Starting phenix.real_space_refine
on Thu Sep 18 09:44:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9krg_62526/09_2025/9krg_62526.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9krg_62526/09_2025/9krg_62526.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9krg_62526/09_2025/9krg_62526.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9krg_62526/09_2025/9krg_62526.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9krg_62526/09_2025/9krg_62526.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9krg_62526/09_2025/9krg_62526.map"
  }
  resolution = 2.9
  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=   0.007 sd=   0.237
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C   10395      2.51       5
     N    2639      2.21       5
     O    2772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15876
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2268
          Classifications: {'peptide': 291}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 13, 'TRANS': 277}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 50
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 1.78, per 1000 atoms: 0.11
  Number of scatterers: 15876
  At special positions: 0
  Unit cell: (117.18, 117.18, 119.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      70     16.00
     O    2772      8.00
     N    2639      7.00
     C   10395      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  84 " - pdb=" SG  CYS A 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  66 " - pdb=" SG  CYS D 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  66 " - pdb=" SG  CYS E 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  66 " - pdb=" SG  CYS F 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  66 " - pdb=" SG  CYS G 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  84 " - pdb=" SG  CYS B 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  84 " - pdb=" SG  CYS C 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  84 " - pdb=" SG  CYS D 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  84 " - pdb=" SG  CYS E 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  84 " - pdb=" SG  CYS F 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  84 " - pdb=" SG  CYS G 242 " 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: 1.27
  Conformation dependent library (CDL) restraints added in 722.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3976

  Finding SS restraints...
    Secondary structure from input PDB file:
      84 helices and 7 sheets defined
      69.8% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 61
      Proline residue:  A  46  - end of helix
      removed outlier: 4.291A  pdb=" N   GLN A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU A  57 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 88
    Processing helix  chain 'A' and resid 104 through 109
      removed outlier: 4.442A  pdb=" N   LYS A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 132
      removed outlier: 3.545A  pdb=" N   ALA A 118 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      Proline residue:  A 124  - end of helix
    Processing helix  chain 'A' and resid 132 through 159
      removed outlier: 3.825A  pdb=" N   ARG A 156 " --> pdb=" O   ASN A 152 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU A 157 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLN A 159 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 201
      removed outlier: 3.991A  pdb=" N   LEU A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 231
      removed outlier: 3.809A  pdb=" N   ASN A 213 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 235
      removed outlier: 3.592A  pdb=" N   PHE A 235 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 232 through 235'
    Processing helix  chain 'A' and resid 265 through 294
      removed outlier: 3.966A  pdb=" N   VAL A 284 " --> pdb=" O   TYR A 280 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
      removed outlier: 4.574A  pdb=" N   LEU A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 317
      removed outlier: 3.634A  pdb=" N   LYS A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 336
    Processing helix  chain 'A' and resid 368 through 374
      removed outlier: 4.295A  pdb=" N   GLY A 374 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 61
      Proline residue:  B  46  - end of helix
      removed outlier: 4.291A  pdb=" N   GLN B  56 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU B  57 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 88
    Processing helix  chain 'B' and resid 104 through 109
      removed outlier: 4.442A  pdb=" N   LYS B 108 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 132
      removed outlier: 3.545A  pdb=" N   ALA B 118 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      Proline residue:  B 124  - end of helix
    Processing helix  chain 'B' and resid 132 through 159
      removed outlier: 3.824A  pdb=" N   ARG B 156 " --> pdb=" O   ASN B 152 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU B 157 " --> pdb=" O   ARG B 153 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN B 159 " --> pdb=" O   ILE B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 201
      removed outlier: 3.991A  pdb=" N   LEU B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 231
      removed outlier: 3.809A  pdb=" N   ASN B 213 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 235
      removed outlier: 3.592A  pdb=" N   PHE B 235 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 232 through 235'
    Processing helix  chain 'B' and resid 265 through 294
      removed outlier: 3.966A  pdb=" N   VAL B 284 " --> pdb=" O   TYR B 280 " (cutoff:3.500A)
      Proline residue:  B 285  - end of helix
      removed outlier: 4.574A  pdb=" N   LEU B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 317
      removed outlier: 3.634A  pdb=" N   LYS B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 336
    Processing helix  chain 'B' and resid 368 through 374
      removed outlier: 4.295A  pdb=" N   GLY B 374 " --> pdb=" O   THR B 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 61
      Proline residue:  C  46  - end of helix
      removed outlier: 4.292A  pdb=" N   GLN C  56 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU C  57 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   SER C  59 " --> pdb=" O   ALA C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 88
    Processing helix  chain 'C' and resid 104 through 109
      removed outlier: 4.442A  pdb=" N   LYS C 108 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 132
      removed outlier: 3.545A  pdb=" N   ALA C 118 " --> pdb=" O   LEU C 114 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU C 119 " --> pdb=" O   LEU C 115 " (cutoff:3.500A)
      Proline residue:  C 124  - end of helix
    Processing helix  chain 'C' and resid 132 through 159
      removed outlier: 3.825A  pdb=" N   ARG C 156 " --> pdb=" O   ASN C 152 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU C 157 " --> pdb=" O   ARG C 153 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN C 159 " --> pdb=" O   ILE C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 201
      removed outlier: 3.991A  pdb=" N   LEU C 196 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 231
      removed outlier: 3.809A  pdb=" N   ASN C 213 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 235
      removed outlier: 3.592A  pdb=" N   PHE C 235 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 232 through 235'
    Processing helix  chain 'C' and resid 265 through 294
      removed outlier: 3.966A  pdb=" N   VAL C 284 " --> pdb=" O   TYR C 280 " (cutoff:3.500A)
      Proline residue:  C 285  - end of helix
      removed outlier: 4.574A  pdb=" N   LEU C 294 " --> pdb=" O   ASN C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 310 through 317
      removed outlier: 3.633A  pdb=" N   LYS C 317 " --> pdb=" O   LEU C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 336
    Processing helix  chain 'C' and resid 368 through 374
      removed outlier: 4.296A  pdb=" N   GLY C 374 " --> pdb=" O   THR C 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 61
      Proline residue:  D  46  - end of helix
      removed outlier: 4.292A  pdb=" N   GLN D  56 " --> pdb=" O   LEU D  52 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU D  57 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER D  59 " --> pdb=" O   ALA D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 88
    Processing helix  chain 'D' and resid 104 through 109
      removed outlier: 4.443A  pdb=" N   LYS D 108 " --> pdb=" O   LEU D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 132
      removed outlier: 3.545A  pdb=" N   ALA D 118 " --> pdb=" O   LEU D 114 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU D 119 " --> pdb=" O   LEU D 115 " (cutoff:3.500A)
      Proline residue:  D 124  - end of helix
    Processing helix  chain 'D' and resid 132 through 159
      removed outlier: 3.824A  pdb=" N   ARG D 156 " --> pdb=" O   ASN D 152 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU D 157 " --> pdb=" O   ARG D 153 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN D 159 " --> pdb=" O   ILE D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 201
      removed outlier: 3.991A  pdb=" N   LEU D 196 " --> pdb=" O   LEU D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 231
      removed outlier: 3.809A  pdb=" N   ASN D 213 " --> pdb=" O   TYR D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 235
      removed outlier: 3.592A  pdb=" N   PHE D 235 " --> pdb=" O   LEU D 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 232 through 235'
    Processing helix  chain 'D' and resid 265 through 294
      removed outlier: 3.966A  pdb=" N   VAL D 284 " --> pdb=" O   TYR D 280 " (cutoff:3.500A)
      Proline residue:  D 285  - end of helix
      removed outlier: 4.574A  pdb=" N   LEU D 294 " --> pdb=" O   ASN D 290 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 310 through 317
      removed outlier: 3.634A  pdb=" N   LYS D 317 " --> pdb=" O   LEU D 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 325 through 336
    Processing helix  chain 'D' and resid 368 through 374
