Starting phenix.real_space_refine
on Wed Jun 11 11:03:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cl7_45664/06_2025/9cl7_45664.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cl7_45664/06_2025/9cl7_45664.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cl7_45664/06_2025/9cl7_45664.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cl7_45664/06_2025/9cl7_45664.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cl7_45664/06_2025/9cl7_45664.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cl7_45664/06_2025/9cl7_45664.cif"
  }
  resolution = 3.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      86      5.49       5
     S      75      5.16       5
     C    7742      2.51       5
     N    2187      2.21       5
     O    2624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12714
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 949
          Classifications: {'DNA': 46}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 45}
    Chain: "F"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 817
          Classifications: {'DNA': 40}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 39}
    Chain: "B"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "C"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "D"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "E"
      Number of atoms: 4924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4924
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 22, 'TRANS': 589}
          Chain breaks: 4
  Time building chain proxies: 7.93, per 1000 atoms: 0.62
  Number of scatterers: 12714
  At special positions: 0
  Unit cell: (102.03, 111.696, 147.138, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      75     16.00
     P      86     15.00
     O    2624      8.00
     N    2187      7.00
     C    7742      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 135 " - pdb=" SG  CYS D 162 " distance=2.03

  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: 3.35
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2642

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 14 sheets defined
      41.4% alpha, 18.2% beta
      29 base pairs and 73 stacking pairs defined.
    Time for finding SS restraints: 4.96
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 20
      removed outlier: 3.972A  pdb=" N   LEU B  12 " --> pdb=" O   GLN B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 57
      No H-bonds generated for 'chain 'B' and resid 55 through 57'
    Processing helix  chain 'B' and resid 72 through 81
      removed outlier: 3.603A  pdb=" N   CYS B  81 " --> pdb=" O   LYS B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 155
      removed outlier: 3.913A  pdb=" N   HIS B 153 " --> pdb=" O   ARG B 149 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ILE B 154 " --> pdb=" O   ASP B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 216
    Processing helix  chain 'B' and resid 217 through 222
      Proline residue:  B 220  - end of helix
      No H-bonds generated for 'chain 'B' and resid 217 through 222'
    Processing helix  chain 'B' and resid 255 through 260
    Processing helix  chain 'C' and resid 8 through 21
      removed outlier: 4.041A  pdb=" N   LEU C  12 " --> pdb=" O   GLN C   8 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   ASP C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 82
      removed outlier: 3.795A  pdb=" N   CYS C  81 " --> pdb=" O   LYS C  77 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA C  82 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 155
      removed outlier: 3.825A  pdb=" N   HIS C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ILE C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY C 155 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 194
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'C' and resid 217 through 222
      Proline residue:  C 220  - end of helix
      No H-bonds generated for 'chain 'C' and resid 217 through 222'
    Processing helix  chain 'C' and resid 256 through 261
      removed outlier: 3.749A  pdb=" N   GLY C 260 " --> pdb=" O   GLU C 256 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER C 261 " --> pdb=" O   ASP C 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 256 through 261'
    Processing helix  chain 'D' and resid 8 through 20
      removed outlier: 4.213A  pdb=" N   LEU D  12 " --> pdb=" O   GLN D   8 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 57
      No H-bonds generated for 'chain 'D' and resid 55 through 57'
    Processing helix  chain 'D' and resid 72 through 80
    Processing helix  chain 'D' and resid 141 through 152
    Processing helix  chain 'D' and resid 208 through 216
    Processing helix  chain 'D' and resid 217 through 222
      Proline residue:  D 220  - end of helix
      No H-bonds generated for 'chain 'D' and resid 217 through 222'
    Processing helix  chain 'E' and resid 373 through 389
    Processing helix  chain 'E' and resid 390 through 394
      removed outlier: 3.545A  pdb=" N   MET E 393 " --> pdb=" O   GLU E 390 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 397 through 410
      removed outlier: 3.590A  pdb=" N   LYS E 401 " --> pdb=" O   ASP E 397 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 411 through 424
      removed outlier: 3.580A  pdb=" N   ARG E 424 " --> pdb=" O   ARG E 420 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 432 through 434
      No H-bonds generated for 'chain 'E' and resid 432 through 434'
    Processing helix  chain 'E' and resid 443 through 453
    Processing helix  chain 'E' and resid 460 through 462
      No H-bonds generated for 'chain 'E' and resid 460 through 462'
    Processing helix  chain 'E' and resid 464 through 472
      removed outlier: 3.528A  pdb=" N   VAL E 468 " --> pdb=" O   GLU E 464 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 473 through 485
    Processing helix  chain 'E' and resid 492 through 506
      removed outlier: 3.587A  pdb=" N   LYS E 505 " --> pdb=" O   LEU E 501 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 509 through 513
    Processing helix  chain 'E' and resid 518 through 532
      removed outlier: 3.982A  pdb=" N   VAL E 522 " --> pdb=" O   GLY E 518 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 548
      removed outlier: 3.818A  pdb=" N   ILE E 548 " --> pdb=" O   VAL E 544 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 548 through 554
      removed outlier: 3.680A  pdb=" N   PHE E 552 " --> pdb=" O   ILE E 548 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 578 through 582
    Processing helix  chain 'E' and resid 598 through 622
      removed outlier: 3.730A  pdb=" N   LEU E 602 " --> pdb=" O   ASP E 598 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 623 through 641
      removed outlier: 3.795A  pdb=" N   ALA E 627 " --> pdb=" O   ASN E 623 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   GLU E 629 " --> pdb=" O   GLU E 625 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU E 630 " --> pdb=" O   GLU E 626 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 644 through 653
      removed outlier: 3.886A  pdb=" N   ARG E 648 " --> pdb=" O   HIS E 644 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   CYS E 649 " --> pdb=" O   PRO E 645 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   HIS E 650 " --> pdb=" O   SER E 646 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLU E 651 " --> pdb=" O   LEU E 647 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ASP E 652 " --> pdb=" O   ARG E 648 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU E 653 " --> pdb=" O   CYS E 649 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 644 through 653'
