Starting phenix.real_space_refine
on Wed Mar  4 20:06:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7niv_12366/03_2026/7niv_12366.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7niv_12366/03_2026/7niv_12366.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7niv_12366/03_2026/7niv_12366.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7niv_12366/03_2026/7niv_12366.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7niv_12366/03_2026/7niv_12366.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7niv_12366/03_2026/7niv_12366.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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       1      5.49       5
     S      54      5.16       5
     C   10092      2.51       5
     N    2607      2.21       5
     O    2970      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15724
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "D"
      Number of atoms: 1584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 208, 1578
          Classifications: {'peptide': 208}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197}
      Conformer: "B"
        Number of residues, atoms: 208, 1575
          Classifications: {'peptide': 208}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 1598
    Chain: "E"
      Number of atoms: 1702
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 229, 1702
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217}
    Chain: "A"
      Number of atoms: 8815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1138, 8815
          Classifications: {'peptide': 1138}
          Link IDs: {'PTRANS': 27, 'TRANS': 1110}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1616
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 211, 1610
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200}
      Conformer: "B"
        Number of residues, atoms: 211, 1607
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 1631
    Chain: "C"
      Number of atoms: 1757
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 234, 1757
          Classifications: {'peptide': 234}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222}
    Chain: "A"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 250
          Unusual residues: {'CLR': 7, 'DLP': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
  Time building chain proxies: 4.16, per 1000 atoms: 0.26
  Number of scatterers: 15724
  At special positions: 0
  Unit cell: (159.06, 132, 127.38, 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      54     16.00
     P       1     15.00
     O    2970      8.00
     N    2607      7.00
     C   10092      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 135 " - pdb=" SG  CYS D 195 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  25 " - pdb=" SG  CYS E  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 153 " - pdb=" SG  CYS E 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  25 " - pdb=" SG  CYS C  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 160 " - pdb=" SG  CYS C 216 " 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: 1.46
  Conformation dependent library (CDL) restraints added in 829.8 milliseconds
  