      removed outlier: 4.296A  pdb=" N   GLY D 374 " --> pdb=" O   THR D 370 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 61
      Proline residue:  E  46  - end of helix
      removed outlier: 4.291A  pdb=" N   GLN E  56 " --> pdb=" O   LEU E  52 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER E  59 " --> pdb=" O   ALA E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 88
    Processing helix  chain 'E' and resid 104 through 109
      removed outlier: 4.442A  pdb=" N   LYS E 108 " --> pdb=" O   LEU E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 132
      removed outlier: 3.545A  pdb=" N   ALA E 118 " --> pdb=" O   LEU E 114 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU E 119 " --> pdb=" O   LEU E 115 " (cutoff:3.500A)
      Proline residue:  E 124  - end of helix
    Processing helix  chain 'E' and resid 132 through 159
      removed outlier: 3.824A  pdb=" N   ARG E 156 " --> pdb=" O   ASN E 152 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU E 157 " --> pdb=" O   ARG E 153 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLN E 159 " --> pdb=" O   ILE E 155 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 201
      removed outlier: 3.991A  pdb=" N   LEU E 196 " --> pdb=" O   LEU E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 205 through 231
      removed outlier: 3.809A  pdb=" N   ASN E 213 " --> pdb=" O   TYR E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 232 through 235
      removed outlier: 3.592A  pdb=" N   PHE E 235 " --> pdb=" O   LEU E 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 232 through 235'
    Processing helix  chain 'E' and resid 265 through 294
      removed outlier: 3.966A  pdb=" N   VAL E 284 " --> pdb=" O   TYR E 280 " (cutoff:3.500A)
      Proline residue:  E 285  - end of helix
      removed outlier: 4.574A  pdb=" N   LEU E 294 " --> pdb=" O   ASN E 290 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 310 through 317
      removed outlier: 3.633A  pdb=" N   LYS E 317 " --> pdb=" O   LEU E 313 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 325 through 336
    Processing helix  chain 'E' and resid 368 through 374
      removed outlier: 4.295A  pdb=" N   GLY E 374 " --> pdb=" O   THR E 370 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 32 through 61
      Proline residue:  F  46  - end of helix
      removed outlier: 4.292A  pdb=" N   GLN F  56 " --> pdb=" O   LEU F  52 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU F  57 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER F  59 " --> pdb=" O   ALA F  55 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 74 through 88
    Processing helix  chain 'F' and resid 104 through 109
      removed outlier: 4.442A  pdb=" N   LYS F 108 " --> pdb=" O   LEU F 104 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 132
      removed outlier: 3.545A  pdb=" N   ALA F 118 " --> pdb=" O   LEU F 114 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU F 119 " --> pdb=" O   LEU F 115 " (cutoff:3.500A)
      Proline residue:  F 124  - end of helix
    Processing helix  chain 'F' and resid 132 through 159
      removed outlier: 3.825A  pdb=" N   ARG F 156 " --> pdb=" O   ASN F 152 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU F 157 " --> pdb=" O   ARG F 153 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLN F 159 " --> pdb=" O   ILE F 155 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 190 through 201
      removed outlier: 3.991A  pdb=" N   LEU F 196 " --> pdb=" O   LEU F 192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 231
      removed outlier: 3.809A  pdb=" N   ASN F 213 " --> pdb=" O   TYR F 209 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 232 through 235
      removed outlier: 3.592A  pdb=" N   PHE F 235 " --> pdb=" O   LEU F 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 232 through 235'
    Processing helix  chain 'F' and resid 265 through 294
      removed outlier: 3.966A  pdb=" N   VAL F 284 " --> pdb=" O   TYR F 280 " (cutoff:3.500A)
      Proline residue:  F 285  - end of helix
      removed outlier: 4.574A  pdb=" N   LEU F 294 " --> pdb=" O   ASN F 290 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 310 through 317
      removed outlier: 3.634A  pdb=" N   LYS F 317 " --> pdb=" O   LEU F 313 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 325 through 336
    Processing helix  chain 'F' and resid 368 through 374
      removed outlier: 4.296A  pdb=" N   GLY F 374 " --> pdb=" O   THR F 370 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 61
      Proline residue:  G  46  - end of helix
      removed outlier: 4.291A  pdb=" N   GLN G  56 " --> pdb=" O   LEU G  52 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU G  57 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER G  59 " --> pdb=" O   ALA G  55 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 74 through 88
    Processing helix  chain 'G' and resid 104 through 109
      removed outlier: 4.442A  pdb=" N   LYS G 108 " --> pdb=" O   LEU G 104 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 109 through 132
      removed outlier: 3.545A  pdb=" N   ALA G 118 " --> pdb=" O   LEU G 114 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU G 119 " --> pdb=" O   LEU G 115 " (cutoff:3.500A)
      Proline residue:  G 124  - end of helix
    Processing helix  chain 'G' and resid 132 through 159
      removed outlier: 3.824A  pdb=" N   ARG G 156 " --> pdb=" O   ASN G 152 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU G 157 " --> pdb=" O   ARG G 153 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLN G 159 " --> pdb=" O   ILE G 155 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 190 through 201
      removed outlier: 3.991A  pdb=" N   LEU G 196 " --> pdb=" O   LEU G 192 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 205 through 231
      removed outlier: 3.809A  pdb=" N   ASN G 213 " --> pdb=" O   TYR G 209 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 232 through 235
      removed outlier: 3.592A  pdb=" N   PHE G 235 " --> pdb=" O   LEU G 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 232 through 235'
    Processing helix  chain 'G' and resid 265 through 294
      removed outlier: 3.966A  pdb=" N   VAL G 284 " --> pdb=" O   TYR G 280 " (cutoff:3.500A)
      Proline residue:  G 285  - end of helix
      removed outlier: 4.574A  pdb=" N   LEU G 294 " --> pdb=" O   ASN G 290 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 310 through 317
      removed outlier: 3.634A  pdb=" N   LYS G 317 " --> pdb=" O   LEU G 313 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 325 through 336
    Processing helix  chain 'G' and resid 368 through 374
      removed outlier: 4.295A  pdb=" N   GLY G 374 " --> pdb=" O   THR G 370 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 64 through 66
    Processing sheet with id=2, first strand: chain 'B' and resid 64 through 66
    Processing sheet with id=3, first strand: chain 'C' and resid 64 through 66
    Processing sheet with id=4, first strand: chain 'D' and resid 64 through 66
    Processing sheet with id=5, first strand: chain 'E' and resid 64 through 66
    Processing sheet with id=6, first strand: chain 'F' and resid 64 through 66
    Processing sheet with id=7, first strand: chain 'G' and resid 64 through 66

    959 hydrogen bonds defined for protein.
    2856 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: 1.77

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4881
        1.34 -     1.46: 3905
        1.46 -     1.58: 7349
        1.58 -     1.70: 0
        1.70 -     1.81: 91
  Bond restraints: 16226
  Sorted by residual:
  bond pdb=" CB  GLU C 193 "
       pdb=" CG  GLU C 193 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.66e+00
  bond pdb=" CB  GLU D 193 "
       pdb=" CG  GLU D 193 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.64e+00
  bond pdb=" CB  GLU B 193 "
       pdb=" CG  GLU B 193 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.64e+00
  bond pdb=" CB  GLU E 193 "
       pdb=" CG  GLU E 193 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.61e+00
  bond pdb=" CB  GLU A 193 "
       pdb=" CG  GLU A 193 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.60e+00
  ... (remaining 16221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 21452
        1.83 -     3.66: 395
        3.66 -     5.49: 98
        5.49 -     7.31: 98
        7.31 -     9.14: 14
  Bond angle restraints: 22057
  Sorted by residual:
  angle pdb=" CA  GLU B 193 "
        pdb=" CB  GLU B 193 "
        pdb=" CG  GLU B 193 "
      ideal   model   delta    sigma   weight residual
     114.10  121.33   -7.23 2.00e+00 2.50e-01 1.31e+01
  angle pdb=" CA  GLU G 193 "
        pdb=" CB  GLU G 193 "
        pdb=" CG  GLU G 193 "
      ideal   model   delta    sigma   weight residual
     114.10  121.33   -7.23 2.00e+00 2.50e-01 1.31e+01
  angle pdb=" CA  GLU D 193 "
        pdb=" CB  GLU D 193 "
        pdb=" CG  GLU D 193 "
      ideal   model   delta    sigma   weight residual
     114.10  121.33   -7.23 2.00e+00 2.50e-01 1.31e+01
  angle pdb=" CA  GLU A 193 "
        pdb=" CB  GLU A 193 "
        pdb=" CG  GLU A 193 "
      ideal   model   delta    sigma   weight residual
     114.10  121.33   -7.23 2.00e+00 2.50e-01 1.31e+01
  angle pdb=" CA  GLU F 193 "
        pdb=" CB  GLU F 193 "
        pdb=" CG  GLU F 193 "
      ideal   model   delta    sigma   weight residual
     114.10  121.32   -7.22 2.00e+00 2.50e-01 1.30e+01
  ... (remaining 22052 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 7945
       15.99 -    31.99: 1295
       31.99 -    47.98: 420
       47.98 -    63.97: 70
       63.97 -    79.97: 21
  Dihedral angle restraints: 9751
    sinusoidal: 3696
      harmonic: 6055
  Sorted by residual:
  dihedral pdb=" CA  GLU G 252 "
           pdb=" C   GLU G 252 "
           pdb=" N   THR G 253 "
           pdb=" CA  THR G 253 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.64  -15.36     0      5.00e+00 4.00e-02 9.44e+00
  dihedral pdb=" N   ASN C 152 "
           pdb=" CA  ASN C 152 "
           pdb=" CB  ASN C 152 "
           pdb=" CG  ASN C 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.00   57.00     3      1.50e+01 4.44e-03 9.42e+00
  dihedral pdb=" N   ASN A 152 "