    Processing helix  chain 'E' and resid 654 through 659
    Processing helix  chain 'E' and resid 661 through 680
      removed outlier: 3.629A  pdb=" N   GLU E 675 " --> pdb=" O   SER E 671 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU E 680 " --> pdb=" O   ILE E 676 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 682 through 695
      removed outlier: 4.018A  pdb=" N   SER E 695 " --> pdb=" O   GLU E 691 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 704 through 718
      removed outlier: 4.030A  pdb=" N   TRP E 708 " --> pdb=" O   ARG E 704 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ASP E 709 " --> pdb=" O   GLY E 705 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   HIS E 718 " --> pdb=" O   ASN E 714 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 721 through 733
    Processing helix  chain 'E' and resid 740 through 756
      removed outlier: 4.167A  pdb=" N   LEU E 746 " --> pdb=" O   HIS E 742 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN E 748 " --> pdb=" O   LEU E 744 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 813 through 825
      removed outlier: 4.279A  pdb=" N   LEU E 817 " --> pdb=" O   SER E 813 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA E 818 " --> pdb=" O   VAL E 814 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   HIS E 821 " --> pdb=" O   LEU E 817 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 835 through 846
      removed outlier: 3.698A  pdb=" N   LEU E 844 " --> pdb=" O   THR E 840 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU E 845 " --> pdb=" O   LEU E 841 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 846 through 852
    Processing helix  chain 'E' and resid 872 through 879
      removed outlier: 4.288A  pdb=" N   PHE E 876 " --> pdb=" O   THR E 872 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ARG E 879 " --> pdb=" O   PHE E 875 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 879 through 893
    Processing helix  chain 'E' and resid 894 through 909
    Processing helix  chain 'E' and resid 918 through 922
    Processing helix  chain 'E' and resid 924 through 935
    Processing helix  chain 'E' and resid 937 through 948
      removed outlier: 4.336A  pdb=" N   SER E 941 " --> pdb=" O   GLY E 937 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   VAL E 943 " --> pdb=" O   VAL E 939 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   HIS E 946 " --> pdb=" O   GLY E 942 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA E 948 " --> pdb=" O   CYS E 944 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 984 through 996
      removed outlier: 3.579A  pdb=" N   MET E 988 " --> pdb=" O   SER E 984 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE E 989 " --> pdb=" O   HIS E 985 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 62
      removed outlier: 3.602A  pdb=" N   THR B  59 " --> pdb=" O   ARG B   5 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ARG B  61 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU B 104 " --> pdb=" O   ILE B  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 62
      removed outlier: 3.602A  pdb=" N   THR B  59 " --> pdb=" O   ARG B   5 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ARG B  61 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LEU B 101 " --> pdb=" O   TYR B 114 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 29
    Processing sheet with id=AA4, first strand: chain 'B' and resid 34 through 40
      removed outlier: 4.360A  pdb=" N   HIS B 246 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 197 through 198
      removed outlier: 3.680A  pdb=" N   VAL B 136 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 139 through 140
    Processing sheet with id=AA7, first strand: chain 'B' and resid 207 through 208
      removed outlier: 3.515A  pdb=" N   PHE B 207 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER B 170 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 182 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ASN B 177 " --> pdb=" O   GLU D 115 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU D 115 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG D  91 " --> pdb=" O   ALA D 100 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   THR D  59 " --> pdb=" O   ARG D   5 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 208
      removed outlier: 3.515A  pdb=" N   PHE B 207 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER B 170 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 182 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   VAL D 111 " --> pdb=" O   LYS B 181 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 62
      removed outlier: 3.643A  pdb=" N   ARG C  61 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL C 102 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU C  99 " --> pdb=" O   MET C 116 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   MET C 116 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   VAL C 111 " --> pdb=" O   LYS D 181 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LYS D 181 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LEU D 182 " --> pdb=" O   VAL D 167 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL D 167 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 67 through 71
      removed outlier: 3.580A  pdb=" N   ALA C  26 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   GLU C  25 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   MET C  40 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   CYS C  27 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   GLN C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL C  48 " --> pdb=" O   SER C  39 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLN C  49 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   HIS C 246 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY C 245 " --> pdb=" O   ILE C 241 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   LYS C 240 " --> pdb=" O   THR C 224 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   THR C 224 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 157 through 158
    Processing sheet with id=AB3, first strand: chain 'D' and resid 67 through 69
      removed outlier: 3.624A  pdb=" N   MET D  68 " --> pdb=" O   TRP D  28 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   CYS D  27 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   GLN D  38 " --> pdb=" O   CYS D  27 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   HIS D 246 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   LYS D 240 " --> pdb=" O   THR D 224 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   THR D 224 " --> pdb=" O   LYS D 240 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL D 136 " --> pdb=" O   GLU D 198 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 429 through 430
      removed outlier: 3.606A  pdb=" N   VAL E 535 " --> pdb=" O   ILE E 429 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 975 through 977
      removed outlier: 7.257A  pdb=" N   GLU E 975 " --> pdb=" O   CYS E1004 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    486 hydrogen bonds defined for protein.
