REVERT: A  212 MET cc_start: 0.7356 (mtp) cc_final: 0.7018 (mtp)
REVERT: A  254 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7821 (pp)
REVERT: A  306 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8415 (p)
REVERT: A  679 LYS cc_start: 0.8019 (tttm) cc_final: 0.7577 (tptp)
REVERT: A  693 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.5383 (mm)
REVERT: A  716 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7367 (ttpt)
REVERT: B   72 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7405 (ttt-90)
REVERT: B   79 ARG cc_start: 0.7947 (ppt170) cc_final: 0.6883 (ppt170)
REVERT: B   97 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8257 (mt)
REVERT: B  126 GLN cc_start: 0.6057 (tm-30) cc_final: 0.5718 (tt0)
REVERT: B  130 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.6150 (p0)
REVERT: B  313 MET cc_start: 0.5741 (tmm) cc_final: 0.5283 (tmm)
REVERT: B  676 GLU cc_start: 0.7252 (tp30) cc_final: 0.6755 (pm20)
REVERT: B  701 LYS cc_start: 0.7441 (mtpt) cc_final: 0.6602 (mttp)
REVERT: C   25 LEU cc_start: 0.8176 (mp) cc_final: 0.7753 (tp)
REVERT: E  765 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7351 (tm-30)
REVERT: E  788 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7341 (mm-40)
  outliers start: 46
  outliers final: 29
  residues processed: 207
  average time/residue: 0.1104
  time to fit residues: 34.6449
Evaluate side-chains
  200 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 162
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
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  202 MET
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  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  693 LEU
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  716 LYS
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 B residue   72 ARG
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  130 ASP
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   59 HIS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 138 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0370
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0870
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
C  56 ASN
** C  59 HIS ** 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 = 0.3988 r_free = 0.3988 target = 0.154243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.118315 restraints weight = 18038.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.118077 restraints weight = 15216.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.119489 restraints weight = 15286.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.120411 restraints weight = 9571.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.120944 restraints weight = 8535.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.3026

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= 0.117
  Angle     :  0.573  10.529  19333  Z= 0.289
  Chirality :  0.042   0.193   2176
  Planarity :  0.004   0.056   2361
  Dihedral  : 13.765 161.459   2290
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.61 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.21), residues: 1599
  helix:  1.52 (0.20), residues: 674
  sheet:  0.04 (0.49), residues: 116
  loop : -1.59 (0.22), residues: 809

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   0.018   0.001   PHE C  57 
 TRP   0.023   0.002   TRP A 973 
 HIS   0.014   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (14198)
  covalent geometry    : angle       0.57198 (19330)
  hydrogen bonds       : bond        0.03581 (  568)
  hydrogen bonds       : angle       4.15929 ( 1605)
  metal coordination   : bond        0.00780 (    4)
  metal coordination   : angle       2.19492 (    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
  205 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 165
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8451 (pp)
REVERT: A  181 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7719 (mm-30)
REVERT: A  207 GLN cc_start: 0.7638 (mp10) cc_final: 0.7334 (mm-40)
REVERT: A  212 MET cc_start: 0.7217 (mtp) cc_final: 0.6930 (ttm)
REVERT: A  254 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7739 (pp)
REVERT: A  306 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8269 (p)
REVERT: A  679 LYS cc_start: 0.8030 (tttm) cc_final: 0.7570 (tptp)
REVERT: A  693 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5489 (mm)
REVERT: A  716 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7384 (ttpt)
REVERT: B   79 ARG cc_start: 0.7724 (ppt170) cc_final: 0.6798 (ppt170)
REVERT: B   97 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8188 (mt)
REVERT: B  126 GLN cc_start: 0.6007 (tm-30) cc_final: 0.5634 (tt0)
REVERT: B  130 ASP cc_start: 0.6590 (OUTLIER) cc_final: 0.6130 (p0)
REVERT: B  313 MET cc_start: 0.5667 (tmm) cc_final: 0.5235 (tmm)
REVERT: B  676 GLU cc_start: 0.7280 (tp30) cc_final: 0.6787 (mp0)
REVERT: B  701 LYS cc_start: 0.7449 (mtpt) cc_final: 0.6587 (mttp)
REVERT: C   25 LEU cc_start: 0.8264 (mp) cc_final: 0.7824 (tp)
REVERT: E  765 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7344 (tm-30)
REVERT: E  788 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7326 (mm-40)
REVERT: F  101 ASN cc_start: 0.8089 (t0) cc_final: 0.7741 (t0)
  outliers start: 40
  outliers final: 25
  residues processed: 197
  average time/residue: 0.1039
  time to fit residues: 31.5063
Evaluate side-chains
  193 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 160
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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  202 MET
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  254 ILE
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  812 ASP
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  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:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 145 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 119 optimal weight:    8.9990
   chunk 113 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0370
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4017 r_free = 0.4017 target = 0.157125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.121002 restraints weight = 17918.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.120076 restraints weight = 15236.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.122037 restraints weight = 14551.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.123076 restraints weight = 9828.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.123760 restraints weight = 8723.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14202  Z= 0.112
  Angle     :  0.565  10.593  19333  Z= 0.283
  Chirality :  0.041   0.190   2176
  Planarity :  0.004   0.054   2361
  Dihedral  : 13.680 160.740   2290
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.02 %
    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: -0.07 (0.21), residues: 1599
  helix:  1.60 (0.20), residues: 673
  sheet:  0.02 (0.49), residues: 114
  loop : -1.57 (0.21), residues: 812