           pdb=" CA  ASN A 152 "
           pdb=" CB  ASN A 152 "
           pdb=" CG  ASN A 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.98   56.98     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 9748 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1641
       0.030 -    0.061: 641
       0.061 -    0.091: 252
       0.091 -    0.121: 105
       0.121 -    0.152: 28
  Chirality restraints: 2667
  Sorted by residual:
  chirality pdb=" CA  SER B  45 "
            pdb=" N   SER B  45 "
            pdb=" C   SER B  45 "
            pdb=" CB  SER B  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" CA  SER D  45 "
            pdb=" N   SER D  45 "
            pdb=" C   SER D  45 "
            pdb=" CB  SER D  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.67e-01
  chirality pdb=" CA  SER C  45 "
            pdb=" N   SER C  45 "
            pdb=" C   SER C  45 "
            pdb=" CB  SER C  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.62e-01
  ... (remaining 2664 not shown)

  Planarity restraints: 2681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU D 193 "    0.010 2.00e-02 2.50e+03   2.14e-02 4.59e+00
        pdb=" CD  GLU D 193 "   -0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLU D 193 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU D 193 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 193 "    0.010 2.00e-02 2.50e+03   2.14e-02 4.58e+00
        pdb=" CD  GLU B 193 "   -0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 193 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 193 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU F 193 "    0.010 2.00e-02 2.50e+03   2.14e-02 4.56e+00
        pdb=" CD  GLU F 193 "   -0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLU F 193 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU F 193 "    0.013 2.00e-02 2.50e+03
  ... (remaining 2678 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 3559
        2.78 -     3.31: 14888
        3.31 -     3.84: 25882
        3.84 -     4.37: 25205
        4.37 -     4.90: 46288
  Nonbonded interactions: 115822
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 224 "
            pdb=" OG1 THR D 281 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OH  TYR G 224 "
            pdb=" OG1 THR G 281 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OH  TYR F 224 "
            pdb=" OG1 THR F 281 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OH  TYR B 224 "
            pdb=" OG1 THR B 281 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OH  TYR C 224 "
            pdb=" OG1 THR C 281 "
     model   vdw
     2.245 3.040
  ... (remaining 115817 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     11.460
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5216
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      :  0.004   0.042  16240  Z= 0.168
  Angle     :  0.787   9.144  22085  Z= 0.400
  Chirality :  0.042   0.152   2667
  Planarity :  0.004   0.040   2681
  Dihedral  : 17.936  79.968   5733
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 41.07 %
    Favored  : 58.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.20), residues: 1967
  helix:  1.06 (0.15), residues: 1323
  sheet: -1.11 (0.50), residues: 126
  loop : -1.55 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 296 
 TYR   0.010   0.001   TYR D 280 
 PHE   0.018   0.002   PHE E 189 
 TRP   0.011   0.001   TRP D 297 
 HIS   0.002   0.001   HIS F 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (16226)
  covalent geometry    : angle       0.78727 (22057)
  SS BOND              : bond        0.00186 (   14)
  SS BOND              : angle       0.35091 (   28)
  hydrogen bonds       : bond        0.17097 (  959)
  hydrogen bonds       : angle       5.48455 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 291
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.5371 (ttt90) cc_final: 0.5080 (ttt-90)
REVERT: A   39 LYS cc_start: 0.5801 (tttt) cc_final: 0.5593 (pttt)
REVERT: A   75 ARG cc_start: 0.5739 (mmm-85) cc_final: 0.5188 (mmp-170)
REVERT: A  201 ARG cc_start: 0.6365 (mmm-85) cc_final: 0.6039 (mtm-85)
REVERT: A  229 HIS cc_start: 0.5663 (t-90) cc_final: 0.5369 (t-90)
REVERT: A  281 THR cc_start: 0.6518 (m) cc_final: 0.6274 (m)
REVERT: B  229 HIS cc_start: 0.5173 (t-90) cc_final: 0.4705 (t-90)
REVERT: B  281 THR cc_start: 0.6767 (m) cc_final: 0.6504 (m)
REVERT: B  296 ARG cc_start: 0.4562 (tpp-160) cc_final: 0.4037 (ptt-90)
REVERT: C  201 ARG cc_start: 0.6671 (mmm-85) cc_final: 0.6160 (mpp80)
REVERT: C  229 HIS cc_start: 0.5705 (t-90) cc_final: 0.5476 (t-90)
REVERT: D   75 ARG cc_start: 0.5157 (mmm-85) cc_final: 0.4767 (mmm160)
REVERT: D  201 ARG cc_start: 0.6475 (mmm-85) cc_final: 0.6168 (ttt-90)
REVERT: D  229 HIS cc_start: 0.5512 (t-90) cc_final: 0.4998 (t70)
REVERT: E   36 ARG cc_start: 0.5429 (ttt90) cc_final: 0.5205 (ttt-90)
REVERT: E   75 ARG cc_start: 0.5041 (mmm-85) cc_final: 0.4306 (mmm160)
REVERT: E  229 HIS cc_start: 0.5137 (t-90) cc_final: 0.4540 (t70)
REVERT: E  233 ASP cc_start: 0.6388 (m-30) cc_final: 0.6153 (m-30)
REVERT: F  218 ILE cc_start: 0.6481 (mm) cc_final: 0.6241 (mt)
REVERT: F  229 HIS cc_start: 0.5267 (t-90) cc_final: 0.4548 (t70)
REVERT: F  238 GLU cc_start: 0.6427 (pm20) cc_final: 0.6130 (pm20)
REVERT: G  201 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6679 (tpp-160)
REVERT: G  229 HIS cc_start: 0.5710 (t-90) cc_final: 0.5094 (t70)
REVERT: G  233 ASP cc_start: 0.6419 (m-30) cc_final: 0.6190 (m-30)
  outliers start: 14
  outliers final: 0
  residues processed: 305
  average time/residue: 0.5870
  time to fit residues: 197.8648
Evaluate side-chains
  197 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 194 optimal weight:    0.6980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 200 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.4980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 336 ASN
D 336 ASN
E 336 ASN
** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 336 ASN ** 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 = 0.4263 r_free = 0.4263 target = 0.204721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.145141 restraints weight = 16787.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.34
r_work: 0.3509 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16240  Z= 0.148
  Angle     :  0.624   7.929  22085  Z= 0.313
  Chirality :  0.040   0.135   2667
  Planarity :  0.005   0.042   2681
  Dihedral  :  3.827  18.022   2177
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 37.79 %
    Favored  : 56.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.19), residues: 1967
  helix:  1.38 (0.14), residues: 1337
  sheet: -1.24 (0.49), residues: 126
  loop : -2.06 (0.23), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  36 
 TYR   0.016   0.002   TYR E 112 
 PHE   0.013   0.002   PHE D 230 
 TRP   0.009   0.002   TRP C 297 
 HIS   0.002   0.001   HIS D 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (16226)
  covalent geometry    : angle       0.62400 (22057)
  SS BOND              : bond        0.00248 (   14)
  SS BOND              : angle       0.75137 (   28)
  hydrogen bonds       : bond        0.04515 (  959)
  hydrogen bonds       : angle       4.21954 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 244
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.6942 (ttt90) cc_final: 0.6617 (ttt-90)
REVERT: A   37 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6264 (tp)
REVERT: A   72 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7639 (m-80)
REVERT: A   75 ARG cc_start: 0.7247 (mmm-85) cc_final: 0.6577 (mmp-170)
REVERT: A  201 ARG cc_start: 0.6805 (mmm-85) cc_final: 0.6242 (mpp80)
REVERT: A  229 HIS cc_start: 0.7429 (t-90) cc_final: 0.7191 (t-90)
REVERT: A  238 GLU cc_start: 0.8439 (pm20) cc_final: 0.8229 (pm20)
REVERT: A  254 HIS cc_start: 0.6790 (t-170) cc_final: 0.6208 (t-90)
REVERT: A  257 ASN cc_start: 0.7859 (t0) cc_final: 0.7562 (m-40)
REVERT: A  281 THR cc_start: 0.8278 (m) cc_final: 0.7910 (m)
REVERT: B   75 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.6859 (mmp-170)
REVERT: B  229 HIS cc_start: 0.7162 (t-90) cc_final: 0.6863 (t-90)
REVERT: B  238 GLU cc_start: 0.8262 (pm20) cc_final: 0.7965 (pm20)
REVERT: B  248 LEU cc_start: 0.5780 (mp) cc_final: 0.5405 (mt)
REVERT: B  262 ARG cc_start: 0.8309 (ttt90) cc_final: 0.7745 (ttt90)
REVERT: C   72 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.6187 (t80)
REVERT: C  201 ARG cc_start: 0.6512 (mmm-85) cc_final: 0.6248 (mtm180)
REVERT: C  229 HIS cc_start: 0.7741 (t-90) cc_final: 0.7484 (t-90)
REVERT: C  238 GLU cc_start: 0.8404 (pm20) cc_final: 0.7797 (pt0)
REVERT: C  248 LEU cc_start: 0.5754 (mp) cc_final: 0.5448 (mt)
REVERT: D   75 ARG cc_start: 0.7190 (mmm-85) cc_final: 0.6684 (mmp-170)
REVERT: D  218 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7658 (mp)
REVERT: D  229 HIS cc_start: 0.7637 (t-90) cc_final: 0.7073 (t70)
REVERT: D  248 LEU cc_start: 0.6330 (mp) cc_final: 0.5925 (mt)
REVERT: D  281 THR cc_start: 0.8318 (m) cc_final: 0.8050 (m)
REVERT: E   36 ARG cc_start: 0.6998 (ttt90) cc_final: 0.6724 (ttt-90)
REVERT: E   37 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6435 (tp)
REVERT: E   72 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.6125 (t80)
REVERT: E   75 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.6791 (mmp-170)
REVERT: E   81 ASP cc_start: 0.8195 (m-30) cc_final: 0.7989 (m-30)
REVERT: E  201 ARG cc_start: 0.6565 (ttt-90) cc_final: 0.6283 (mpp80)
REVERT: E  229 HIS cc_start: 0.7020 (t-90) cc_final: 0.6453 (t-90)
REVERT: E  331 LEU cc_start: 0.6179 (mt) cc_final: 0.5976 (mp)
REVERT: F  218 ILE cc_start: 0.8158 (mm) cc_final: 0.7892 (mt)
REVERT: F  229 HIS cc_start: 0.7592 (t-90) cc_final: 0.6903 (t70)
REVERT: F  238 GLU cc_start: 0.8267 (pm20) cc_final: 0.8063 (pm20)
REVERT: F  281 THR cc_start: 0.8268 (m) cc_final: 0.7926 (m)
REVERT: G   36 ARG cc_start: 0.7106 (ttt90) cc_final: 0.6730 (ttt-90)
REVERT: G  121 MET cc_start: 0.8360 (mmt) cc_final: 0.7977 (mmt)
REVERT: G  218 ILE cc_start: 0.7824 (mm) cc_final: 0.7536 (mt)
REVERT: G  229 HIS cc_start: 0.7406 (t-90) cc_final: 0.6792 (t-90)
  outliers start: 96
  outliers final: 17
  residues processed: 321
  average time/residue: 0.4660