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3732

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 24 sheets defined
      36.6% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'D' and resid 122 through 127
    Processing helix  chain 'D' and resid 184 through 188
      removed outlier: 3.911A  pdb=" N   GLU D 188 " --> pdb=" O   LYS D 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 184 through 188'
    Processing helix  chain 'E' and resid 31 through 35
    Processing helix  chain 'E' and resid 213 through 217
    Processing helix  chain 'A' and resid 50 through 69
    Processing helix  chain 'A' and resid 69 through 92
      removed outlier: 3.929A  pdb=" N   LEU A  73 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET A  74 " --> pdb=" O   GLY A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 160
    Processing helix  chain 'A' and resid 163 through 168
    Processing helix  chain 'A' and resid 169 through 190
      removed outlier: 4.961A  pdb=" N   ILE A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   SER A 182 " --> pdb=" O   THR A 178 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 211
    Processing helix  chain 'A' and resid 214 through 244
      removed outlier: 3.639A  pdb=" N   ILE A 223 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
      Proline residue:  A 225  - end of helix
      removed outlier: 3.835A  pdb=" N   LEU A 238 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER A 239 " --> pdb=" O   ALA A 235 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   SER A 242 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ASP A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 259
      removed outlier: 4.921A  pdb=" N   VAL A 255 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 322
      removed outlier: 4.484A  pdb=" N   ASN A 285 " --> pdb=" O   LYS A 281 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   ILE A 289 " --> pdb=" O   ASN A 285 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   LYS A 292 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 349
    Processing helix  chain 'A' and resid 350 through 372
      removed outlier: 3.741A  pdb=" N   ALA A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   VAL A 366 " --> pdb=" O   GLY A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 442
      removed outlier: 3.549A  pdb=" N   VAL A 439 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ILE A 442 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 469
    Processing helix  chain 'A' and resid 485 through 492
      removed outlier: 3.835A  pdb=" N   TYR A 492 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 508
    Processing helix  chain 'A' and resid 512 through 517
    Processing helix  chain 'A' and resid 540 through 549
      removed outlier: 4.168A  pdb=" N   ALA A 544 " --> pdb=" O   ARG A 540 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ALA A 546 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG A 549 " --> pdb=" O   ARG A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 577
      removed outlier: 5.170A  pdb=" N   ALA A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   ALA A 574 " --> pdb=" O   GLU A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 618
    Processing helix  chain 'A' and resid 623 through 628
    Processing helix  chain 'A' and resid 696 through 703
      removed outlier: 3.536A  pdb=" N   VAL A 700 " --> pdb=" O   SER A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 720
    Processing helix  chain 'A' and resid 723 through 739
      removed outlier: 3.966A  pdb=" N   ILE A 736 " --> pdb=" O   PHE A 732 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA A 737 " --> pdb=" O   SER A 733 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A 739 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 794
      removed outlier: 3.639A  pdb=" N   LYS A 750 " --> pdb=" O   VAL A 746 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   CYS A 751 " --> pdb=" O   LYS A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 853
      removed outlier: 3.760A  pdb=" N   LEU A 813 " --> pdb=" O   SER A 809 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A 821 " --> pdb=" O   LEU A 817 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   ALA A 822 " --> pdb=" O   ALA A 818 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   GLY A 829 " --> pdb=" O   GLN A 825 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   ARG A 831 " --> pdb=" O   ALA A 827 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   LEU A 832 " --> pdb=" O   THR A 828 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASN A 838 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU A 842 " --> pdb=" O   ASN A 838 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   THR A 844 " --> pdb=" O   ALA A 840 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY A 845 " --> pdb=" O   ASN A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 868
      removed outlier: 3.587A  pdb=" N   THR A 857 " --> pdb=" O   GLY A 853 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL A 863 " --> pdb=" O   LEU A 859 " (cutoff:3.500A)
      Proline residue:  A 865  - end of helix
    Processing helix  chain 'A' and resid 869 through 874
    Processing helix  chain 'A' and resid 881 through 902
      removed outlier: 5.391A  pdb=" N   ILE A 895 " --> pdb=" O   ALA A 891 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   ALA A 896 " --> pdb=" O   ALA A 892 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASN A 902 " --> pdb=" O   GLU A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 902 through 910
      removed outlier: 3.992A  pdb=" N   VAL A 906 " --> pdb=" O   ASN A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 965
      removed outlier: 4.943A  pdb=" N   GLY A 925 " --> pdb=" O   GLU A 921 " (cutoff:3.500A)
      Proline residue:  A 926  - end of helix
      removed outlier: 3.630A  pdb=" N   TYR A 949 " --> pdb=" O   GLN A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 992
      removed outlier: 3.895A  pdb=" N   SER A 978 " --> pdb=" O   ILE A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1013
      removed outlier: 4.415A  pdb=" N   LEU A1002 " --> pdb=" O   ALA A 998 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER A1003 " --> pdb=" O   LYS A 999 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG A1013 " --> pdb=" O   MET A1009 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1083
    Processing helix  chain 'A' and resid 1104 through 1112
      removed outlier: 3.774A  pdb=" N   GLN A1111 " --> pdb=" O   TRP A1107 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   LEU A1112 " --> pdb=" O   LEU A1108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1130 through 1134
      removed outlier: 4.018A  pdb=" N   GLY A1133 " --> pdb=" O   ILE A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1140 through 1151
      removed outlier: 3.818A  pdb=" N   ILE A1144 " --> pdb=" O   SER A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1153 through 1158
      removed outlier: 3.839A  pdb=" N   GLU A1158 " --> pdb=" O   HIS A1154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1179 through 1183
    Processing helix  chain 'A' and resid 1185 through 1190
    Processing helix  chain 'A' and resid 1206 through 1211
      removed outlier: 4.187A  pdb=" N   LYS A1211 " --> pdb=" O   THR A1207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1212 through 1215
    Processing helix  chain 'A' and resid 1232 through 1237
      removed outlier: 4.374A  pdb=" N   GLN A1237 " --> pdb=" O   LEU A1233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 188
    Processing helix  chain 'C' and resid 31 through 35
      removed outlier: 3.543A  pdb=" N   SER C  34 " --> pdb=" O   ASN C  31 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER C  35 " --> pdb=" O   LEU C  32 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 31 through 35'
    Processing helix  chain 'C' and resid 176 through 178
      No H-bonds generated for 'chain 'C' and resid 176 through 178'
    Processing helix  chain 'C' and resid 222 through 224
      No H-bonds generated for 'chain 'C' and resid 222 through 224'
    Processing sheet with id=AA1, first strand: chain 'D' and resid 20 through 25
      removed outlier: 3.794A  pdb=" N   THR D  73 " --> pdb=" O   SER D  66 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER D  66 " --> pdb=" O   THR D  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 47
      removed outlier: 3.591A  pdb=" N   LYS D  46 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 115 through 118
      removed outlier: 5.105A  pdb=" N   SER D 132 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   LEU D 182 " --> pdb=" O   SER D 132 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   VAL D 134 " --> pdb=" O   LEU D 180 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU D 180 " --> pdb=" O   VAL D 134 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   LEU D 136 " --> pdb=" O   SER D 178 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   SER D 178 " --> pdb=" O   LEU D 136 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   ASN D 138 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   LEU D 176 " --> pdb=" O   ASN D 138 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 146 through 151
    Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 25
      removed outlier: 3.556A  pdb=" N   CYS E  25 " --> pdb=" O   ALA E  82 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA E  82 " --> pdb=" O   CYS E  25 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 38 through 41
      removed outlier: 7.009A  pdb=" N   TRP E  39 " --> pdb=" O   VAL E  51 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 133 through 137
      removed outlier: 3.854A  pdb=" N   GLY E 152 " --> pdb=" O   LEU E 137 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   CYS E 153 " --> pdb=" O   SER E 193 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   SER E 193 " --> pdb=" O   CYS E 153 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL E 194 " --> pdb=" O   HIS E 177 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 164 through 167
      removed outlier: 3.761A  pdb=" N   TYR E 207 " --> pdb=" O   VAL E 224 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LYS E 222 " --> pdb=" O   CYS E 209 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 182 through 183
    Processing sheet with id=AB1, first strand: chain 'A' and resid 416 through 418
    Processing sheet with id=AB2, first strand: chain 'A' and resid 427 through 428
      removed outlier: 3.593A  pdb=" N   VAL A 428 " --> pdb=" O   ALA A 601 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 472 through 473
      removed outlier: 6.493A  pdb=" N   GLY A 473 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   ASP A 557 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1050 through 1057
      removed outlier: 7.040A  pdb=" N   VAL A1051 " --> pdb=" O   ASN A1042 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   ASN A1042 " --> pdb=" O   VAL A1051 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   GLN A1053 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   VAL A1040 " --> pdb=" O   GLN A1053 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   LEU A1055 " --> pdb=" O   GLU A1038 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU A1038 " --> pdb=" O   LEU A1055 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1195 through 1197
      removed outlier: 5.232A  pdb=" N   LEU A1196 " --> pdb=" O   ILE A1227 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1245 through 1246
    Processing sheet with id=AB7, first strand: chain 'B' and resid 6 through 7
      removed outlier: 3.804A  pdb=" N   CYS B  24 " --> pdb=" O   PHE B  72 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   PHE B  72 " --> pdb=" O   CYS B  24 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 55
      removed outlier: 3.578A  pdb=" N   SER B  54 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ALA B  35 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN B  90 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 115 through 119
      removed outlier: 5.931A  pdb=" N   TYR B 174 " --> pdb=" O   ASN B 139 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.201A  pdb=" N   CYS B 195 " --> pdb=" O   LYS B 208 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LYS B 208 " --> pdb=" O   CYS B 195 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL B 197 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL B 206 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   HIS B 199 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   SER B 204 " --> pdb=" O   HIS B 199 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 6 through 10
      removed outlier: 3.657A  pdb=" N   SER C  24 " --> pdb=" O   SER C  10 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 14 through 15
      removed outlier: 4.220A  pdb=" N   VAL C  15 " --> pdb=" O   THR C 130 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC3
    Processing sheet with id=AC4, first strand: chain 'C' and resid 60 through 63
      removed outlier: 6.564A  pdb=" N   TRP C  39 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   TYR C  53 " --> pdb=" O   ILE C  37 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ILE C  37 " --> pdb=" O   TYR C  53 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 140 through 142
      removed outlier: 5.904A  pdb=" N   TYR C 196 " --> pdb=" O   ASP C 164 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 170 through 174