    1350 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      66 hydrogen bonds
      112 hydrogen bond angles
      0 basepair planarities
      29 basepair parallelities
      73 stacking parallelities
  Total time for adding SS restraints: 5.52

  Time building geometry restraints manager: 3.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3844
        1.34 -     1.46: 2626
        1.46 -     1.58: 6353
        1.58 -     1.70: 170
        1.70 -     1.82: 116
  Bond restraints: 13109
  Sorted by residual:
  bond pdb=" CG  LEU E 472 "
       pdb=" CD2 LEU E 472 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.56e+00
  bond pdb=" C   MET C  68 "
       pdb=" N   GLY C  69 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 5.00e-03 4.00e+04 2.00e+00
  bond pdb=" CB  MET E 558 "
       pdb=" CG  MET E 558 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.57e+00
  bond pdb=" CA  VAL C 233 "
       pdb=" C   VAL C 233 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.012 1.05e-02 9.07e+03 1.23e+00
  bond pdb=" CB  MET E 772 "
       pdb=" CG  MET E 772 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.09e+00
  ... (remaining 13104 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.13: 17959
        3.13 -     6.25: 103
        6.25 -     9.38: 19
        9.38 -    12.51: 6
       12.51 -    15.64: 2
  Bond angle restraints: 18089
  Sorted by residual:
  angle pdb=" CB  MET E 558 "
        pdb=" CG  MET E 558 "
        pdb=" SD  MET E 558 "
      ideal   model   delta    sigma   weight residual
     112.70  128.34  -15.64 3.00e+00 1.11e-01 2.72e+01
  angle pdb=" CA  MET E 772 "
        pdb=" CB  MET E 772 "
        pdb=" CG  MET E 772 "
      ideal   model   delta    sigma   weight residual
     114.10  122.63   -8.53 2.00e+00 2.50e-01 1.82e+01
  angle pdb=" CA  LEU E 524 "
        pdb=" CB  LEU E 524 "
        pdb=" CG  LEU E 524 "
      ideal   model   delta    sigma   weight residual
     116.30  130.62  -14.32 3.50e+00 8.16e-02 1.68e+01
  angle pdb=" CB  MET C 116 "
        pdb=" CG  MET C 116 "
        pdb=" SD  MET C 116 "
      ideal   model   delta    sigma   weight residual
     112.70  124.01  -11.31 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" CB  MET D 244 "
        pdb=" CG  MET D 244 "
        pdb=" SD  MET D 244 "
      ideal   model   delta    sigma   weight residual
     112.70  123.59  -10.89 3.00e+00 1.11e-01 1.32e+01
  ... (remaining 18084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 6067
       18.00 -    35.99: 1063
       35.99 -    53.99: 494
       53.99 -    71.99: 111
       71.99 -    89.98: 23
  Dihedral angle restraints: 7758
    sinusoidal: 3695
      harmonic: 4063
  Sorted by residual:
  dihedral pdb=" CA  SER B 161 "
           pdb=" C   SER B 161 "
           pdb=" N   CYS B 162 "
           pdb=" CA  CYS B 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.33  -25.67     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  GLU E 476 "
           pdb=" C   GLU E 476 "
           pdb=" N   LEU E 477 "
           pdb=" CA  LEU E 477 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.05   18.95     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CB  CYS B 135 "
           pdb=" SG  CYS B 135 "
           pdb=" SG  CYS B 162 "
           pdb=" CB  CYS B 162 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.47   31.47     1      1.00e+01 1.00e-02 1.41e+01
  ... (remaining 7755 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1463
       0.038 -    0.075: 446
       0.075 -    0.113: 144
       0.113 -    0.150: 16
       0.150 -    0.188: 2
  Chirality restraints: 2071
  Sorted by residual:
  chirality pdb=" CB  VAL E 544 "
            pdb=" CA  VAL E 544 "
            pdb=" CG1 VAL E 544 "
            pdb=" CG2 VAL E 544 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.82e-01
  chirality pdb=" CA  GLU E 476 "
            pdb=" N   GLU E 476 "
            pdb=" C   GLU E 476 "
            pdb=" CB  GLU E 476 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.78e-01
  chirality pdb=" CG  LEU E 477 "
            pdb=" CB  LEU E 477 "
            pdb=" CD1 LEU E 477 "
            pdb=" CD2 LEU E 477 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.31e-01
  ... (remaining 2068 not shown)

  Planarity restraints: 2018
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 215 "    0.020 2.00e-02 2.50e+03   1.66e-02 4.81e+00
        pdb=" CG  PHE B 215 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 215 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 215 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 215 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 215 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 215 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 233 "   -0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO B 234 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 234 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 234 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C  89 "   -0.008 2.00e-02 2.50e+03   1.59e-02 2.54e+00
        pdb=" C   THR C  89 "    0.028 2.00e-02 2.50e+03
        pdb=" O   THR C  89 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU C  90 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2015 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 795
        2.72 -     3.26: 13465
        3.26 -     3.81: 22828
        3.81 -     4.35: 26329
        4.35 -     4.90: 40479
  Nonbonded interactions: 103896
  Sorted by model distance:
  nonbonded pdb=" O   ARG E 721 "
            pdb=" OG1 THR E 725 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" O   SER C  31 "
            pdb=" OH  TYR C  60 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O   LEU E 550 "
            pdb=" OG  SER E 553 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OD2 ASP D  41 "
            pdb=" OG  SER D  43 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OD2 ASP B  41 "
            pdb=" OH  TYR B 211 "
     model   vdw
     2.216 3.040
  ... (remaining 103891 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             1.040
  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:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     36.300
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
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   0.053  13112  Z= 0.149
  Angle     :  0.703  15.635  18095  Z= 0.351
  Chirality :  0.040   0.188   2071
  Planarity :  0.003   0.051   2018
  Dihedral  : 21.866  89.983   5107
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 21.56
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.73 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 35.19 %
    Favored  : 64.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.23), residues: 1379
  helix:  0.56 (0.25), residues: 440
  sheet: -0.80 (0.28), residues: 363
  loop : -1.20 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 708 
 HIS   0.003   0.001   HIS E 650 
 PHE   0.037   0.002   PHE B 215 
 TYR   0.011   0.001   TYR D 249 
 ARG   0.008   0.000   ARG E 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24494 (  539)
  hydrogen bonds       : angle       8.85765 ( 1462)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       0.82350 (    6)
  covalent geometry    : bond        0.00316 (13109)
  covalent geometry    : angle       0.70265 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 1.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  199 MET cc_start: 0.6875 (tpt) cc_final: 0.6624 (tpt)