  time to fit residues: 168.5501
Evaluate side-chains
  244 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 221
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   72 PHE
Chi-restraints excluded: chain E residue  218 ILE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue   72 PHE
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue   72 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 154 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 53 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 147 optimal weight:    0.6980
   chunk 165 optimal weight:    0.8980
   chunk 57 optimal weight:   40.0000
   chunk 117 optimal weight:    2.9990
   chunk 156 optimal weight:    9.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 ASN
** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 336 ASN ** 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 = 0.4238 r_free = 0.4238 target = 0.202204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.141511 restraints weight = 16769.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.98
r_work: 0.3473 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16240  Z= 0.120
  Angle     :  0.564   8.391  22085  Z= 0.274
  Chirality :  0.037   0.134   2667
  Planarity :  0.004   0.041   2681
  Dihedral  :  3.535  16.630   2177
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 35.31 %
    Favored  : 57.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.19), residues: 1967
  helix:  1.82 (0.15), residues: 1344
  sheet: -1.11 (0.48), residues: 126
  loop : -1.78 (0.24), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  36 
 TYR   0.013   0.001   TYR F 112 
 PHE   0.015   0.001   PHE F 269 
 TRP   0.009   0.001   TRP G 297 
 HIS   0.003   0.001   HIS G 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (16226)
  covalent geometry    : angle       0.56387 (22057)
  SS BOND              : bond        0.00146 (   14)
  SS BOND              : angle       0.57432 (   28)
  hydrogen bonds       : bond        0.04082 (  959)
  hydrogen bonds       : angle       3.91408 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 117
    poor density    : 227
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.6916 (ttt90) cc_final: 0.6642 (ttt-90)
REVERT: A   37 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6381 (tp)
REVERT: A   72 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7666 (m-10)
REVERT: A   75 ARG cc_start: 0.7076 (mmm-85) cc_final: 0.6799 (mmp-170)
REVERT: A  229 HIS cc_start: 0.7346 (t-90) cc_final: 0.7085 (t-90)
REVERT: A  235 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6356 (m-80)
REVERT: A  238 GLU cc_start: 0.8549 (pm20) cc_final: 0.8235 (pt0)
REVERT: A  254 HIS cc_start: 0.7242 (t-170) cc_final: 0.6584 (t-90)
REVERT: A  257 ASN cc_start: 0.8144 (t0) cc_final: 0.7779 (m-40)
REVERT: A  281 THR cc_start: 0.8175 (m) cc_final: 0.7777 (m)
REVERT: B   75 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.6931 (mmp-170)
REVERT: B  229 HIS cc_start: 0.7105 (t-90) cc_final: 0.6820 (t-90)
REVERT: B  238 GLU cc_start: 0.8355 (pm20) cc_final: 0.7921 (pt0)
REVERT: B  257 ASN cc_start: 0.8346 (t0) cc_final: 0.7885 (m-40)
REVERT: C  229 HIS cc_start: 0.7616 (t-90) cc_final: 0.7381 (t-90)
REVERT: C  238 GLU cc_start: 0.8414 (pm20) cc_final: 0.8044 (pt0)
REVERT: C  257 ASN cc_start: 0.8000 (t0) cc_final: 0.7760 (m110)
REVERT: D   75 ARG cc_start: 0.7341 (mmm-85) cc_final: 0.6891 (mmp-170)
REVERT: D  229 HIS cc_start: 0.7538 (t-90) cc_final: 0.6952 (t70)
REVERT: D  238 GLU cc_start: 0.8432 (pm20) cc_final: 0.8078 (pt0)
REVERT: D  257 ASN cc_start: 0.8210 (t0) cc_final: 0.7861 (m-40)
REVERT: D  281 THR cc_start: 0.8357 (m) cc_final: 0.8146 (m)
REVERT: E   36 ARG cc_start: 0.6948 (ttt90) cc_final: 0.6547 (ttt-90)
REVERT: E   75 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.6977 (mmp-170)
REVERT: E   81 ASP cc_start: 0.8182 (m-30) cc_final: 0.7745 (m-30)
REVERT: E  201 ARG cc_start: 0.6923 (ttt-90) cc_final: 0.6615 (mpp80)
REVERT: E  218 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7862 (mt)
REVERT: E  229 HIS cc_start: 0.7172 (t-90) cc_final: 0.6581 (t-90)
REVERT: F   75 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.6976 (mmp-170)
REVERT: F  218 ILE cc_start: 0.8147 (mm) cc_final: 0.7894 (mt)
REVERT: F  229 HIS cc_start: 0.7577 (t-90) cc_final: 0.6900 (t70)
REVERT: F  238 GLU cc_start: 0.8434 (pm20) cc_final: 0.8080 (pt0)
REVERT: F  248 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6300 (pt)
REVERT: F  257 ASN cc_start: 0.8343 (t0) cc_final: 0.8092 (m-40)
REVERT: F  281 THR cc_start: 0.8252 (m) cc_final: 0.7975 (m)
REVERT: F  293 ARG cc_start: 0.6586 (ttm-80) cc_final: 0.6243 (ttm-80)
REVERT: G  218 ILE cc_start: 0.8168 (mm) cc_final: 0.7856 (mt)
REVERT: G  229 HIS cc_start: 0.7352 (t-90) cc_final: 0.6720 (t-90)
REVERT: G  238 GLU cc_start: 0.8346 (pm20) cc_final: 0.7941 (pt0)
  outliers start: 117
  outliers final: 29
  residues processed: 321
  average time/residue: 0.4137
  time to fit residues: 151.9679
Evaluate side-chains
  250 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 216
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   40 PHE
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   54 PHE
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   39 LYS
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   58 PHE
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   72 PHE
Chi-restraints excluded: chain E residue  218 ILE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue   72 PHE
Chi-restraints excluded: chain F residue  248 LEU
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue   72 PHE
Chi-restraints excluded: chain G residue  248 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 171 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0270
   chunk 144 optimal weight:   30.0000
   chunk 128 optimal weight:    0.6980
   chunk 125 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 99 optimal weight:   20.0000
   chunk 102 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 162 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.9040

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 336 ASN
G 336 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.199902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.139284 restraints weight = 16629.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.95
r_work: 0.3422 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  16240  Z= 0.114
  Angle     :  0.547   9.933  22085  Z= 0.264
  Chirality :  0.037   0.127   2667
  Planarity :  0.004   0.044   2681
  Dihedral  :  3.502  16.739   2177
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 34.27 %
    Favored  : 59.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.19), residues: 1967
  helix:  2.02 (0.14), residues: 1344
  sheet: -1.18 (0.46), residues: 126
  loop : -1.69 (0.24), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  36 
 TYR   0.013   0.001   TYR G 112 
 PHE   0.016   0.001   PHE E 189 
 TRP   0.007   0.001   TRP G 297 
 HIS   0.005   0.001   HIS E 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (16226)
  covalent geometry    : angle       0.54691 (22057)
  SS BOND              : bond        0.00167 (   14)
  SS BOND              : angle       0.65890 (   28)
  hydrogen bonds       : bond        0.03955 (  959)
  hydrogen bonds       : angle       3.76711 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 112
    poor density    : 230
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6227 (tp)
REVERT: A   72 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7618 (m-10)
REVERT: A   75 ARG cc_start: 0.7233 (mmm-85) cc_final: 0.6949 (mmp-170)
REVERT: A  229 HIS cc_start: 0.7441 (t-90) cc_final: 0.7152 (t-90)
REVERT: A  235 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.7050 (m-80)
REVERT: A  238 GLU cc_start: 0.8678 (pm20) cc_final: 0.8243 (pt0)
REVERT: A  254 HIS cc_start: 0.7978 (t-170) cc_final: 0.7657 (t-90)
REVERT: A  257 ASN cc_start: 0.8139 (t0) cc_final: 0.7829 (m-40)
REVERT: A  281 THR cc_start: 0.8219 (m) cc_final: 0.7827 (m)
REVERT: A  285 PRO cc_start: 0.7268 (Cg_exo) cc_final: 0.7054 (Cg_endo)
REVERT: A  325 ASP cc_start: 0.7166 (m-30) cc_final: 0.6724 (t0)
REVERT: B   75 ARG cc_start: 0.7448 (mmm-85) cc_final: 0.6926 (mmp-170)
REVERT: B  229 HIS cc_start: 0.7182 (t-90) cc_final: 0.6959 (t-90)
REVERT: B  235 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6199 (m-80)
REVERT: B  238 GLU cc_start: 0.8381 (pm20) cc_final: 0.7990 (pt0)
REVERT: B  248 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6862 (mt)
REVERT: B  257 ASN cc_start: 0.8444 (t0) cc_final: 0.8140 (m-40)
REVERT: C   75 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7056 (mmp-170)
REVERT: C  189 PHE cc_start: 0.4071 (OUTLIER) cc_final: 0.3714 (m-80)
REVERT: C  238 GLU cc_start: 0.8482 (pm20) cc_final: 0.8108 (pt0)
REVERT: D   75 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.6998 (mmp-170)
REVERT: D  229 HIS cc_start: 0.7595 (t-90) cc_final: 0.6979 (t-90)
REVERT: D  235 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.6712 (m-80)
REVERT: D  238 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8086 (pt0)
REVERT: D  257 ASN cc_start: 0.8406 (t0) cc_final: 0.7993 (m-40)
REVERT: D  281 THR cc_start: 0.8425 (m) cc_final: 0.8159 (m)
REVERT: E   36 ARG cc_start: 0.6983 (ttt90) cc_final: 0.6617 (ttt-90)
REVERT: E   54 PHE cc_start: 0.6195 (OUTLIER) cc_final: 0.5317 (m-10)
REVERT: E   75 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.7214 (mmp-170)
REVERT: E   81 ASP cc_start: 0.8232 (m-30) cc_final: 0.7871 (m-30)
REVERT: E  129 GLN cc_start: 0.7620 (tp40) cc_final: 0.7417 (tt0)
REVERT: E  201 ARG cc_start: 0.6998 (ttt-90) cc_final: 0.6705 (mpp80)
REVERT: E  229 HIS cc_start: 0.7182 (t-90) cc_final: 0.6586 (t-90)
REVERT: E  257 ASN cc_start: 0.8522 (t0) cc_final: 0.8145 (m-40)
REVERT: E  285 PRO cc_start: 0.7004 (Cg_exo) cc_final: 0.6724 (Cg_endo)
REVERT: F   75 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7106 (mmp-170)
REVERT: F  218 ILE cc_start: 0.8263 (mm) cc_final: 0.7966 (mt)
REVERT: F  229 HIS cc_start: 0.7651 (t-90) cc_final: 0.7005 (t70)
REVERT: F  238 GLU cc_start: 0.8410 (pm20) cc_final: 0.8081 (pt0)
REVERT: F  281 THR cc_start: 0.8353 (m) cc_final: 0.8082 (m)