    656 hydrogen bonds defined for protein.
    1836 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.48

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2524
        1.31 -     1.44: 4312
        1.44 -     1.57: 9121
        1.57 -     1.69: 26
        1.69 -     1.82: 81
  Bond restraints: 16064
  Sorted by residual:
  bond pdb=" C11 DLP A1301 "
       pdb=" O3  DLP A1301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.422 -0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" C31 DLP A1301 "
       pdb=" O2  DLP A1301 "
    ideal  model  delta    sigma   weight residual
    1.331  1.426 -0.095 2.00e-02 2.50e+03 2.25e+01
  bond pdb=" N   DLP A1301 "
       pdb=" C7  DLP A1301 "
    ideal  model  delta    sigma   weight residual
    1.491  1.427  0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" N   VAL E 124 "
       pdb=" CA  VAL E 124 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.19e-02 7.06e+03 8.58e+00
  bond pdb=" C23 CLR A1307 "
       pdb=" C24 CLR A1307 "
    ideal  model  delta    sigma   weight residual
    1.525  1.578 -0.053 2.00e-02 2.50e+03 7.07e+00
  ... (remaining 16059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.01: 21335
        3.01 -     6.02: 414
        6.02 -     9.03: 49
        9.03 -    12.04: 7
       12.04 -    15.04: 1
  Bond angle restraints: 21806
  Sorted by residual:
  angle pdb=" N   TYR E 107 "
        pdb=" CA  TYR E 107 "
        pdb=" C   TYR E 107 "
      ideal   model   delta    sigma   weight residual
     111.71  118.65   -6.94 1.15e+00 7.56e-01 3.65e+01
  angle pdb=" O3P DLP A1301 "
        pdb=" P   DLP A1301 "
        pdb=" O4P DLP A1301 "
      ideal   model   delta    sigma   weight residual
      93.58  108.62  -15.04 3.00e+00 1.11e-01 2.51e+01
  angle pdb=" C   ALA E 112 "
        pdb=" CA  ALA E 112 "
        pdb=" CB  ALA E 112 "
      ideal   model   delta    sigma   weight residual
     116.54  110.79    5.75 1.15e+00 7.56e-01 2.50e+01
  angle pdb=" CA  VAL A 609 "
        pdb=" C   VAL A 609 "
        pdb=" N   GLU A 610 "
      ideal   model   delta    sigma   weight residual
     117.15  120.86   -3.71 7.80e-01 1.64e+00 2.26e+01
  angle pdb=" CA  ALA E 112 "
        pdb=" C   ALA E 112 "
        pdb=" N   MET E 113 "
      ideal   model   delta    sigma   weight residual
     119.52  115.97    3.55 7.90e-01 1.60e+00 2.02e+01
  ... (remaining 21801 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.80: 9208
       23.80 -    47.59: 624
       47.59 -    71.38: 71
       71.38 -    95.18: 15
       95.18 -   118.97: 2
  Dihedral angle restraints: 9920
    sinusoidal: 4089
      harmonic: 5831
  Sorted by residual:
  dihedral pdb=" CA  PHE A 732 "
           pdb=" C   PHE A 732 "
           pdb=" N   SER A 733 "
           pdb=" CA  SER A 733 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.12   28.88     0      5.00e+00 4.00e-02 3.34e+01
  dihedral pdb=" CB  CYS B 135 "
           pdb=" SG  CYS B 135 "
           pdb=" SG  CYS B 195 "
           pdb=" CB  CYS B 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.35   47.65     1      1.00e+01 1.00e-02 3.13e+01
  dihedral pdb=" CA  PHE A 982 "
           pdb=" C   PHE A 982 "
           pdb=" N   GLY A 983 "
           pdb=" CA  GLY A 983 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.21   26.79     0      5.00e+00 4.00e-02 2.87e+01
  ... (remaining 9917 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 2169
       0.077 -    0.155: 285
       0.155 -    0.232: 27
       0.232 -    0.309: 14
       0.309 -    0.386: 4
  Chirality restraints: 2499
  Sorted by residual:
  chirality pdb=" C17 CLR A1303 "
            pdb=" C13 CLR A1303 "
            pdb=" C16 CLR A1303 "
            pdb=" C20 CLR A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.94   -0.39 2.00e-01 2.50e+01 3.73e+00
  chirality pdb=" C17 CLR A1302 "
            pdb=" C13 CLR A1302 "
            pdb=" C16 CLR A1302 "
            pdb=" C20 CLR A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.91   -0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" C17 CLR A1304 "
            pdb=" C13 CLR A1304 "
            pdb=" C16 CLR A1304 "
            pdb=" C20 CLR A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.91   -0.35 2.00e-01 2.50e+01 3.13e+00
  ... (remaining 2496 not shown)

  Planarity restraints: 2727
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 305 "   -0.021 2.00e-02 2.50e+03   2.62e-02 1.20e+01
        pdb=" CG  PHE A 305 "    0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 305 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 305 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 305 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 305 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 305 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 175 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.31e+00
        pdb=" C   THR A 175 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   THR A 175 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ARG A 176 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 958 "    0.016 2.00e-02 2.50e+03   1.62e-02 4.61e+00
        pdb=" CG  PHE A 958 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 958 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 958 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 958 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 958 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 958 "    0.002 2.00e-02 2.50e+03
  ... (remaining 2724 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1670
        2.74 -     3.28: 16241
        3.28 -     3.82: 25161
        3.82 -     4.36: 30743
        4.36 -     4.90: 51375
  Nonbonded interactions: 125190
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 243 "
            pdb=" OD1 ASP A 243 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OE1 GLN A 443 "
            pdb=" OG  SER A 908 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" NE2 GLN B  39 "
            pdb=" O   LYS B  43 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OD1 ASP A 166 "
            pdb=" OH  TYR A 446 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   GLY A 845 "
            pdb=" OG  SER A 849 "
     model   vdw
     2.216 3.040
  ... (remaining 125185 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' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid  \ 
116 through 156 or resid 158 through 203 or resid 205 through 213))
  selection = (chain 'D' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid  \ 
116 through 156 or resid 158 through 203 or resid 205 through 213))
}
ncs_group {
  reference = (chain 'C' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ 
 or resid 54 through 56 or resid 59 through 101 or resid 109 or resid 111 throug \ 
h 112 or resid 115 or resid 121 through 236))
  selection = (chain 'E' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ 
 or resid 54 through 56 or resid 59 through 101 or resid 103 or resid 105 throug \ 
h 106 or resid 108 or resid 114 through 229))
}