REVERT: E  848 ASP cc_start: 0.9715 (m-30) cc_final: 0.9434 (p0)
  outliers start: 3
  outliers final: 1
  residues processed: 84
  average time/residue: 0.2304
  time to fit residues: 30.1627
Evaluate side-chains
  79 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  113 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 111 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 115 optimal weight:    8.9990
   chunk 44 optimal weight:    0.4980
   chunk 70 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 133 optimal weight:   10.0000
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
B 125 GLN
E 891 HIS
** E 909 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 = 0.4049 r_free = 0.4049 target = 0.089332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.059387 restraints weight = 82733.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.061087 restraints weight = 44098.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.062325 restraints weight = 30323.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13112  Z= 0.191
  Angle     :  0.657  10.436  18095  Z= 0.347
  Chirality :  0.041   0.196   2071
  Planarity :  0.004   0.051   2018
  Dihedral  : 21.788  80.941   2438
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.74 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 31.17 %
    Favored  : 65.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.23), residues: 1379
  helix:  0.60 (0.24), residues: 462
  sheet: -0.61 (0.30), residues: 340
  loop : -1.27 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  28 
 HIS   0.003   0.001   HIS E 594 
 PHE   0.030   0.002   PHE B 215 
 TYR   0.024   0.002   TYR E 842 
 ARG   0.004   0.000   ARG E 982 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07722 (  539)
  hydrogen bonds       : angle       6.20684 ( 1462)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       0.73339 (    6)
  covalent geometry    : bond        0.00401 (13109)
  covalent geometry    : angle       0.65722 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 77
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.9434 (tmm) cc_final: 0.9169 (tmm)
REVERT: B  199 MET cc_start: 0.6756 (tpt) cc_final: 0.6455 (tpt)
REVERT: C    1 MET cc_start: 0.7732 (tpp) cc_final: 0.7295 (tpp)
REVERT: C  116 MET cc_start: 0.8468 (ppp) cc_final: 0.7321 (ppp)
REVERT: C  119 MET cc_start: 0.8612 (tmm) cc_final: 0.7950 (tmm)
REVERT: D   40 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7999 (tmm)
REVERT: E  848 ASP cc_start: 0.9760 (m-30) cc_final: 0.9433 (p0)
  outliers start: 43
  outliers final: 22
  residues processed: 114
  average time/residue: 0.2214
  time to fit residues: 38.8864
Evaluate side-chains
  96 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   62 CYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  162 CYS
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  207 PHE
Chi-restraints excluded: chain B residue  215 PHE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 MET
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue   64 ARG
Chi-restraints excluded: chain D residue   72 LEU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain E residue  612 LEU
Chi-restraints excluded: chain E residue  814 VAL
Chi-restraints excluded: chain E residue  872 THR
Chi-restraints excluded: chain E residue  940 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 116 optimal weight:    6.9990
   chunk 124 optimal weight:    0.7980
   chunk 112 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 20 optimal weight:   30.0000
   chunk 142 optimal weight:   30.0000
   chunk 101 optimal weight:    3.9990
   chunk 121 optimal weight:    6.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** E 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.089620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.062961 restraints weight = 83722.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.062276 restraints weight = 45328.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.062702 restraints weight = 37292.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13112  Z= 0.149
  Angle     :  0.629  12.552  18095  Z= 0.327
  Chirality :  0.041   0.130   2071
  Planarity :  0.004   0.046   2018
  Dihedral  : 21.821  78.669   2436
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.16 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 29.86 %
    Favored  : 65.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.23), residues: 1379
  helix:  0.83 (0.25), residues: 449
  sheet: -0.77 (0.29), residues: 350
  loop : -1.17 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 638 
 HIS   0.003   0.001   HIS C 153 
 PHE   0.029   0.001   PHE B 215 
 TYR   0.023   0.002   TYR E 842 
 ARG   0.003   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06407 (  539)
  hydrogen bonds       : angle       5.55995 ( 1462)
  SS BOND              : bond        0.00478 (    3)
  SS BOND              : angle       0.83722 (    6)
  covalent geometry    : bond        0.00313 (13109)
  covalent geometry    : angle       0.62891 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 81
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.9494 (tmm) cc_final: 0.9183 (tmm)
REVERT: B  199 MET cc_start: 0.6940 (tpt) cc_final: 0.6615 (tpt)
REVERT: C    1 MET cc_start: 0.8075 (tpp) cc_final: 0.7769 (tpp)
REVERT: C   54 SER cc_start: 0.9470 (OUTLIER) cc_final: 0.8890 (m)
REVERT: C   79 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9422 (tt)
REVERT: C  116 MET cc_start: 0.8593 (ppp) cc_final: 0.7469 (ppp)
REVERT: C  119 MET cc_start: 0.8683 (tmm) cc_final: 0.8118 (tmm)
REVERT: D    1 MET cc_start: 0.8723 (tpt) cc_final: 0.8470 (tpp)
REVERT: D   40 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8077 (tmm)
REVERT: E  457 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6842 (pm20)
REVERT: E  848 ASP cc_start: 0.9738 (m-30) cc_final: 0.9349 (p0)
  outliers start: 53
  outliers final: 28
  residues processed: 129
  average time/residue: 0.2154
  time to fit residues: 42.7048
Evaluate side-chains
  106 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 74
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   62 CYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  162 CYS
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  207 PHE
Chi-restraints excluded: chain B residue  215 PHE
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 MET
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   72 LEU
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain E residue  441 LEU
Chi-restraints excluded: chain E residue  457 GLN
Chi-restraints excluded: chain E residue  473 SER
Chi-restraints excluded: chain E residue  555 THR
Chi-restraints excluded: chain E residue  814 VAL
Chi-restraints excluded: chain E residue  872 THR
Chi-restraints excluded: chain E residue  940 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 130 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0370
   chunk 58 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    1.3460

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   8 GLN
** E 909 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 = 0.4060 r_free = 0.4060 target = 0.090029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.063207 restraints weight = 82609.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.062769 restraints weight = 42701.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.063004 restraints weight = 34644.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13112  Z= 0.131
  Angle     :  0.613  11.486  18095  Z= 0.317