REVERT: F  293 ARG cc_start: 0.6548 (ttm-80) cc_final: 0.6280 (ttm-80)
REVERT: G  218 ILE cc_start: 0.8073 (mm) cc_final: 0.7775 (mt)
REVERT: G  229 HIS cc_start: 0.7385 (t-90) cc_final: 0.6723 (t-90)
REVERT: G  235 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7389 (m-80)
REVERT: G  238 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7902 (pt0)
REVERT: G  257 ASN cc_start: 0.8097 (t0) cc_final: 0.7883 (m-40)
REVERT: G  285 PRO cc_start: 0.7005 (Cg_exo) cc_final: 0.6708 (Cg_endo)
  outliers start: 112
  outliers final: 47
  residues processed: 321
  average time/residue: 0.4293
  time to fit residues: 158.0165
Evaluate side-chains
  281 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 223
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 PHE
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  233 ASP
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain D residue  233 ASP
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  294 LEU
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   39 LYS
Chi-restraints excluded: chain E residue   54 PHE
Chi-restraints excluded: chain E residue   58 PHE
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   72 PHE
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain F residue   38 VAL
Chi-restraints excluded: chain F residue   72 PHE
Chi-restraints excluded: chain F residue  147 LEU
Chi-restraints excluded: chain F residue  189 PHE
Chi-restraints excluded: chain F residue  233 ASP
Chi-restraints excluded: chain F residue  248 LEU
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain F residue  294 LEU
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue   54 PHE
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  238 GLU
Chi-restraints excluded: chain G residue  263 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 192 optimal weight:    6.9990
   chunk 106 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   chunk 92 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0370
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 187 optimal weight:   10.0000
   chunk 143 optimal weight:    9.9990
   chunk 198 optimal weight:    1.9990
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.200312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.140136 restraints weight = 16767.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.92
r_work: 0.3433 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.4228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  16240  Z= 0.104
  Angle     :  0.534   9.653  22085  Z= 0.254
  Chirality :  0.036   0.126   2667
  Planarity :  0.004   0.046   2681
  Dihedral  :  3.384  15.413   2177
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 35.54 %
    Favored  : 58.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.19), residues: 1967
  helix:  2.17 (0.14), residues: 1344
  sheet: -1.20 (0.57), residues: 84
  loop : -1.55 (0.23), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  36 
 TYR   0.012   0.001   TYR G 112 
 PHE   0.017   0.001   PHE E 189 
 TRP   0.007   0.001   TRP C 297 
 HIS   0.005   0.001   HIS B 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (16226)
  covalent geometry    : angle       0.53397 (22057)
  SS BOND              : bond        0.00148 (   14)
  SS BOND              : angle       0.60646 (   28)
  hydrogen bonds       : bond        0.03595 (  959)
  hydrogen bonds       : angle       3.68378 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 95
    poor density    : 229
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.6605 (OUTLIER) cc_final: 0.6134 (tp)
REVERT: A   72 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7534 (m-10)
REVERT: A   75 ARG cc_start: 0.7322 (mmm-85) cc_final: 0.6988 (mmp-170)
REVERT: A  229 HIS cc_start: 0.7361 (t-90) cc_final: 0.7030 (t-90)
REVERT: A  235 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6324 (m-80)
REVERT: A  238 GLU cc_start: 0.8648 (pm20) cc_final: 0.8248 (pt0)
REVERT: A  248 LEU cc_start: 0.7554 (mp) cc_final: 0.7294 (mt)
REVERT: A  254 HIS cc_start: 0.8099 (t-170) cc_final: 0.7832 (t-90)
REVERT: A  257 ASN cc_start: 0.8181 (t0) cc_final: 0.7932 (m-40)
REVERT: A  281 THR cc_start: 0.8200 (m) cc_final: 0.7809 (m)
REVERT: A  285 PRO cc_start: 0.7180 (Cg_exo) cc_final: 0.6943 (Cg_endo)
REVERT: B   75 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.6880 (mmp-170)
REVERT: B  235 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6061 (m-80)
REVERT: B  238 GLU cc_start: 0.8332 (pm20) cc_final: 0.7848 (pt0)
REVERT: B  257 ASN cc_start: 0.8403 (t0) cc_final: 0.8118 (m-40)
REVERT: B  325 ASP cc_start: 0.7213 (m-30) cc_final: 0.6711 (t70)
REVERT: C   75 ARG cc_start: 0.7497 (mmm-85) cc_final: 0.6899 (mmp-170)
REVERT: C  218 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7571 (mt)
REVERT: C  238 GLU cc_start: 0.8456 (pm20) cc_final: 0.8111 (pt0)
REVERT: D   75 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.6908 (mmp-170)
REVERT: D  229 HIS cc_start: 0.7523 (t-90) cc_final: 0.6905 (t-90)
REVERT: D  235 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6689 (m-80)
REVERT: D  238 GLU cc_start: 0.8322 (pm20) cc_final: 0.7869 (pt0)
REVERT: D  257 ASN cc_start: 0.8294 (t0) cc_final: 0.7914 (m-40)
REVERT: D  281 THR cc_start: 0.8328 (m) cc_final: 0.8074 (m)
REVERT: D  285 PRO cc_start: 0.7436 (Cg_exo) cc_final: 0.7079 (Cg_endo)
REVERT: E   37 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.5994 (tp)
REVERT: E   52 LEU cc_start: 0.6162 (mp) cc_final: 0.5956 (tp)
REVERT: E   54 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5104 (m-10)
REVERT: E   75 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7054 (mmp-170)
REVERT: E   81 ASP cc_start: 0.8172 (m-30) cc_final: 0.7831 (m-30)
REVERT: E  201 ARG cc_start: 0.6982 (ttt-90) cc_final: 0.6664 (mpp80)
REVERT: E  229 HIS cc_start: 0.7114 (t-90) cc_final: 0.6516 (t-90)
REVERT: E  257 ASN cc_start: 0.8426 (t0) cc_final: 0.8017 (m-40)
REVERT: E  285 PRO cc_start: 0.6895 (Cg_exo) cc_final: 0.6601 (Cg_endo)
REVERT: F   75 ARG cc_start: 0.7564 (mmm-85) cc_final: 0.7056 (mmp-170)
REVERT: F  218 ILE cc_start: 0.8190 (mm) cc_final: 0.7857 (mt)
REVERT: F  229 HIS cc_start: 0.7655 (t-90) cc_final: 0.7017 (t70)
REVERT: F  238 GLU cc_start: 0.8392 (pm20) cc_final: 0.8077 (pt0)
REVERT: F  281 THR cc_start: 0.8294 (m) cc_final: 0.8009 (m)
REVERT: F  293 ARG cc_start: 0.6323 (ttm-80) cc_final: 0.6070 (ttm-80)
REVERT: G   37 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6029 (tp)
REVERT: G  218 ILE cc_start: 0.8108 (mm) cc_final: 0.7818 (mt)
REVERT: G  229 HIS cc_start: 0.7339 (t-90) cc_final: 0.6684 (t-90)
REVERT: G  235 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7287 (m-80)
REVERT: G  238 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7917 (pt0)
REVERT: G  285 PRO cc_start: 0.6942 (Cg_exo) cc_final: 0.6637 (Cg_endo)
  outliers start: 95
  outliers final: 45
  residues processed: 310
  average time/residue: 0.4259
  time to fit residues: 151.1041
Evaluate side-chains
  279 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 223
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain C residue   54 PHE
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain C residue  218 ILE
Chi-restraints excluded: chain C residue  233 ASP
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  294 LEU
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   39 LYS
Chi-restraints excluded: chain E residue   54 PHE
Chi-restraints excluded: chain E residue   58 PHE
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   72 PHE
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  324 ASN
Chi-restraints excluded: chain F residue   38 VAL
Chi-restraints excluded: chain F residue   72 PHE
Chi-restraints excluded: chain F residue  147 LEU
Chi-restraints excluded: chain F residue  248 LEU
Chi-restraints excluded: chain F residue  263 LEU
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain F residue  294 LEU
Chi-restraints excluded: chain G residue   37 ILE
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue   54 PHE
Chi-restraints excluded: chain G residue  127 LEU
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  238 GLU
Chi-restraints excluded: chain G residue  263 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 175 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 101 optimal weight:    0.2980
   chunk 124 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 148 optimal weight:   10.0000
   chunk 184 optimal weight:    3.9990
   chunk 186 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0010
   overall best weight:    0.9990

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

Flipped N/Q/H residues before XYZ refinement:
G 290 ASN
G 324 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.198283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.137638 restraints weight = 16670.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.92
r_work: 0.3421 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16240  Z= 0.114
  Angle     :  0.558   9.399  22085  Z= 0.263
  Chirality :  0.037   0.128   2667
  Planarity :  0.004   0.044   2681
  Dihedral  :  3.417  15.565   2177
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 35.02 %
    Favored  : 59.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.19), residues: 1967
  helix:  2.23 (0.14), residues: 1344
  sheet: -1.17 (0.44), residues: 119
  loop : -1.58 (0.23), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 293 
 TYR   0.014   0.002   TYR G 112 
 PHE   0.019   0.001   PHE F 189 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.006   0.001   HIS E 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (16226)
  covalent geometry    : angle       0.55718 (22057)
  SS BOND              : bond        0.00201 (   14)
  SS BOND              : angle       0.81648 (   28)
  hydrogen bonds       : bond        0.03939 (  959)
  hydrogen bonds       : angle       3.61640 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 230
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6339 (tp)
REVERT: A   54 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6384 (m-80)
REVERT: A   72 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7468 (m-80)
REVERT: A   75 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.7008 (mmp-170)