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=0.30 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:             7.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.560
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6054
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      :  0.008   0.095  16072  Z= 0.350
  Angle     :  1.042  15.045  21822  Z= 0.568
  Chirality :  0.058   0.386   2499
  Planarity :  0.006   0.047   2727
  Dihedral  : 15.580 118.974   6164
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 22.54
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.62 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  7.72 %
    Favored  : 91.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.19 (0.15), residues: 2010
  helix: -3.96 (0.12), residues: 688
  sheet: -2.34 (0.24), residues: 406
  loop : -3.48 (0.17), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 831 
 TYR   0.031   0.003   TYR A 710 
 PHE   0.059   0.003   PHE A 305 
 TRP   0.022   0.002   TRP C 112 
 HIS   0.008   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00755 (16064)
  covalent geometry    : angle       1.04190 (21806)
  SS BOND              : bond        0.00375 (    8)
  SS BOND              : angle       1.45484 (   16)
  hydrogen bonds       : bond        0.16208 (  656)
  hydrogen bonds       : angle       8.40589 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   88 TYR cc_start: 0.5676 (m-80) cc_final: 0.5361 (m-80)
REVERT: A  206 PHE cc_start: 0.6256 (t80) cc_final: 0.5800 (t80)
REVERT: A  246 LEU cc_start: 0.1126 (OUTLIER) cc_final: 0.0761 (mt)
REVERT: A  738 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7744 (pt)
REVERT: B   95 LYS cc_start: 0.5449 (mmmt) cc_final: 0.4585 (mtmt)
  outliers start: 15
  outliers final: 7
  residues processed: 193
  average time/residue: 0.1543
  time to fit residues: 42.0655
Evaluate side-chains
  142 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  747 LYS
Chi-restraints excluded: chain A residue 1019 SER
Chi-restraints excluded: chain A residue 1065 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 194 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    9.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
E 108 GLN
A 151 GLN
A 332 ASN
A 400 HIS
A 537 GLN
A 748 GLN
A 837 GLN
A 838 ASN
A 841 ASN
A 881 ASN
A 902 ASN
A 935 HIS
A1033 ASN
A1111 GLN
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1152 ASN
A1214 GLN
B   4 GLN
B  90 GLN
B  91 GLN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  42 GLN
C  80 ASN
C  87 ASN
C 175 ASN
** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4984 r_free = 0.4984 target = 0.256167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.231527 restraints weight = 41979.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.233854 restraints weight = 58081.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4740 r_free = 0.4740 target = 0.234693 restraints weight = 15171.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.235535 restraints weight = 10091.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.235360 restraints weight = 8320.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.4731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4740 r_free = 0.4740    target_work(ls_wunit_k1) = 0.227         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4740 r_free = 0.4740    target_work(ls_wunit_k1) = 0.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.4740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5775
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16072  Z= 0.134
  Angle     :  0.661   8.996  21822  Z= 0.342
  Chirality :  0.044   0.176   2499
  Planarity :  0.005   0.076   2727
  Dihedral  :  8.868  83.526   2690
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.23 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.17), residues: 2010
  helix: -1.69 (0.17), residues: 694
  sheet: -1.72 (0.24), residues: 406
  loop : -2.53 (0.19), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  25 
 TYR   0.016   0.002   TYR A 116 
 PHE   0.026   0.002   PHE A 732 
 TRP   0.034   0.002   TRP E 106 
 HIS   0.004   0.001   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (16064)
  covalent geometry    : angle       0.66071 (21806)
  SS BOND              : bond        0.00360 (    8)
  SS BOND              : angle       1.00433 (   16)
  hydrogen bonds       : bond        0.04947 (  656)
  hydrogen bonds       : angle       5.88014 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 PHE cc_start: 0.6500 (t80) cc_final: 0.6231 (t80)
REVERT: A  206 PHE cc_start: 0.5783 (t80) cc_final: 0.5350 (t80)
REVERT: A  501 GLU cc_start: 0.5880 (mt-10) cc_final: 0.5521 (mt-10)
REVERT: A  552 LYS cc_start: 0.6760 (tppt) cc_final: 0.6379 (mmtm)
REVERT: A  738 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7676 (pt)
REVERT: B   95 LYS cc_start: 0.5320 (mmmt) cc_final: 0.4369 (mtmt)
REVERT: C   86 MET cc_start: 0.4683 (ptp) cc_final: 0.4208 (ptm)
  outliers start: 31
  outliers final: 14
  residues processed: 178
  average time/residue: 0.1261
  time to fit residues: 33.5577
Evaluate side-chains
  141 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue  902 ASN
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue  121 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 17 optimal weight:   50.0000
   chunk 57 optimal weight:    3.9990
   chunk 115 optimal weight:    0.6980
   chunk 33 optimal weight:   50.0000
   chunk 198 optimal weight:   10.0000
   chunk 98 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 95 optimal weight:    8.9990
   chunk 119 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  67 HIS
A 332 ASN
A 902 ASN
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  38 GLN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4970 r_free = 0.4970 target = 0.254919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.228728 restraints weight = 42733.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.231127 restraints weight = 53798.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.231552 restraints weight = 16406.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.232319 restraints weight = 11883.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.232317 restraints weight = 7193.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4690
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4691 r_free = 0.4691    target_work(ls_wunit_k1) = 0.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4691 r_free = 0.4691    target_work(ls_wunit_k1) = 0.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.4691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5841
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16072  Z= 0.149
  Angle     :  0.629   8.592  21822  Z= 0.324
  Chirality :  0.043   0.213   2499
  Planarity :  0.005   0.062   2727
  Dihedral  :  8.369  88.516   2682
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.56 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.18), residues: 2010
  helix: -0.91 (0.19), residues: 698
  sheet: -1.43 (0.24), residues: 422
  loop : -2.14 (0.20), residues: 890