  Chirality :  0.040   0.148   2071
  Planarity :  0.003   0.044   2018
  Dihedral  : 21.736  76.168   2436
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.95 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 30.19 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.23), residues: 1379
  helix:  0.80 (0.24), residues: 457
  sheet: -0.75 (0.28), residues: 349
  loop : -1.17 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 638 
 HIS   0.003   0.001   HIS E 742 
 PHE   0.029   0.001   PHE B 215 
 TYR   0.022   0.001   TYR E 842 
 ARG   0.003   0.000   ARG E 704 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05958 (  539)
  hydrogen bonds       : angle       5.25512 ( 1462)
  SS BOND              : bond        0.00372 (    3)
  SS BOND              : angle       0.95980 (    6)
  covalent geometry    : bond        0.00276 (13109)
  covalent geometry    : angle       0.61247 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 80
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.9096 (ppp)
REVERT: B  154 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9142 (tp)
REVERT: B  199 MET cc_start: 0.6911 (tpt) cc_final: 0.6565 (tpt)
REVERT: C    1 MET cc_start: 0.7993 (tpp) cc_final: 0.7785 (tpp)
REVERT: C   54 SER cc_start: 0.9425 (OUTLIER) cc_final: 0.8854 (m)
REVERT: C  119 MET cc_start: 0.8617 (tmm) cc_final: 0.8101 (tmm)
REVERT: D    1 MET cc_start: 0.8807 (tpt) cc_final: 0.8436 (tpp)
REVERT: D   40 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8042 (tmm)
REVERT: D   99 LEU cc_start: 0.9424 (tp) cc_final: 0.9075 (pp)
REVERT: E  457 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6821 (pm20)
REVERT: E  848 ASP cc_start: 0.9739 (m-30) cc_final: 0.9377 (p0)
  outliers start: 42
  outliers final: 31
  residues processed: 116
  average time/residue: 0.2033
  time to fit residues: 37.2904
Evaluate side-chains
  110 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 74
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  162 CYS
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  215 PHE
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  199 MET
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 MET
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain E residue  441 LEU
Chi-restraints excluded: chain E residue  457 GLN
Chi-restraints excluded: chain E residue  602 LEU
Chi-restraints excluded: chain E residue  612 LEU
Chi-restraints excluded: chain E residue  624 TRP
Chi-restraints excluded: chain E residue  814 VAL
Chi-restraints excluded: chain E residue  870 LEU
Chi-restraints excluded: chain E residue  872 THR
Chi-restraints excluded: chain E residue  931 LEU
Chi-restraints excluded: chain E residue  940 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 140 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 213 ASN
D  44 HIS
E 492 GLN
** E 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.087584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.060247 restraints weight = 83891.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.060260 restraints weight = 46547.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.060465 restraints weight = 35923.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13112  Z= 0.205
  Angle     :  0.639  11.714  18095  Z= 0.332
  Chirality :  0.040   0.179   2071
  Planarity :  0.004   0.041   2018
  Dihedral  : 21.861  74.908   2436
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 18.72
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.38 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 28.96 %
    Favored  : 65.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.23), residues: 1379
  helix:  0.79 (0.24), residues: 453
  sheet: -0.92 (0.27), residues: 371
  loop : -1.15 (0.27), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  28 
 HIS   0.003   0.001   HIS D  44 
 PHE   0.033   0.002   PHE B 215 
 TYR   0.022   0.002   TYR E 842 
 ARG   0.004   0.000   ARG D  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06330 (  539)
  hydrogen bonds       : angle       5.34552 ( 1462)
  SS BOND              : bond        0.00394 (    3)
  SS BOND              : angle       1.03429 (    6)
  covalent geometry    : bond        0.00436 (13109)
  covalent geometry    : angle       0.63851 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 75
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8913 (mm)
REVERT: B  112 SER cc_start: 0.9102 (OUTLIER) cc_final: 0.8623 (p)
REVERT: B  139 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.9093 (ppp)
REVERT: B  199 MET cc_start: 0.7005 (tpt) cc_final: 0.6349 (tpt)
REVERT: C    1 MET cc_start: 0.8194 (tpp) cc_final: 0.7971 (tpp)
REVERT: C   54 SER cc_start: 0.9442 (OUTLIER) cc_final: 0.8866 (m)
REVERT: C  119 MET cc_start: 0.8601 (tmm) cc_final: 0.8193 (tmm)
REVERT: C  229 MET cc_start: 0.8792 (pmt) cc_final: 0.8512 (pmt)
REVERT: D   40 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8003 (tmm)
REVERT: D   99 LEU cc_start: 0.9452 (tp) cc_final: 0.9200 (pp)
REVERT: D  207 PHE cc_start: 0.8710 (m-80) cc_final: 0.8311 (m-80)
REVERT: E  457 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6957 (pm20)
REVERT: E  477 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9403 (mm)
REVERT: E  848 ASP cc_start: 0.9770 (m-30) cc_final: 0.9432 (p0)
  outliers start: 67
  outliers final: 42
  residues processed: 137
  average time/residue: 0.2236
  time to fit residues: 47.5472
Evaluate side-chains
  121 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 72
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   62 CYS
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  207 PHE
Chi-restraints excluded: chain B residue  215 PHE
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  213 ASN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 MET
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  110 LYS
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain E residue  407 PHE
Chi-restraints excluded: chain E residue  441 LEU
Chi-restraints excluded: chain E residue  457 GLN
Chi-restraints excluded: chain E residue  477 LEU
Chi-restraints excluded: chain E residue  492 GLN
Chi-restraints excluded: chain E residue  510 CYS
Chi-restraints excluded: chain E residue  602 LEU
Chi-restraints excluded: chain E residue  612 LEU
Chi-restraints excluded: chain E residue  624 TRP
Chi-restraints excluded: chain E residue  661 THR
Chi-restraints excluded: chain E residue  870 LEU
Chi-restraints excluded: chain E residue  872 THR
Chi-restraints excluded: chain E residue  931 LEU
Chi-restraints excluded: chain E residue  940 LEU
Chi-restraints excluded: chain E residue  984 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 62 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 96 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 139 optimal weight:   30.0000
   chunk 83 optimal weight:    8.9990
   chunk 115 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    3.8988

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 213 ASN
E 492 GLN