REVERT: A  229 HIS cc_start: 0.7467 (t-90) cc_final: 0.7146 (t-90)
REVERT: A  238 GLU cc_start: 0.8757 (pm20) cc_final: 0.8375 (pt0)
REVERT: A  248 LEU cc_start: 0.7864 (mp) cc_final: 0.7524 (mt)
REVERT: A  254 HIS cc_start: 0.8325 (t-170) cc_final: 0.8037 (t-90)
REVERT: A  257 ASN cc_start: 0.8309 (t0) cc_final: 0.8098 (m-40)
REVERT: A  281 THR cc_start: 0.8232 (m) cc_final: 0.7866 (m)
REVERT: A  285 PRO cc_start: 0.7367 (Cg_exo) cc_final: 0.7084 (Cg_endo)
REVERT: B   75 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7061 (mmp-170)
REVERT: B  235 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6304 (m-80)
REVERT: B  238 GLU cc_start: 0.8319 (pm20) cc_final: 0.8063 (pt0)
REVERT: B  257 ASN cc_start: 0.8402 (t0) cc_final: 0.8189 (m-40)
REVERT: C   75 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7046 (mmp-170)
REVERT: C  122 TYR cc_start: 0.8372 (t80) cc_final: 0.8110 (t80)
REVERT: C  218 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7652 (mt)
REVERT: C  238 GLU cc_start: 0.8535 (pm20) cc_final: 0.8205 (pt0)
REVERT: D   75 ARG cc_start: 0.7476 (mmm-85) cc_final: 0.7028 (mmp-170)
REVERT: D  218 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7713 (mp)
REVERT: D  229 HIS cc_start: 0.7610 (t-90) cc_final: 0.6974 (t-90)
REVERT: D  235 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.6749 (m-80)
REVERT: D  238 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7959 (pt0)
REVERT: D  281 THR cc_start: 0.8462 (m) cc_final: 0.8177 (m)
REVERT: D  285 PRO cc_start: 0.7407 (Cg_exo) cc_final: 0.7114 (Cg_endo)
REVERT: E   54 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5127 (m-10)
REVERT: E   75 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7248 (mmp-170)
REVERT: E   81 ASP cc_start: 0.8246 (m-30) cc_final: 0.7941 (m-30)
REVERT: E  201 ARG cc_start: 0.7068 (ttt-90) cc_final: 0.6754 (mpp80)
REVERT: E  229 HIS cc_start: 0.7194 (t-90) cc_final: 0.6568 (t-90)
REVERT: E  257 ASN cc_start: 0.8632 (t0) cc_final: 0.8287 (m-40)
REVERT: E  285 PRO cc_start: 0.7053 (Cg_exo) cc_final: 0.6695 (Cg_endo)
REVERT: E  334 ARG cc_start: 0.6541 (tmm-80) cc_final: 0.6125 (ttm110)
REVERT: F   75 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7216 (mmp-170)
REVERT: F  218 ILE cc_start: 0.8140 (mm) cc_final: 0.7800 (mt)
REVERT: F  229 HIS cc_start: 0.7752 (t-90) cc_final: 0.7093 (t70)
REVERT: F  238 GLU cc_start: 0.8475 (pm20) cc_final: 0.8174 (pt0)
REVERT: F  281 THR cc_start: 0.8306 (m) cc_final: 0.8038 (m)
REVERT: G   37 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.6057 (tp)
REVERT: G   75 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7218 (mmp-170)
REVERT: G  218 ILE cc_start: 0.8100 (mm) cc_final: 0.7810 (mt)
REVERT: G  229 HIS cc_start: 0.7451 (t-90) cc_final: 0.6774 (t-90)
REVERT: G  238 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8004 (pt0)
REVERT: G  285 PRO cc_start: 0.7018 (Cg_exo) cc_final: 0.6653 (Cg_endo)
REVERT: G  290 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7157 (t0)
  outliers start: 101
  outliers final: 52
  residues processed: 316
  average time/residue: 0.4384
  time to fit residues: 158.3208
Evaluate side-chains
  289 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 225
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 PHE
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain C residue  127 LEU
Chi-restraints excluded: chain C residue  218 ILE
Chi-restraints excluded: chain C residue  233 ASP
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  325 ASP
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  294 LEU
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   39 LYS
Chi-restraints excluded: chain E residue   54 PHE
Chi-restraints excluded: chain E residue   58 PHE
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   72 PHE
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  324 ASN
Chi-restraints excluded: chain F residue   38 VAL
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue   72 PHE
Chi-restraints excluded: chain F residue  147 LEU
Chi-restraints excluded: chain F residue  189 PHE
Chi-restraints excluded: chain F residue  233 ASP
Chi-restraints excluded: chain F residue  248 LEU
Chi-restraints excluded: chain F residue  263 LEU
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain F residue  294 LEU
Chi-restraints excluded: chain G residue   37 ILE
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue  127 LEU
Chi-restraints excluded: chain G residue  198 CYS
Chi-restraints excluded: chain G residue  238 GLU
Chi-restraints excluded: chain G residue  263 LEU
Chi-restraints excluded: chain G residue  290 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 150 optimal weight:    3.9990
   chunk 157 optimal weight:   20.0000
   chunk 152 optimal weight:    3.9990
   chunk 127 optimal weight:   10.0000
   chunk 185 optimal weight:   20.0000
   chunk 70 optimal weight:   20.0000
   chunk 172 optimal weight:    0.4980
   chunk 63 optimal weight:    0.6980
   chunk 119 optimal weight:    9.9990
   chunk 131 optimal weight:    1.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
G  76 GLN
G 254 HIS
G 290 ASN
G 324 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.189662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143256 restraints weight = 16805.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.57
r_work: 0.3277 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.4886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  16240  Z= 0.175
  Angle     :  0.638  12.253  22085  Z= 0.306
  Chirality :  0.041   0.183   2667
  Planarity :  0.004   0.044   2681
  Dihedral  :  3.810  19.096   2177
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 34.27 %
    Favored  : 59.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.19), residues: 1967
  helix:  2.07 (0.14), residues: 1344
  sheet:  0.63 (0.52), residues: 77
  loop : -2.10 (0.22), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 293 
 TYR   0.017   0.002   TYR B 112 
 PHE   0.021   0.002   PHE E 189 
 TRP   0.008   0.002   TRP B  85 
 HIS   0.006   0.001   HIS G 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (16226)
  covalent geometry    : angle       0.63682 (22057)
  SS BOND              : bond        0.00304 (   14)
  SS BOND              : angle       1.28778 (   28)
  hydrogen bonds       : bond        0.05279 (  959)
  hydrogen bonds       : angle       3.82409 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 109
    poor density    : 225
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.6694 (tp)
REVERT: A   72 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7603 (m-80)
REVERT: A   75 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7467 (mmp-170)
REVERT: A  229 HIS cc_start: 0.7820 (t-90) cc_final: 0.7527 (t-90)
REVERT: A  238 GLU cc_start: 0.8709 (pm20) cc_final: 0.8426 (pt0)
REVERT: A  248 LEU cc_start: 0.8256 (mp) cc_final: 0.7980 (mt)
REVERT: A  281 THR cc_start: 0.8455 (m) cc_final: 0.8117 (m)
REVERT: A  285 PRO cc_start: 0.7654 (Cg_exo) cc_final: 0.7328 (Cg_endo)
REVERT: B   75 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.7609 (mmp-170)
REVERT: B  194 ARG cc_start: 0.4191 (mmm160) cc_final: 0.3971 (mmm-85)
REVERT: B  235 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6525 (m-80)
REVERT: B  238 GLU cc_start: 0.8490 (pm20) cc_final: 0.8236 (pt0)
REVERT: C   51 SER cc_start: 0.8597 (t) cc_final: 0.8334 (p)
REVERT: C   75 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7440 (mmp-170)
REVERT: C  122 TYR cc_start: 0.8605 (t80) cc_final: 0.8368 (t80)
REVERT: C  238 GLU cc_start: 0.8757 (pm20) cc_final: 0.8497 (pt0)
REVERT: D   72 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.5876 (t80)
REVERT: D   75 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7625 (mmp-170)
REVERT: D  218 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7721 (mt)
REVERT: D  229 HIS cc_start: 0.8012 (t-90) cc_final: 0.7419 (t-90)
REVERT: D  235 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.6821 (m-80)
REVERT: D  238 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8299 (pt0)
REVERT: D  281 THR cc_start: 0.8578 (m) cc_final: 0.8204 (m)
REVERT: E   36 ARG cc_start: 0.7350 (ttt90) cc_final: 0.7045 (ttt-90)
REVERT: E   75 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7408 (mmp-170)
REVERT: E   81 ASP cc_start: 0.8530 (m-30) cc_final: 0.8257 (m-30)
REVERT: E  201 ARG cc_start: 0.7315 (ttt-90) cc_final: 0.7083 (mpp80)
REVERT: E  229 HIS cc_start: 0.7520 (t-90) cc_final: 0.6999 (t-90)
REVERT: E  238 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8269 (pt0)
REVERT: E  257 ASN cc_start: 0.8738 (t0) cc_final: 0.8427 (m-40)
REVERT: F   75 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7465 (mmp-170)
REVERT: F   81 ASP cc_start: 0.8567 (m-30) cc_final: 0.8254 (m-30)
REVERT: F  218 ILE cc_start: 0.8284 (mm) cc_final: 0.7962 (mt)
REVERT: F  235 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.6360 (m-80)
REVERT: F  238 GLU cc_start: 0.8676 (pm20) cc_final: 0.8414 (pt0)
REVERT: F  281 THR cc_start: 0.8465 (m) cc_final: 0.8213 (m)
REVERT: G   72 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7894 (m-10)
REVERT: G   75 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7634 (mmp-170)
REVERT: G  201 ARG cc_start: 0.7049 (mmm-85) cc_final: 0.6545 (tpp-160)
REVERT: G  229 HIS cc_start: 0.7842 (t-90) cc_final: 0.7217 (t-90)
REVERT: G  238 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8243 (pt0)
  outliers start: 109
  outliers final: 59
  residues processed: 311
  average time/residue: 0.4788
  time to fit residues: 168.1691
Evaluate side-chains
  287 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 217
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   54 PHE
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain C residue  127 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  325 ASP
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain D residue  198 CYS
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  233 ASP
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  294 LEU
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   39 LYS
Chi-restraints excluded: chain E residue   58 PHE
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   72 PHE
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  233 ASP