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 957 
 TYR   0.019   0.002   TYR A1132 
 PHE   0.026   0.002   PHE A 982 
 TRP   0.018   0.001   TRP E 106 
 HIS   0.005   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (16064)
  covalent geometry    : angle       0.62876 (21806)
  SS BOND              : bond        0.00272 (    8)
  SS BOND              : angle       0.75956 (   16)
  hydrogen bonds       : bond        0.04890 (  656)
  hydrogen bonds       : angle       5.54799 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   88 TYR cc_start: 0.5430 (m-80) cc_final: 0.5143 (m-80)
REVERT: E  192 SER cc_start: -0.1385 (OUTLIER) cc_final: -0.1946 (t)
REVERT: A  501 GLU cc_start: 0.5906 (mt-10) cc_final: 0.5654 (mt-10)
REVERT: A  738 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7733 (pt)
REVERT: A  957 ARG cc_start: 0.8431 (tpt90) cc_final: 0.8149 (tpt90)
REVERT: A 1002 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7298 (tp)
REVERT: A 1031 GLU cc_start: 0.4812 (mm-30) cc_final: 0.4510 (mm-30)
REVERT: B   47 LEU cc_start: 0.6904 (tt) cc_final: 0.6658 (tp)
REVERT: B   95 LYS cc_start: 0.5321 (mmmt) cc_final: 0.4402 (mtmt)
  outliers start: 32
  outliers final: 14
  residues processed: 166
  average time/residue: 0.1239
  time to fit residues: 31.2985
Evaluate side-chains
  142 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue  121 ASP
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 26 optimal weight:    0.0170
   chunk 160 optimal weight:   30.0000
   chunk 91 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 128 optimal weight:    0.6980
   chunk 28 optimal weight:   20.0000
   chunk 47 optimal weight:    0.8980
   chunk 39 optimal weight:    9.9990
   chunk 172 optimal weight:   40.0000
   chunk 87 optimal weight:    8.9990
   chunk 127 optimal weight:    0.9980
   overall best weight:    2.3220

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

Flipped N/Q/H residues before XYZ refinement:
D   7 GLN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
A 902 ASN
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4936 r_free = 0.4936 target = 0.250921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.221796 restraints weight = 41946.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.224621 restraints weight = 56281.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.224991 restraints weight = 18025.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.226071 restraints weight = 10604.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.226015 restraints weight = 7668.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.4592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4589 r_free = 0.4589    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4589 r_free = 0.4589    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5992
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  16072  Z= 0.185
  Angle     :  0.658   9.579  21822  Z= 0.336
  Chirality :  0.045   0.272   2499
  Planarity :  0.005   0.058   2727
  Dihedral  :  8.367  87.866   2682
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 16.16 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.18), residues: 2010
  helix: -0.84 (0.19), residues: 698
  sheet: -1.26 (0.25), residues: 419
  loop : -1.94 (0.20), residues: 893

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1221 
 TYR   0.017   0.002   TYR A1132 
 PHE   0.035   0.002   PHE A 206 
 TRP   0.013   0.001   TRP E 167 
 HIS   0.006   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (16064)
  covalent geometry    : angle       0.65817 (21806)
  SS BOND              : bond        0.00243 (    8)
  SS BOND              : angle       0.68578 (   16)
  hydrogen bonds       : bond        0.05221 (  656)
  hydrogen bonds       : angle       5.52974 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 132
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 PHE cc_start: 0.5451 (OUTLIER) cc_final: 0.5138 (m-80)
REVERT: E  192 SER cc_start: -0.1529 (OUTLIER) cc_final: -0.2007 (t)
REVERT: A  501 GLU cc_start: 0.5940 (mt-10) cc_final: 0.5683 (mt-10)
REVERT: A  552 LYS cc_start: 0.6831 (tppt) cc_final: 0.6459 (mmtm)
REVERT: A  738 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7775 (pt)
REVERT: A  895 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.6917 (mt)
REVERT: A 1002 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7343 (tp)
REVERT: B   95 LYS cc_start: 0.5408 (mmmt) cc_final: 0.4405 (mtmt)
  outliers start: 55
  outliers final: 32
  residues processed: 174
  average time/residue: 0.1243
  time to fit residues: 33.4222
Evaluate side-chains
  157 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain E residue   71 PHE
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  872 ILE
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  949 TYR
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 2 optimal weight:   40.0000
   chunk 93 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 151 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 120 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 187 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 119 optimal weight:    0.7980
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 ASN
** C 220 HIS ** 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 = 0.4921 r_free = 0.4921 target = 0.249050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.216332 restraints weight = 44231.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.213840 restraints weight = 56885.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.210089 restraints weight = 37744.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.210675 restraints weight = 31896.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.210199 restraints weight = 23035.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.4551
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4554 r_free = 0.4554    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4554 r_free = 0.4554    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.4554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6073
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  16072  Z= 0.227
  Angle     :  0.698   9.639  21822  Z= 0.357
  Chirality :  0.046   0.218   2499
  Planarity :  0.005   0.056   2727
  Dihedral  :  8.649  87.750   2682
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 18.06 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.18), residues: 2010
  helix: -1.00 (0.18), residues: 698
  sheet: -1.16 (0.25), residues: 409
  loop : -1.85 (0.20), residues: 903