** E 909 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 = 0.4004 r_free = 0.4004 target = 0.086379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.059659 restraints weight = 84986.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.058998 restraints weight = 45892.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.059336 restraints weight = 39392.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13112  Z= 0.236
  Angle     :  0.688  15.874  18095  Z= 0.354
  Chirality :  0.041   0.155   2071
  Planarity :  0.004   0.040   2018
  Dihedral  : 22.085  75.091   2436
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.53 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 29.53 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.23), residues: 1379
  helix:  0.63 (0.24), residues: 458
  sheet: -1.04 (0.28), residues: 351
  loop : -1.27 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  28 
 HIS   0.006   0.001   HIS B 153 
 PHE   0.035   0.002   PHE B 215 
 TYR   0.022   0.002   TYR E 842 
 ARG   0.004   0.000   ARG E 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06294 (  539)
  hydrogen bonds       : angle       5.40347 ( 1462)
  SS BOND              : bond        0.00767 (    3)
  SS BOND              : angle       2.19226 (    6)
  covalent geometry    : bond        0.00501 (13109)
  covalent geometry    : angle       0.68679 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 75
  time to evaluate  : 1.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8983 (mm)
REVERT: B  112 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8640 (p)
REVERT: B  139 MET cc_start: 0.9528 (OUTLIER) cc_final: 0.9112 (ppp)
REVERT: B  229 MET cc_start: 0.8243 (ptt) cc_final: 0.7724 (tpp)
REVERT: C    1 MET cc_start: 0.8219 (tpp) cc_final: 0.7981 (tpp)
REVERT: C   54 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.8817 (m)
REVERT: C  119 MET cc_start: 0.8602 (tmm) cc_final: 0.8302 (tmm)
REVERT: C  229 MET cc_start: 0.8843 (pmt) cc_final: 0.8595 (pmt)
REVERT: D    1 MET cc_start: 0.9026 (tpp) cc_final: 0.8347 (tpp)
REVERT: D   40 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8005 (tmm)
REVERT: D   99 LEU cc_start: 0.9516 (tp) cc_final: 0.9261 (pp)
REVERT: D  207 PHE cc_start: 0.8694 (m-80) cc_final: 0.8318 (m-80)
REVERT: E  457 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6948 (pm20)
REVERT: E  468 VAL cc_start: 0.9866 (OUTLIER) cc_final: 0.9664 (p)
REVERT: E  472 LEU cc_start: 0.9658 (pp) cc_final: 0.9443 (pp)
REVERT: E  477 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9348 (mm)
REVERT: E  492 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8389 (mm-40)
REVERT: E  848 ASP cc_start: 0.9778 (m-30) cc_final: 0.9486 (p0)
  outliers start: 65
  outliers final: 45
  residues processed: 135
  average time/residue: 0.2438
  time to fit residues: 50.8012
Evaluate side-chains
  125 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 71
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   62 CYS
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  215 PHE
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  213 ASN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 MET
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  110 LYS
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain E residue  407 PHE
Chi-restraints excluded: chain E residue  441 LEU
Chi-restraints excluded: chain E residue  457 GLN
Chi-restraints excluded: chain E residue  461 GLU
Chi-restraints excluded: chain E residue  468 VAL
Chi-restraints excluded: chain E residue  477 LEU
Chi-restraints excluded: chain E residue  492 GLN
Chi-restraints excluded: chain E residue  602 LEU
Chi-restraints excluded: chain E residue  612 LEU
Chi-restraints excluded: chain E residue  624 TRP
Chi-restraints excluded: chain E residue  661 THR
Chi-restraints excluded: chain E residue  708 TRP
Chi-restraints excluded: chain E residue  870 LEU
Chi-restraints excluded: chain E residue  872 THR
Chi-restraints excluded: chain E residue  931 LEU
Chi-restraints excluded: chain E residue  940 LEU
Chi-restraints excluded: chain E residue  984 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 116 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 140 optimal weight:    7.9990
   chunk 4 optimal weight:   20.0000
   chunk 82 optimal weight:    1.9990
   chunk 144 optimal weight:    8.9990
   chunk 111 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 24 optimal weight:    0.3980
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
B 125 GLN
** E 492 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 = 0.4033 r_free = 0.4033 target = 0.087973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.061269 restraints weight = 82794.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.061221 restraints weight = 46094.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.061023 restraints weight = 33738.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13112  Z= 0.135
  Angle     :  0.645  12.443  18095  Z= 0.327
  Chirality :  0.040   0.159   2071
  Planarity :  0.004   0.041   2018
  Dihedral  : 22.021  74.801   2436
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.95 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 29.70 %
    Favored  : 65.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.23), residues: 1379
  helix:  0.86 (0.24), residues: 457
  sheet: -0.98 (0.27), residues: 371
  loop : -1.12 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  28 
 HIS   0.002   0.001   HIS E 650 
 PHE   0.034   0.001   PHE B 215 
 TYR   0.020   0.001   TYR E 842 
 ARG   0.006   0.000   ARG E 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05499 (  539)
  hydrogen bonds       : angle       5.13534 ( 1462)
  SS BOND              : bond        0.00417 (    3)
  SS BOND              : angle       1.71397 (    6)
  covalent geometry    : bond        0.00289 (13109)
  covalent geometry    : angle       0.64399 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 76
  time to evaluate  : 1.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8899 (mm)
REVERT: B  112 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8694 (p)
REVERT: B  139 MET cc_start: 0.9551 (OUTLIER) cc_final: 0.9121 (ppp)
REVERT: B  229 MET cc_start: 0.8390 (ptt) cc_final: 0.7852 (tpp)
REVERT: C    1 MET cc_start: 0.8311 (tpp) cc_final: 0.8103 (tpp)
REVERT: C   54 SER cc_start: 0.9444 (OUTLIER) cc_final: 0.8791 (m)
REVERT: C  119 MET cc_start: 0.8569 (tmm) cc_final: 0.8231 (tmm)
REVERT: C  229 MET cc_start: 0.8819 (pmt) cc_final: 0.8569 (pmt)
REVERT: D    1 MET cc_start: 0.9152 (tpp) cc_final: 0.8566 (tpp)
REVERT: D   40 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7975 (tmm)
REVERT: D   99 LEU cc_start: 0.9571 (tp) cc_final: 0.9293 (pp)
REVERT: D  207 PHE cc_start: 0.8672 (m-80) cc_final: 0.8299 (m-80)
REVERT: E  457 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6841 (pm20)
REVERT: E  472 LEU cc_start: 0.9620 (pp) cc_final: 0.9399 (pp)
REVERT: E  477 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9326 (mm)
REVERT: E  848 ASP cc_start: 0.9762 (m-30) cc_final: 0.9452 (p0)
  outliers start: 57
  outliers final: 38
  residues processed: 127
  average time/residue: 0.2629
  time to fit residues: 54.4702
Evaluate side-chains
  119 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 74
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   62 CYS
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  207 PHE
Chi-restraints excluded: chain B residue  215 PHE
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain E residue  441 LEU
Chi-restraints excluded: chain E residue  457 GLN
Chi-restraints excluded: chain E residue  477 LEU