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  238 GLU
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  324 ASN
Chi-restraints excluded: chain E residue  331 LEU
Chi-restraints excluded: chain F residue   72 PHE
Chi-restraints excluded: chain F residue  147 LEU
Chi-restraints excluded: chain F residue  233 ASP
Chi-restraints excluded: chain F residue  235 PHE
Chi-restraints excluded: chain F residue  248 LEU
Chi-restraints excluded: chain F residue  263 LEU
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain F residue  294 LEU
Chi-restraints excluded: chain G residue   37 ILE
Chi-restraints excluded: chain G residue   72 PHE
Chi-restraints excluded: chain G residue  198 CYS
Chi-restraints excluded: chain G residue  238 GLU
Chi-restraints excluded: chain G residue  263 LEU
Chi-restraints excluded: chain G residue  292 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 188 optimal weight:    6.9990
   chunk 113 optimal weight:    0.3980
   chunk 199 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   chunk 10 optimal weight:    9.9990
   chunk 177 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:
C 254 HIS
G 254 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.193941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.147374 restraints weight = 16856.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.38
r_work: 0.3392 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.4984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  16240  Z= 0.107
  Angle     :  0.549   9.511  22085  Z= 0.259
  Chirality :  0.037   0.128   2667
  Planarity :  0.004   0.043   2681
  Dihedral  :  3.480  16.116   2177
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 36.18 %
    Favored  : 59.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.19), residues: 1967
  helix:  2.49 (0.14), residues: 1316
  sheet: -0.99 (0.61), residues: 84
  loop : -1.69 (0.22), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 201 
 TYR   0.012   0.001   TYR B 112 
 PHE   0.017   0.001   PHE E 189 
 TRP   0.007   0.001   TRP E 105 
 HIS   0.006   0.001   HIS G 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (16226)
  covalent geometry    : angle       0.54827 (22057)
  SS BOND              : bond        0.00152 (   14)
  SS BOND              : angle       0.74851 (   28)
  hydrogen bonds       : bond        0.03751 (  959)
  hydrogen bonds       : angle       3.62269 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 231
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6674 (tp)
REVERT: A   72 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7736 (m-80)
REVERT: A   75 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7425 (mmp-170)
REVERT: A  229 HIS cc_start: 0.7616 (t-90) cc_final: 0.7334 (t-90)
REVERT: A  238 GLU cc_start: 0.8663 (pm20) cc_final: 0.8370 (pt0)
REVERT: A  248 LEU cc_start: 0.8150 (mp) cc_final: 0.7875 (mt)
REVERT: A  281 THR cc_start: 0.8317 (m) cc_final: 0.8034 (m)
REVERT: A  285 PRO cc_start: 0.7569 (Cg_exo) cc_final: 0.7265 (Cg_endo)
REVERT: B   75 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7525 (mmp-170)
REVERT: B  235 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6459 (m-80)
REVERT: B  238 GLU cc_start: 0.8438 (pm20) cc_final: 0.8202 (pt0)
REVERT: B  325 ASP cc_start: 0.7612 (m-30) cc_final: 0.7258 (t0)
REVERT: C   51 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8409 (p)
REVERT: C   75 ARG cc_start: 0.7968 (mmm-85) cc_final: 0.7303 (mmp-170)
REVERT: C  122 TYR cc_start: 0.8551 (t80) cc_final: 0.8319 (t80)
REVERT: C  238 GLU cc_start: 0.8650 (pm20) cc_final: 0.8415 (pt0)
REVERT: D   72 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.6221 (t80)
REVERT: D   75 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7546 (mmp-170)
REVERT: D  218 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7915 (mt)
REVERT: D  229 HIS cc_start: 0.7930 (t-90) cc_final: 0.7356 (t-90)
REVERT: D  235 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6860 (m-80)
REVERT: D  238 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8115 (pt0)
REVERT: D  285 PRO cc_start: 0.7441 (Cg_exo) cc_final: 0.7199 (Cg_endo)
REVERT: E   37 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6348 (tp)
REVERT: E   75 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7666 (mmp-170)
REVERT: E   81 ASP cc_start: 0.8431 (m-30) cc_final: 0.8191 (m-30)
REVERT: E  201 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.7056 (mpp80)
REVERT: E  229 HIS cc_start: 0.7385 (t-90) cc_final: 0.6880 (t-90)
REVERT: E  257 ASN cc_start: 0.8667 (t0) cc_final: 0.8371 (m-40)
REVERT: E  318 MET cc_start: 0.4527 (tpt) cc_final: 0.4040 (mmt)
REVERT: E  334 ARG cc_start: 0.6852 (tmm-80) cc_final: 0.6443 (ttm110)
REVERT: F   75 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7618 (mmp-170)
REVERT: F  218 ILE cc_start: 0.8336 (mm) cc_final: 0.7998 (mt)
REVERT: F  238 GLU cc_start: 0.8515 (pm20) cc_final: 0.8303 (pt0)
REVERT: F  281 THR cc_start: 0.8409 (m) cc_final: 0.8120 (m)
REVERT: G   37 ILE cc_start: 0.6974 (OUTLIER) cc_final: 0.6435 (tp)
REVERT: G   75 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7622 (mmp-170)
REVERT: G  194 ARG cc_start: 0.4914 (mmm160) cc_final: 0.4695 (mmm-85)
REVERT: G  218 ILE cc_start: 0.8362 (mm) cc_final: 0.8096 (mt)
REVERT: G  229 HIS cc_start: 0.7703 (t-90) cc_final: 0.7075 (t-90)
REVERT: G  238 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8057 (pt0)
REVERT: G  285 PRO cc_start: 0.7320 (Cg_exo) cc_final: 0.6943 (Cg_endo)
  outliers start: 74
  outliers final: 46
  residues processed: 292
  average time/residue: 0.4697
  time to fit residues: 154.8246
Evaluate side-chains
  282 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 225
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 PHE
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain C residue  127 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  325 ASP
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  294 LEU
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   39 LYS
Chi-restraints excluded: chain E residue   58 PHE
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   72 PHE
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  324 ASN
Chi-restraints excluded: chain F residue   51 SER
Chi-restraints excluded: chain F residue   72 PHE
Chi-restraints excluded: chain F residue  121 MET
Chi-restraints excluded: chain F residue  198 CYS
Chi-restraints excluded: chain F residue  248 LEU
Chi-restraints excluded: chain F residue  263 LEU
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain F residue  294 LEU
Chi-restraints excluded: chain F residue  325 ASP
Chi-restraints excluded: chain G residue   37 ILE
Chi-restraints excluded: chain G residue  238 GLU
Chi-restraints excluded: chain G residue  263 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 170 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 143 optimal weight:    0.5980
   chunk 125 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
C 254 HIS
G 254 HIS
G 290 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.193039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.146592 restraints weight = 16812.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.28
r_work: 0.3394 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16240  Z= 0.112
  Angle     :  0.552   9.488  22085  Z= 0.261
  Chirality :  0.037   0.128   2667
  Planarity :  0.004   0.043   2681
  Dihedral  :  3.445  15.387   2177
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 36.29 %
    Favored  : 59.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.19), residues: 1967
  helix:  2.58 (0.14), residues: 1316
  sheet: -1.01 (0.60), residues: 84
  loop : -1.65 (0.22), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 201 
 TYR   0.014   0.002   TYR G 112 
 PHE   0.016   0.001   PHE E 189 
 TRP   0.006   0.001   TRP D 105 
 HIS   0.006   0.001   HIS C 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (16226)
  covalent geometry    : angle       0.55168 (22057)
  SS BOND              : bond        0.00192 (   14)
  SS BOND              : angle       0.84932 (   28)
  hydrogen bonds       : bond        0.03950 (  959)
  hydrogen bonds       : angle       3.57179 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 228
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6654 (tp)
REVERT: A   72 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7663 (m-80)
REVERT: A   75 ARG cc_start: 0.7803 (mmm-85) cc_final: 0.7397 (mmp-170)
REVERT: A  229 HIS cc_start: 0.7660 (t-90) cc_final: 0.7361 (t-90)
REVERT: A  238 GLU cc_start: 0.8710 (pm20) cc_final: 0.8418 (pt0)
REVERT: A  248 LEU cc_start: 0.8260 (mp) cc_final: 0.8031 (mt)
REVERT: A  281 THR cc_start: 0.8419 (m) cc_final: 0.8096 (m)
REVERT: B   75 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7556 (mmp-170)
REVERT: B  235 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.6534 (m-80)
REVERT: B  325 ASP cc_start: 0.7567 (m-30) cc_final: 0.7219 (t0)
REVERT: C   51 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8437 (p)
REVERT: C   75 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7393 (mmp-170)
REVERT: C  122 TYR cc_start: 0.8559 (t80) cc_final: 0.8340 (t80)
REVERT: C  238 GLU cc_start: 0.8646 (pm20) cc_final: 0.8385 (pt0)
REVERT: D   75 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7395 (mmp-170)
REVERT: D  218 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7935 (mt)
REVERT: D  229 HIS cc_start: 0.7939 (t-90) cc_final: 0.7331 (t-90)
REVERT: D  235 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7018 (m-80)
REVERT: D  238 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8155 (pt0)
REVERT: D  285 PRO cc_start: 0.7347 (Cg_exo) cc_final: 0.7085 (Cg_endo)
REVERT: E   54 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.5743 (m-10)
REVERT: E   75 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7680 (mmp-170)
REVERT: E   81 ASP cc_start: 0.8400 (m-30) cc_final: 0.8162 (m-30)
REVERT: E  201 ARG cc_start: 0.7242 (ttt-90) cc_final: 0.6963 (mpp80)
REVERT: E  229 HIS cc_start: 0.7393 (t-90) cc_final: 0.6881 (t-90)
REVERT: E  257 ASN cc_start: 0.8705 (t0) cc_final: 0.8394 (m-40)
REVERT: E  318 MET cc_start: 0.4495 (tpt) cc_final: 0.4036 (mmt)
REVERT: F   75 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7549 (mmp-170)