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 957 
 TYR   0.016   0.002   TYR B 174 
 PHE   0.037   0.002   PHE A 982 
 TRP   0.036   0.002   TRP E 106 
 HIS   0.006   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (16064)
  covalent geometry    : angle       0.69777 (21806)
  SS BOND              : bond        0.00250 (    8)
  SS BOND              : angle       0.69869 (   16)
  hydrogen bonds       : bond        0.05713 (  656)
  hydrogen bonds       : angle       5.65711 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 123
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 PHE cc_start: 0.5383 (OUTLIER) cc_final: 0.5128 (m-80)
REVERT: E  192 SER cc_start: -0.1313 (OUTLIER) cc_final: -0.1833 (t)
REVERT: A  501 GLU cc_start: 0.5981 (mt-10) cc_final: 0.5774 (mt-10)
REVERT: A  552 LYS cc_start: 0.6852 (tppt) cc_final: 0.6449 (mmtm)
REVERT: A  800 MET cc_start: 0.6883 (ttt) cc_final: 0.6549 (ttt)
REVERT: A  877 LEU cc_start: 0.3726 (OUTLIER) cc_final: 0.3463 (pt)
REVERT: A  895 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7043 (mp)
REVERT: A  947 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6591 (m-80)
REVERT: A 1002 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7367 (tp)
REVERT: B   95 LYS cc_start: 0.5253 (mmmt) cc_final: 0.4291 (mtmt)
REVERT: C   86 MET cc_start: 0.4537 (ptp) cc_final: 0.3662 (ptm)
  outliers start: 62
  outliers final: 39
  residues processed: 171
  average time/residue: 0.1158
  time to fit residues: 31.0492
Evaluate side-chains
  159 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 114
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   87 TYR
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain E residue   71 PHE
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  872 ILE
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  947 PHE
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  202 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 196 optimal weight:   50.0000
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 116 optimal weight:    0.6980
   chunk 189 optimal weight:    0.0060
   chunk 115 optimal weight:    0.8980
   chunk 160 optimal weight:   10.0000
   chunk 198 optimal weight:   20.0000
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:   20.0000
   chunk 161 optimal weight:    3.9990
   overall best weight:    1.5200

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.254473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.223920 restraints weight = 29944.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.221690 restraints weight = 44957.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.218920 restraints weight = 33799.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.218740 restraints weight = 31419.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.216936 restraints weight = 27687.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.4639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4641 r_free = 0.4641    target_work(ls_wunit_k1) = 0.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4641 r_free = 0.4641    target_work(ls_wunit_k1) = 0.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.4641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5988
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  16072  Z= 0.148
  Angle     :  0.619  11.330  21822  Z= 0.314
  Chirality :  0.043   0.193   2499
  Planarity :  0.004   0.057   2727
  Dihedral  :  8.038  88.970   2680
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 19.13 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.19), residues: 2010
  helix: -0.50 (0.19), residues: 693
  sheet: -1.03 (0.25), residues: 409
  loop : -1.69 (0.21), residues: 908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 957 
 TYR   0.018   0.001   TYR C 122 
 PHE   0.034   0.002   PHE A 206 
 TRP   0.055   0.002   TRP E 106 
 HIS   0.004   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (16064)
  covalent geometry    : angle       0.61893 (21806)
  SS BOND              : bond        0.00223 (    8)
  SS BOND              : angle       0.59364 (   16)
  hydrogen bonds       : bond        0.04846 (  656)
  hydrogen bonds       : angle       5.30287 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 121
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 PHE cc_start: 0.6392 (t80) cc_final: 0.6140 (t80)
REVERT: A  552 LYS cc_start: 0.6788 (tppt) cc_final: 0.6408 (mmtm)
REVERT: A  800 MET cc_start: 0.6744 (ttt) cc_final: 0.6325 (ttt)
REVERT: A  877 LEU cc_start: 0.3817 (OUTLIER) cc_final: 0.3582 (pt)
REVERT: A  895 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.6981 (mt)
REVERT: A  947 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6364 (m-80)
REVERT: A  969 ARG cc_start: 0.6838 (mtm110) cc_final: 0.6506 (mtm-85)
REVERT: A 1002 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7256 (tp)
REVERT: A 1249 ARG cc_start: 0.3189 (OUTLIER) cc_final: 0.2988 (mmt-90)
REVERT: B   95 LYS cc_start: 0.5283 (mmmt) cc_final: 0.4343 (mtmt)
REVERT: C   89 LEU cc_start: 0.4588 (OUTLIER) cc_final: 0.4231 (tp)
  outliers start: 54
  outliers final: 33
  residues processed: 166
  average time/residue: 0.1271
  time to fit residues: 32.2963
Evaluate side-chains
  154 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 115
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   87 TYR
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  872 ILE
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  947 PHE
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1138 VAL
Chi-restraints excluded: chain A residue 1249 ARG
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  170 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 141 optimal weight:    4.9990
   chunk 129 optimal weight:    7.9990
   chunk 75 optimal weight:    9.9990
   chunk 185 optimal weight:    6.9990
   chunk 172 optimal weight:   40.0000
   chunk 57 optimal weight:    1.9990
   chunk 133 optimal weight:    6.9990
   chunk 170 optimal weight:    8.9990
   chunk 64 optimal weight:    0.6980
   chunk 28 optimal weight:   10.0000
   chunk 174 optimal weight:    0.0030
   overall best weight:    2.9396

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

Flipped N/Q/H residues before XYZ refinement:
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 168 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
A 841 ASN
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 ASN
** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4923 r_free = 0.4923 target = 0.249364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.217138 restraints weight = 27410.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.213637 restraints weight = 37250.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.209809 restraints weight = 22013.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.208386 restraints weight = 27546.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.206934 restraints weight = 22840.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4536 r_free = 0.4536    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4536 r_free = 0.4536    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.4536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6144
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  16072  Z= 0.214
  Angle     :  0.683  10.997  21822  Z= 0.348
  Chirality :  0.046   0.218   2499
  Planarity :  0.005   0.062   2727
  Dihedral  :  8.303  86.332   2677
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 18.72 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.18), residues: 2010
  helix: -0.72 (0.19), residues: 692
  sheet: -1.04 (0.25), residues: 409
  loop : -1.72 (0.21), residues: 909