Chi-restraints excluded: chain E residue  510 CYS
Chi-restraints excluded: chain E residue  602 LEU
Chi-restraints excluded: chain E residue  604 ARG
Chi-restraints excluded: chain E residue  612 LEU
Chi-restraints excluded: chain E residue  624 TRP
Chi-restraints excluded: chain E residue  661 THR
Chi-restraints excluded: chain E residue  814 VAL
Chi-restraints excluded: chain E residue  870 LEU
Chi-restraints excluded: chain E residue  872 THR
Chi-restraints excluded: chain E residue  940 LEU
Chi-restraints excluded: chain E residue  964 TRP
Chi-restraints excluded: chain E residue  984 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 105 optimal weight:    0.0170
   chunk 112 optimal weight:   20.0000
   chunk 52 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 114 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 119 optimal weight:    0.3980
   chunk 139 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    2.2824

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 213 ASN
** E 492 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 = 0.4021 r_free = 0.4021 target = 0.087209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.060729 restraints weight = 83923.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.060252 restraints weight = 48181.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.060250 restraints weight = 36875.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13112  Z= 0.161
  Angle     :  0.654  13.521  18095  Z= 0.331
  Chirality :  0.041   0.254   2071
  Planarity :  0.004   0.040   2018
  Dihedral  : 21.979  74.707   2436
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.24 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 29.37 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.23), residues: 1379
  helix:  0.89 (0.24), residues: 457
  sheet: -0.92 (0.27), residues: 371
  loop : -1.11 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 638 
 HIS   0.002   0.001   HIS E 594 
 PHE   0.034   0.001   PHE B 215 
 TYR   0.020   0.002   TYR E 842 
 ARG   0.005   0.000   ARG E 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05711 (  539)
  hydrogen bonds       : angle       5.13228 ( 1462)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       1.53914 (    6)
  covalent geometry    : bond        0.00350 (13109)
  covalent geometry    : angle       0.65374 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 77
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8931 (mm)
REVERT: B  112 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8691 (p)
REVERT: B  139 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.9124 (ppp)
REVERT: B  229 MET cc_start: 0.8349 (ptt) cc_final: 0.8055 (ptt)
REVERT: C   54 SER cc_start: 0.9469 (OUTLIER) cc_final: 0.8836 (m)
REVERT: C  119 MET cc_start: 0.8603 (tmm) cc_final: 0.8261 (tmm)
REVERT: C  229 MET cc_start: 0.8872 (pmt) cc_final: 0.8647 (pmt)
REVERT: D   40 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7990 (tmm)
REVERT: D   99 LEU cc_start: 0.9534 (tp) cc_final: 0.9327 (pp)
REVERT: D  207 PHE cc_start: 0.8665 (m-80) cc_final: 0.8307 (m-80)
REVERT: E  457 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6767 (pm20)
REVERT: E  472 LEU cc_start: 0.9622 (pp) cc_final: 0.9364 (pp)
REVERT: E  477 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9351 (mm)
REVERT: E  848 ASP cc_start: 0.9767 (m-30) cc_final: 0.9467 (p0)
  outliers start: 57
  outliers final: 44
  residues processed: 129
  average time/residue: 0.2249
  time to fit residues: 44.9744
Evaluate side-chains
  126 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 75
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   62 CYS
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  215 PHE
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  213 ASN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain E residue  407 PHE
Chi-restraints excluded: chain E residue  441 LEU
Chi-restraints excluded: chain E residue  457 GLN
Chi-restraints excluded: chain E residue  477 LEU
Chi-restraints excluded: chain E residue  510 CYS
Chi-restraints excluded: chain E residue  602 LEU
Chi-restraints excluded: chain E residue  604 ARG
Chi-restraints excluded: chain E residue  612 LEU
Chi-restraints excluded: chain E residue  624 TRP
Chi-restraints excluded: chain E residue  661 THR
Chi-restraints excluded: chain E residue  710 ARG
Chi-restraints excluded: chain E residue  814 VAL
Chi-restraints excluded: chain E residue  870 LEU
Chi-restraints excluded: chain E residue  872 THR
Chi-restraints excluded: chain E residue  940 LEU
Chi-restraints excluded: chain E residue  964 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 129 optimal weight:   30.0000
   chunk 9 optimal weight:    5.9990
   chunk 119 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9980
   chunk 75 optimal weight:    9.9990
   chunk 82 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 99 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.5982

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

Flipped N/Q/H residues before XYZ refinement:
B 125 GLN
** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 492 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 = 0.4033 r_free = 0.4033 target = 0.087861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.060335 restraints weight = 83192.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.061149 restraints weight = 47016.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.060937 restraints weight = 31601.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13112  Z= 0.135
  Angle     :  0.678  15.098  18095  Z= 0.334
  Chirality :  0.041   0.163   2071
  Planarity :  0.004   0.041   2018
  Dihedral  : 21.912  74.527   2436
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.09 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 30.27 %
    Favored  : 65.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.23), residues: 1379
  helix:  0.96 (0.24), residues: 451
  sheet: -0.84 (0.27), residues: 371
  loop : -1.14 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 847 
 HIS   0.004   0.001   HIS E 718 
 PHE   0.033   0.001   PHE B 215 
 TYR   0.020   0.002   TYR E 842 
 ARG   0.006   0.000   ARG E 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05461 (  539)
  hydrogen bonds       : angle       5.02404 ( 1462)
  SS BOND              : bond        0.00348 (    3)
  SS BOND              : angle       1.44330 (    6)
  covalent geometry    : bond        0.00291 (13109)
  covalent geometry    : angle       0.67730 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 79
  time to evaluate  : 1.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: B  112 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8804 (p)
REVERT: B  139 MET cc_start: 0.9533 (OUTLIER) cc_final: 0.9108 (ppp)
REVERT: B  229 MET cc_start: 0.8318 (ptt) cc_final: 0.7882 (tpp)
REVERT: C   54 SER cc_start: 0.9449 (OUTLIER) cc_final: 0.8810 (m)
REVERT: C  119 MET cc_start: 0.8599 (tmm) cc_final: 0.8275 (tmm)
REVERT: D    1 MET cc_start: 0.9105 (tpp) cc_final: 0.8514 (tpp)
REVERT: D   40 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8058 (tmm)
REVERT: D  207 PHE cc_start: 0.8685 (m-80) cc_final: 0.8355 (m-80)
REVERT: E  457 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6874 (pm20)
REVERT: E  461 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8658 (pm20)
REVERT: E  472 LEU cc_start: 0.9619 (pp) cc_final: 0.9357 (pp)