REVERT: F  218 ILE cc_start: 0.8355 (mm) cc_final: 0.8003 (mt)
REVERT: F  238 GLU cc_start: 0.8611 (pm20) cc_final: 0.8400 (pt0)
REVERT: F  281 THR cc_start: 0.8494 (m) cc_final: 0.8237 (m)
REVERT: F  323 ILE cc_start: 0.7719 (mm) cc_final: 0.7252 (pp)
REVERT: G   37 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6360 (tp)
REVERT: G   75 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7574 (mmp-170)
REVERT: G  218 ILE cc_start: 0.8376 (mm) cc_final: 0.8116 (mt)
REVERT: G  229 HIS cc_start: 0.7699 (t-90) cc_final: 0.7059 (t-90)
REVERT: G  238 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8059 (pt0)
REVERT: G  285 PRO cc_start: 0.7362 (Cg_exo) cc_final: 0.6980 (Cg_endo)
REVERT: G  290 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7389 (t0)
  outliers start: 76
  outliers final: 52
  residues processed: 289
  average time/residue: 0.4695
  time to fit residues: 153.7156
Evaluate side-chains
  281 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 218
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 PHE
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain C residue  127 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  325 ASP
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain D residue  198 CYS
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  294 LEU
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   39 LYS
Chi-restraints excluded: chain E residue   54 PHE
Chi-restraints excluded: chain E residue   58 PHE
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   72 PHE
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  324 ASN
Chi-restraints excluded: chain F residue   51 SER
Chi-restraints excluded: chain F residue   72 PHE
Chi-restraints excluded: chain F residue  121 MET
Chi-restraints excluded: chain F residue  198 CYS
Chi-restraints excluded: chain F residue  248 LEU
Chi-restraints excluded: chain F residue  263 LEU
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain F residue  294 LEU
Chi-restraints excluded: chain F residue  325 ASP
Chi-restraints excluded: chain G residue   37 ILE
Chi-restraints excluded: chain G residue  198 CYS
Chi-restraints excluded: chain G residue  238 GLU
Chi-restraints excluded: chain G residue  263 LEU
Chi-restraints excluded: chain G residue  290 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 172 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 183 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 113 optimal weight:    0.6980
   chunk 85 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0050
   chunk 163 optimal weight:    5.9990
   chunk 174 optimal weight:    0.0570
   overall best weight:    0.4912

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

Flipped N/Q/H residues before XYZ refinement:
C 254 HIS
D 254 HIS
G 254 HIS
G 290 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.195638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.149338 restraints weight = 16946.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.41
r_work: 0.3397 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.5187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  16240  Z= 0.099
  Angle     :  0.529   9.678  22085  Z= 0.249
  Chirality :  0.036   0.125   2667
  Planarity :  0.004   0.043   2681
  Dihedral  :  3.343  15.547   2177
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 37.62 %
    Favored  : 58.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.19), residues: 1967
  helix:  2.67 (0.14), residues: 1316
  sheet: -0.99 (0.60), residues: 84
  loop : -1.53 (0.22), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 201 
 TYR   0.014   0.001   TYR G 289 
 PHE   0.016   0.001   PHE E 189 
 TRP   0.008   0.001   TRP E 105 
 HIS   0.008   0.001   HIS C 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 (16226)
  covalent geometry    : angle       0.52885 (22057)
  SS BOND              : bond        0.00147 (   14)
  SS BOND              : angle       0.67833 (   28)
  hydrogen bonds       : bond        0.03404 (  959)
  hydrogen bonds       : angle       3.51541 ( 2856)

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

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

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3934 Ramachandran restraints generated.
    1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 233
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6694 (tp)
REVERT: A   72 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7827 (m-10)
REVERT: A   75 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7369 (mmp-170)
REVERT: A  229 HIS cc_start: 0.7637 (t-90) cc_final: 0.7322 (t-90)
REVERT: A  238 GLU cc_start: 0.8658 (pm20) cc_final: 0.8341 (pt0)
REVERT: A  248 LEU cc_start: 0.8073 (mp) cc_final: 0.7835 (mt)
REVERT: A  281 THR cc_start: 0.8345 (m) cc_final: 0.8039 (m)
REVERT: B   75 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7619 (mmp-170)
REVERT: B  235 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6544 (m-80)
REVERT: B  238 GLU cc_start: 0.8477 (pt0) cc_final: 0.8065 (pt0)
REVERT: C   51 SER cc_start: 0.8667 (t) cc_final: 0.8426 (p)
REVERT: C   75 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7217 (mmp-170)
REVERT: C  122 TYR cc_start: 0.8532 (t80) cc_final: 0.8300 (t80)
REVERT: C  238 GLU cc_start: 0.8627 (pm20) cc_final: 0.8417 (pt0)
REVERT: D   75 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7388 (mmp-170)
REVERT: D  218 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8069 (mt)
REVERT: D  229 HIS cc_start: 0.7927 (t-90) cc_final: 0.7314 (t-90)
REVERT: D  235 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7000 (m-80)
REVERT: D  238 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8138 (pt0)
REVERT: D  285 PRO cc_start: 0.7312 (Cg_exo) cc_final: 0.7044 (Cg_endo)
REVERT: E   37 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6271 (tp)
REVERT: E   54 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.5627 (m-10)
REVERT: E   75 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7662 (mmp-170)
REVERT: E   81 ASP cc_start: 0.8363 (m-30) cc_final: 0.8118 (m-30)
REVERT: E  201 ARG cc_start: 0.7268 (ttt-90) cc_final: 0.6976 (mpp80)
REVERT: E  229 HIS cc_start: 0.7357 (t-90) cc_final: 0.6842 (t-90)
REVERT: E  257 ASN cc_start: 0.8698 (t0) cc_final: 0.8373 (m-40)
REVERT: E  318 MET cc_start: 0.4483 (tpt) cc_final: 0.4020 (mmt)
REVERT: F   75 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7531 (mmp-170)
REVERT: F  218 ILE cc_start: 0.8325 (mm) cc_final: 0.7980 (mt)
REVERT: F  281 THR cc_start: 0.8432 (m) cc_final: 0.8150 (m)
REVERT: F  323 ILE cc_start: 0.7637 (mm) cc_final: 0.7179 (pp)
REVERT: G   37 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6325 (tp)
REVERT: G   75 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7592 (tpt170)
REVERT: G  218 ILE cc_start: 0.8276 (mm) cc_final: 0.7977 (mt)
REVERT: G  229 HIS cc_start: 0.7671 (t-90) cc_final: 0.7029 (t-90)
REVERT: G  238 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8020 (pt0)
REVERT: G  285 PRO cc_start: 0.7362 (Cg_exo) cc_final: 0.6978 (Cg_endo)
REVERT: G  290 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7382 (t0)
  outliers start: 62
  outliers final: 42
  residues processed: 282
  average time/residue: 0.4509
  time to fit residues: 144.4582
Evaluate side-chains
  280 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 227
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   54 PHE
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain C residue  127 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  325 ASP
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  198 CYS
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   39 LYS
Chi-restraints excluded: chain E residue   54 PHE
Chi-restraints excluded: chain E residue   58 PHE
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   72 PHE
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  324 ASN
Chi-restraints excluded: chain F residue   51 SER
Chi-restraints excluded: chain F residue   72 PHE
Chi-restraints excluded: chain F residue  198 CYS
Chi-restraints excluded: chain F residue  248 LEU
Chi-restraints excluded: chain F residue  294 LEU
Chi-restraints excluded: chain F residue  325 ASP
Chi-restraints excluded: chain G residue   37 ILE
Chi-restraints excluded: chain G residue  198 CYS
Chi-restraints excluded: chain G residue  238 GLU
Chi-restraints excluded: chain G residue  290 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 82 optimal weight:    0.4980
   chunk 181 optimal weight:    0.4980
   chunk 159 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 173 optimal weight:   20.0000
   chunk 62 optimal weight:    2.9990
   chunk 162 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 128 optimal weight:    3.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
C 254 HIS
F 324 ASN
G 254 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.191286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.145153 restraints weight = 16884.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.77
r_work: 0.3343 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.5278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16240  Z= 0.135
  Angle     :  0.584   9.762  22085  Z= 0.277
  Chirality :  0.038   0.134   2667
  Planarity :  0.004   0.043   2681
  Dihedral  :  3.527  15.459   2177
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 36.81 %
    Favored  : 58.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.19), residues: 1967
  helix:  2.58 (0.14), residues: 1316
  sheet: -1.07 (0.60), residues: 84
  loop : -1.61 (0.22), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 201 
 TYR   0.026   0.002   TYR G 289 
 PHE   0.016   0.002   PHE E 189 
 TRP   0.006   0.001   TRP A 128 
 HIS   0.007   0.001   HIS C 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (16226)
  covalent geometry    : angle       0.58321 (22057)
  SS BOND              : bond        0.00243 (   14)
  SS BOND              : angle       1.07367 (   28)
  hydrogen bonds       : bond        0.04430 (  959)
  hydrogen bonds       : angle       3.59513 ( 2856)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6014.94 seconds
wall clock time: 102 minutes 56.18 seconds (6176.18 seconds total)