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 494 
 TYR   0.018   0.002   TYR C 122 
 PHE   0.037   0.002   PHE A 982 
 TRP   0.077   0.002   TRP E 106 
 HIS   0.006   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (16064)
  covalent geometry    : angle       0.68274 (21806)
  SS BOND              : bond        0.00226 (    8)
  SS BOND              : angle       0.64551 (   16)
  hydrogen bonds       : bond        0.05583 (  656)
  hydrogen bonds       : angle       5.51457 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 118
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
REVERT: E   89 LEU cc_start: 0.5654 (mm) cc_final: 0.5398 (mm)
REVERT: E  172 LEU cc_start: 0.1963 (pt) cc_final: 0.1480 (tp)
REVERT: A  552 LYS cc_start: 0.6871 (tppt) cc_final: 0.6525 (mmtm)
REVERT: A  800 MET cc_start: 0.6856 (ttt) cc_final: 0.6474 (ttt)
REVERT: A  877 LEU cc_start: 0.3784 (OUTLIER) cc_final: 0.3454 (pt)
REVERT: A  895 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7081 (mp)
REVERT: A  947 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6569 (m-80)
REVERT: A 1002 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7348 (tp)
REVERT: A 1137 ARG cc_start: 0.6957 (ptm-80) cc_final: 0.6698 (ttp80)
REVERT: A 1249 ARG cc_start: 0.3125 (OUTLIER) cc_final: 0.2913 (mmt-90)
REVERT: B   95 LYS cc_start: 0.5237 (mmmt) cc_final: 0.4259 (mtmt)
  outliers start: 70
  outliers final: 43
  residues processed: 177
  average time/residue: 0.1141
  time to fit residues: 31.9224
Evaluate side-chains
  159 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 111
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   87 TYR
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain E residue    8 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  872 ILE
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 SER
Chi-restraints excluded: chain A residue  947 PHE
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1138 VAL
Chi-restraints excluded: chain A residue 1249 ARG
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 101 optimal weight:    0.0980
   chunk 195 optimal weight:   20.0000
   chunk 21 optimal weight:    0.0870
   chunk 67 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 121 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 157 optimal weight:    6.9990
   chunk 173 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 841 ASN
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 GLN
** C 220 HIS ** 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 = 0.4964 r_free = 0.4964 target = 0.253986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4807 r_free = 0.4807 target = 0.235635 restraints weight = 40980.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.231827 restraints weight = 49201.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.229661 restraints weight = 47450.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.229759 restraints weight = 42419.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.228003 restraints weight = 36888.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.4755
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4758
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4758 r_free = 0.4758    target_work(ls_wunit_k1) = 0.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4758 r_free = 0.4758    target_work(ls_wunit_k1) = 0.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.4758
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5694
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  16072  Z= 0.125
  Angle     :  0.595  10.172  21822  Z= 0.303
  Chirality :  0.042   0.182   2499
  Planarity :  0.004   0.056   2727
  Dihedral  :  7.689  86.708   2677
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.26 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.19), residues: 2010
  helix: -0.13 (0.20), residues: 685
  sheet: -1.01 (0.25), residues: 414
  loop : -1.49 (0.21), residues: 911