REVERT: E  477 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9353 (mm)
REVERT: E  848 ASP cc_start: 0.9778 (m-30) cc_final: 0.9492 (p0)
  outliers start: 50
  outliers final: 38
  residues processed: 122
  average time/residue: 0.2112
  time to fit residues: 40.5277
Evaluate side-chains
  121 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 75
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   62 CYS
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  215 PHE
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  189 ASP
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain E residue  393 MET
Chi-restraints excluded: chain E residue  407 PHE
Chi-restraints excluded: chain E residue  441 LEU
Chi-restraints excluded: chain E residue  457 GLN
Chi-restraints excluded: chain E residue  461 GLU
Chi-restraints excluded: chain E residue  468 VAL
Chi-restraints excluded: chain E residue  477 LEU
Chi-restraints excluded: chain E residue  510 CYS
Chi-restraints excluded: chain E residue  602 LEU
Chi-restraints excluded: chain E residue  604 ARG
Chi-restraints excluded: chain E residue  624 TRP
Chi-restraints excluded: chain E residue  661 THR
Chi-restraints excluded: chain E residue  870 LEU
Chi-restraints excluded: chain E residue  872 THR
Chi-restraints excluded: chain E residue  940 LEU
Chi-restraints excluded: chain E residue  964 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 112 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0020
   chunk 129 optimal weight:   20.0000
   chunk 9 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 143 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 145 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    3.3996

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

Flipped N/Q/H residues before XYZ refinement:
B 125 GLN
B 246 HIS
C 213 ASN
** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.085875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.058883 restraints weight = 84089.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.058914 restraints weight = 46638.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.058865 restraints weight = 34931.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13112  Z= 0.213
  Angle     :  0.718  14.807  18095  Z= 0.357
  Chirality :  0.041   0.171   2071
  Planarity :  0.004   0.041   2018
  Dihedral  : 21.964  74.924   2436
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.82 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 30.52 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.23), residues: 1379
  helix:  0.84 (0.24), residues: 457
  sheet: -0.92 (0.29), residues: 339
  loop : -1.25 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 847 
 HIS   0.010   0.001   HIS C  44 
 PHE   0.035   0.002   PHE B 215 
 TYR   0.024   0.002   TYR D 249 
 ARG   0.004   0.000   ARG E 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06137 (  539)
  hydrogen bonds       : angle       5.20116 ( 1462)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       1.38503 (    6)
  covalent geometry    : bond        0.00457 (13109)
  covalent geometry    : angle       0.71725 (18089)

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

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

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2758 Ramachandran restraints generated.
    1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 73
  time to evaluate  : 1.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8962 (mm)
REVERT: B  112 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8684 (p)
REVERT: B  139 MET cc_start: 0.9558 (OUTLIER) cc_final: 0.9131 (ppp)
REVERT: B  229 MET cc_start: 0.8329 (ptt) cc_final: 0.8032 (ptt)
REVERT: C    1 MET cc_start: 0.8194 (tpp) cc_final: 0.7871 (tpp)
REVERT: C   54 SER cc_start: 0.9466 (OUTLIER) cc_final: 0.8841 (m)
REVERT: C  119 MET cc_start: 0.8569 (tmm) cc_final: 0.8240 (tmm)
REVERT: D    1 MET cc_start: 0.9194 (tpp) cc_final: 0.8670 (tpp)
REVERT: D   40 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7952 (tmm)
REVERT: D  207 PHE cc_start: 0.8761 (m-80) cc_final: 0.8419 (m-80)
REVERT: E  457 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6851 (pm20)
REVERT: E  472 LEU cc_start: 0.9643 (pp) cc_final: 0.9392 (pp)
REVERT: E  477 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9396 (mm)
REVERT: E  848 ASP cc_start: 0.9793 (m-30) cc_final: 0.9504 (p0)
  outliers start: 53
  outliers final: 41
  residues processed: 121
  average time/residue: 0.2883
  time to fit residues: 54.2121
Evaluate side-chains
  120 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 72
  time to evaluate  : 1.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   62 CYS
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  215 PHE
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  213 ASN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain E residue  407 PHE
Chi-restraints excluded: chain E residue  441 LEU
Chi-restraints excluded: chain E residue  457 GLN
Chi-restraints excluded: chain E residue  461 GLU
Chi-restraints excluded: chain E residue  477 LEU
Chi-restraints excluded: chain E residue  510 CYS
Chi-restraints excluded: chain E residue  602 LEU
Chi-restraints excluded: chain E residue  604 ARG
Chi-restraints excluded: chain E residue  624 TRP
Chi-restraints excluded: chain E residue  661 THR
Chi-restraints excluded: chain E residue  870 LEU
Chi-restraints excluded: chain E residue  872 THR
Chi-restraints excluded: chain E residue  940 LEU
Chi-restraints excluded: chain E residue  964 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 142 optimal weight:    8.9990
   chunk 78 optimal weight:    5.9990
   chunk 128 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 112 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 135 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 213 ASN
** E 492 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 = 0.3984 r_free = 0.3984 target = 0.084770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.057894 restraints weight = 84496.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.057792 restraints weight = 46432.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.057799 restraints weight = 35815.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  13112  Z= 0.263
  Angle     :  0.743  15.649  18095  Z= 0.374
  Chirality :  0.042   0.204   2071
  Planarity :  0.004   0.041   2018
  Dihedral  : 22.113  77.767   2436
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 20.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.53 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 30.52 %
    Favored  : 65.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.23), residues: 1379
  helix:  0.68 (0.24), residues: 456
  sheet: -1.09 (0.27), residues: 360
  loop : -1.19 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 847 
 HIS   0.015   0.001   HIS C  44 
 PHE   0.038   0.002   PHE B 215 
 TYR   0.026   0.002   TYR D 249 
 ARG   0.005   0.001   ARG E 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06500 (  539)
  hydrogen bonds       : angle       5.34944 ( 1462)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       1.43298 (    6)
  covalent geometry    : bond        0.00560 (13109)
  covalent geometry    : angle       0.74297 (18089)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5745.10 seconds
wall clock time: 104 minutes 32.16 seconds (6272.16 seconds total)