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   0.001   PHE C  54 
 TRP   0.023   0.001   TRP A 973 
 HIS   0.003   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (14198)
  covalent geometry    : angle       0.56399 (19330)
  hydrogen bonds       : bond        0.03352 (  568)
  hydrogen bonds       : angle       4.06592 ( 1605)
  metal coordination   : bond        0.00735 (    4)
  metal coordination   : angle       2.04866 (    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
  197 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 164
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8436 (pp)
REVERT: A  181 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7728 (mm-30)
REVERT: A  207 GLN cc_start: 0.7613 (mp10) cc_final: 0.7348 (mm-40)
REVERT: A  212 MET cc_start: 0.7205 (mtp) cc_final: 0.6903 (ttm)
REVERT: A  254 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7679 (pp)
REVERT: A  306 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8333 (p)
REVERT: A  624 VAL cc_start: 0.8706 (t) cc_final: 0.8487 (m)
REVERT: A  679 LYS cc_start: 0.8037 (tttm) cc_final: 0.7454 (tptp)
REVERT: A  693 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5468 (mm)
REVERT: A 1004 LEU cc_start: 0.7653 (tp) cc_final: 0.7211 (tp)
REVERT: B   79 ARG cc_start: 0.7676 (ppt170) cc_final: 0.6765 (ppt170)
REVERT: B   97 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8160 (mt)
REVERT: B  126 GLN cc_start: 0.6030 (tm-30) cc_final: 0.5640 (tt0)
REVERT: B  130 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6171 (p0)
REVERT: B  244 MET cc_start: 0.7895 (tpp) cc_final: 0.7517 (tpt)
REVERT: B  313 MET cc_start: 0.5734 (tmm) cc_final: 0.5300 (tmm)
REVERT: B  676 GLU cc_start: 0.7241 (tp30) cc_final: 0.6836 (pm20)
REVERT: C   25 LEU cc_start: 0.8295 (mp) cc_final: 0.7853 (tp)
REVERT: E  765 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7324 (tm-30)
REVERT: E  788 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7355 (mm-40)
REVERT: F  101 ASN cc_start: 0.8071 (t0) cc_final: 0.7721 (t0)
  outliers start: 33
  outliers final: 24
  residues processed: 191
  average time/residue: 0.1066
  time to fit residues: 31.6057
Evaluate side-chains
  188 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 157
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
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  202 MET
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  254 ILE
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  746 ILE
Chi-restraints excluded: chain A residue  812 ASP
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 160 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 141 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 105 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 126 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 = 0.4026 r_free = 0.4026 target = 0.157920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.122137 restraints weight = 17819.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.121387 restraints weight = 14986.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.122997 restraints weight = 15126.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.124287 restraints weight = 9507.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.125042 restraints weight = 8293.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14202  Z= 0.127
  Angle     :  0.580  12.102  19333  Z= 0.291
  Chirality :  0.042   0.189   2176
  Planarity :  0.004   0.054   2361
  Dihedral  : 13.668 160.323   2290
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.16 %
    Favored  : 80.23 %
  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 (0.21), residues: 1599
  helix:  1.50 (0.20), residues: 677
  sheet:  0.01 (0.49), residues: 114
  loop : -1.57 (0.22), residues: 808

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   0.022   0.001   PHE C  54 
 TRP   0.022   0.001   TRP A 973 
 HIS   0.003   0.001   HIS E 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (14198)
  covalent geometry    : angle       0.57981 (19330)
  hydrogen bonds       : bond        0.03519 (  568)
  hydrogen bonds       : angle       4.06846 ( 1605)
  metal coordination   : bond        0.00708 (    4)
  metal coordination   : angle       2.04824 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3409.85 seconds
wall clock time: 59 minutes 12.46 seconds (3552.46 seconds total)