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1187 
 TYR   0.015   0.001   TYR B 174 
 PHE   0.033   0.002   PHE A 206 
 TRP   0.066   0.002   TRP E 106 
 HIS   0.003   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (16064)
  covalent geometry    : angle       0.59516 (21806)
  SS BOND              : bond        0.00218 (    8)
  SS BOND              : angle       0.54924 (   16)
  hydrogen bonds       : bond        0.04473 (  656)
  hydrogen bonds       : angle       5.10866 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 114
  time to evaluate  : 0.575 
Fit side-chains
REVERT: E  172 LEU cc_start: 0.1940 (pt) cc_final: 0.1344 (tp)
REVERT: A  552 LYS cc_start: 0.6605 (tppt) cc_final: 0.6292 (mmtm)
REVERT: A  800 MET cc_start: 0.6714 (ttt) cc_final: 0.6268 (ttt)
REVERT: A  877 LEU cc_start: 0.3833 (OUTLIER) cc_final: 0.3606 (pt)
REVERT: A  895 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.6957 (mt)
REVERT: A  947 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6317 (m-80)
REVERT: A  971 ARG cc_start: 0.5433 (OUTLIER) cc_final: 0.5046 (ptm160)
REVERT: A 1002 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7390 (tp)
REVERT: A 1137 ARG cc_start: 0.6641 (ptm-80) cc_final: 0.6390 (ttp80)
REVERT: B   95 LYS cc_start: 0.5220 (mmmt) cc_final: 0.4331 (mtmt)
REVERT: C   89 LEU cc_start: 0.4574 (OUTLIER) cc_final: 0.4267 (tp)
  outliers start: 47
  outliers final: 27
  residues processed: 155
  average time/residue: 0.1221
  time to fit residues: 29.6934
Evaluate side-chains
  139 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   87 TYR
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  872 ILE
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 SER
Chi-restraints excluded: chain A residue  947 PHE
Chi-restraints excluded: chain A residue  971 ARG
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1138 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 171 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 149 optimal weight:    5.9990
   chunk 192 optimal weight:   10.0000
   chunk 113 optimal weight:    0.7980
   chunk 198 optimal weight:    7.9990
   chunk 179 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
A 614 HIS
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 HIS ** 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 = 0.4958 r_free = 0.4958 target = 0.253382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.233383 restraints weight = 35474.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.231386 restraints weight = 50205.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4742 r_free = 0.4742 target = 0.228557 restraints weight = 32326.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.227139 restraints weight = 34460.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.225516 restraints weight = 40235.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.4763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4763 r_free = 0.4763    target_work(ls_wunit_k1) = 0.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4763 r_free = 0.4763    target_work(ls_wunit_k1) = 0.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.4763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5801
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  16072  Z= 0.166
  Angle     :  0.634  10.100  21822  Z= 0.323
  Chirality :  0.044   0.199   2499
  Planarity :  0.004   0.055   2727
  Dihedral  :  7.888  86.868   2677
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.44 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.19), residues: 2010
  helix: -0.33 (0.19), residues: 698
  sheet: -0.93 (0.26), residues: 408
  loop : -1.41 (0.21), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1249 
 TYR   0.026   0.002   TYR A1132 
 PHE   0.034   0.002   PHE A 982 
 TRP   0.051   0.002   TRP E 106 
 HIS   0.005   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (16064)
  covalent geometry    : angle       0.63358 (21806)
  SS BOND              : bond        0.00223 (    8)
  SS BOND              : angle       0.56965 (   16)
  hydrogen bonds       : bond        0.04957 (  656)
  hydrogen bonds       : angle       5.20992 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 107
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
REVERT: E  172 LEU cc_start: 0.1744 (pt) cc_final: 0.1179 (tp)
REVERT: A  552 LYS cc_start: 0.6508 (tppt) cc_final: 0.6214 (mmtm)
REVERT: A  800 MET cc_start: 0.6774 (ttt) cc_final: 0.6371 (ttt)
REVERT: A  877 LEU cc_start: 0.4012 (OUTLIER) cc_final: 0.3705 (pt)
REVERT: A  895 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7002 (mt)
REVERT: A  947 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6443 (m-80)
REVERT: A 1002 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7263 (tp)
REVERT: A 1137 ARG cc_start: 0.6545 (ptm-80) cc_final: 0.6316 (ttp80)
REVERT: B   95 LYS cc_start: 0.5341 (mmmt) cc_final: 0.4473 (mtmt)
  outliers start: 50
  outliers final: 41
  residues processed: 149
  average time/residue: 0.1178
  time to fit residues: 27.4460
Evaluate side-chains
  148 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 103
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   87 TYR
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain E residue    8 VAL
Chi-restraints excluded: chain E residue  108 GLN
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  872 ILE
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 SER
Chi-restraints excluded: chain A residue  947 PHE
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1138 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 137 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 163 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 182 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 166 optimal weight:    5.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 285 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
A 841 ASN
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 HIS ** 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 = 0.4918 r_free = 0.4918 target = 0.248517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.217708 restraints weight = 30171.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.214384 restraints weight = 43618.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.211495 restraints weight = 36912.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.211591 restraints weight = 37909.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.209851 restraints weight = 29702.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.4558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4559 r_free = 0.4559    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4559 r_free = 0.4559    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.4559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6040
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  16072  Z= 0.208
  Angle     :  0.680  10.120  21822  Z= 0.348
  Chirality :  0.045   0.215   2499
  Planarity :  0.005   0.055   2727
  Dihedral  :  8.148  85.769   2677
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.68 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.19), residues: 2010
  helix: -0.63 (0.19), residues: 694
  sheet: -1.00 (0.26), residues: 412
  loop : -1.37 (0.21), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 969 
 TYR   0.025   0.002   TYR A1132 
 PHE   0.038   0.002   PHE A 206 
 TRP   0.060   0.002   TRP E 106 
 HIS   0.006   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (16064)
  covalent geometry    : angle       0.67975 (21806)
  SS BOND              : bond        0.00361 (    8)
  SS BOND              : angle       0.81323 (   16)
  hydrogen bonds       : bond        0.05445 (  656)
  hydrogen bonds       : angle       5.41516 ( 1836)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 105
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
REVERT: A  552 LYS cc_start: 0.6715 (tppt) cc_final: 0.6454 (mmtm)
REVERT: A  877 LEU cc_start: 0.3941 (OUTLIER) cc_final: 0.3651 (pt)
REVERT: A  895 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7085 (mp)
REVERT: A  947 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6516 (m-80)
REVERT: A 1002 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7329 (tp)
REVERT: A 1137 ARG cc_start: 0.6964 (ptm-80) cc_final: 0.6717 (ttp80)
REVERT: B   95 LYS cc_start: 0.5184 (mmmt) cc_final: 0.4161 (mtmt)
  outliers start: 48
  outliers final: 38
  residues processed: 146
  average time/residue: 0.1177
  time to fit residues: 26.7274
Evaluate side-chains
  146 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 104
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   87 TYR
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain E residue    8 VAL
Chi-restraints excluded: chain E residue  108 GLN
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  872 ILE
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 SER
Chi-restraints excluded: chain A residue  947 PHE
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1138 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 29 optimal weight:    8.9990
   chunk 173 optimal weight:    7.9990
   chunk 129 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 125 optimal weight:    0.6980
   chunk 155 optimal weight:    4.9990
   chunk 134 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 GLN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 841 ASN
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 HIS ** 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 = 0.4979 r_free = 0.4979 target = 0.255632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4813 r_free = 0.4813 target = 0.236086 restraints weight = 32871.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.233989 restraints weight = 49636.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.231369 restraints weight = 31129.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4753 r_free = 0.4753 target = 0.229966 restraints weight = 35238.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.228359 restraints weight = 35612.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.4788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4788 r_free = 0.4788    target_work(ls_wunit_k1) = 0.232         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4788 r_free = 0.4788    target_work(ls_wunit_k1) = 0.232         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.4788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5740
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  16072  Z= 0.137
  Angle     :  0.611   9.779  21822  Z= 0.312
  Chirality :  0.042   0.181   2499
  Planarity :  0.004   0.057   2727
  Dihedral  :  7.740  89.301   2677
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.09 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.19), residues: 2010
  helix: -0.19 (0.20), residues: 702
  sheet: -0.93 (0.26), residues: 401
  loop : -1.28 (0.21), residues: 907

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 969 
 TYR   0.021   0.001   TYR A1132 
 PHE   0.044   0.002   PHE B 140 
 TRP   0.050   0.002   TRP E 106 
 HIS   0.004   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (16064)
  covalent geometry    : angle       0.61064 (21806)
  SS BOND              : bond        0.00289 (    8)
  SS BOND              : angle       1.06725 (   16)
  hydrogen bonds       : bond        0.04605 (  656)
  hydrogen bonds       : angle       5.10941 ( 1836)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3196.98 seconds
wall clock time: 55 minutes 55.04 seconds (3355.04 seconds total)