Starting phenix.real_space_refine
on Sat Jan 18 07:11:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uvu_42629/01_2025/8uvu_42629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uvu_42629/01_2025/8uvu_42629.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uvu_42629/01_2025/8uvu_42629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uvu_42629/01_2025/8uvu_42629.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uvu_42629/01_2025/8uvu_42629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uvu_42629/01_2025/8uvu_42629.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.102
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     120      5.16       5
     C    7784      2.51       5
     N    2000      2.21       5
     O    2072      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 11976
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2970
          Classifications: {'peptide': 379}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 366}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 24
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 12
          Unusual residues: {'BDF': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 12
          Unusual residues: {'FRU': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" C1 ABDF A 501 " occ=0.75
      ... (10 atoms not shown)
      pdb=" O6 ABDF A 501 " occ=0.75
    residue:
      pdb=" C1 BFRU A 502 " occ=0.25
      ... (10 atoms not shown)
      pdb=" O6 BFRU A 502 " occ=0.25
    residue:
      pdb=" C1 ABDF B 501 " occ=0.75
      ... (10 atoms not shown)
      pdb=" O6 ABDF B 501 " occ=0.75
    residue:
      pdb=" C1 BFRU B 502 " occ=0.25
      ... (10 atoms not shown)
      pdb=" O6 BFRU B 502 " occ=0.25
    residue:
      pdb=" C1 ABDF C 501 " occ=0.75
      ... (10 atoms not shown)
      pdb=" O6 ABDF C 501 " occ=0.75
    residue:
      pdb=" C1 BFRU C 502 " occ=0.25
      ... (10 atoms not shown)
      pdb=" O6 BFRU C 502 " occ=0.25
    residue:
      pdb=" C1 ABDF D 501 " occ=0.75
      ... (10 atoms not shown)
      pdb=" O6 ABDF D 501 " occ=0.75
    residue:
      pdb=" C1 BFRU D 502 " occ=0.25
      ... (10 atoms not shown)
      pdb=" O6 BFRU D 502 " occ=0.25
  Time building chain proxies: 6.82, per 1000 atoms: 0.57
  Number of scatterers: 11976
  At special positions: 0
  Unit cell: (110.004, 110.004, 93.984, 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     120     16.00
     O    2072      8.00
     N    2000      7.00
     C    7784      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.20
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2856

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 4 sheets defined
      85.5% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 32
      removed outlier: 3.817A  pdb=" N   PHE A  24 " --> pdb=" O   GLY A  20 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   LEU A  26 " --> pdb=" O   HIS A  22 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   LYS A  27 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 79
      removed outlier: 3.531A  pdb=" N   TYR A  57 " --> pdb=" O   GLY A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 112
      removed outlier: 4.100A  pdb=" N   VAL A  94 " --> pdb=" O   ARG A  90 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL A  95 " --> pdb=" O   MET A  91 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   SER A  96 " --> pdb=" O   SER A  92 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 134
      removed outlier: 3.916A  pdb=" N   GLU A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   ASN A 127 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU A 134 " --> pdb=" O   ALA A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 176
      removed outlier: 3.773A  pdb=" N   SER A 140 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU A 147 " --> pdb=" O   THR A 143 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   CYS A 148 " --> pdb=" O   GLU A 144 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ALA A 149 " --> pdb=" O   ARG A 145 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   LEU A 150 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A 175 " --> pdb=" O   MET A 171 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   THR A 176 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 186
    Processing helix  chain 'A' and resid 186 through 225
      removed outlier: 4.051A  pdb=" N   TYR A 190 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE A 191 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 341
      removed outlier: 3.645A  pdb=" N   GLY A 292 " --> pdb=" O   CYS A 288 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   LEU A 314 " --> pdb=" O   ASP A 310 " (cutoff:3.500A)
      Proline residue:  A 315  - end of helix
      Proline residue:  A 331  - end of helix
    Processing helix  chain 'A' and resid 344 through 390
      Proline residue:  A 368  - end of helix
    Processing helix  chain 'A' and resid 394 through 410
      removed outlier: 4.121A  pdb=" N   SER A 398 " --> pdb=" O   GLY A 394 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG A 399 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 419
    Processing helix  chain 'A' and resid 423 through 446
      removed outlier: 3.708A  pdb=" N   MET A 427 " --> pdb=" O   ASP A 423 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL A 428 " --> pdb=" O   ARG A 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 32
      removed outlier: 3.816A  pdb=" N   PHE B  24 " --> pdb=" O   GLY B  20 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   LEU B  26 " --> pdb=" O   HIS B  22 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   LYS B  27 " --> pdb=" O   ALA B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 79
      removed outlier: 3.532A  pdb=" N   TYR B  57 " --> pdb=" O   GLY B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 112
      removed outlier: 4.100A  pdb=" N   VAL B  94 " --> pdb=" O   ARG B  90 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL B  95 " --> pdb=" O   MET B  91 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   SER B  96 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 134
      removed outlier: 3.916A  pdb=" N   GLU B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   ASN B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA B 130 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLU B 134 " --> pdb=" O   ALA B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 176
      removed outlier: 3.773A  pdb=" N   SER B 140 " --> pdb=" O   GLY B 136 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU B 147 " --> pdb=" O   THR B 143 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   CYS B 148 " --> pdb=" O   GLU B 144 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ALA B 149 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   LEU B 150 " --> pdb=" O   LYS B 146 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS B 175 " --> pdb=" O   MET B 171 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   THR B 176 " --> pdb=" O   GLN B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 186
    Processing helix  chain 'B' and resid 186 through 225
      removed outlier: 4.052A  pdb=" N   TYR B 190 " --> pdb=" O   TYR B 186 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE B 191 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 341
      removed outlier: 3.645A  pdb=" N   GLY B 292 " --> pdb=" O   CYS B 288 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   LEU B 314 " --> pdb=" O   ASP B 310 " (cutoff:3.500A)
      Proline residue:  B 315  - end of helix
      Proline residue:  B 331  - end of helix
    Processing helix  chain 'B' and resid 344 through 390
      Proline residue:  B 368  - end of helix
    Processing helix  chain 'B' and resid 394 through 410
      removed outlier: 4.122A  pdb=" N   SER B 398 " --> pdb=" O   GLY B 394 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG B 399 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   LEU B 400 " --> pdb=" O   LEU B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 419
    Processing helix  chain 'B' and resid 423 through 446
      removed outlier: 3.708A  pdb=" N   MET B 427 " --> pdb=" O   ASP B 423 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL B 428 " --> pdb=" O   ARG B 424 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 32
      removed outlier: 3.817A  pdb=" N   PHE C  24 " --> pdb=" O   GLY C  20 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   LEU C  26 " --> pdb=" O   HIS C  22 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LYS C  27 " --> pdb=" O   ALA C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 79
      removed outlier: 3.532A  pdb=" N   TYR C  57 " --> pdb=" O   GLY C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 112
      removed outlier: 4.100A  pdb=" N   VAL C  94 " --> pdb=" O   ARG C  90 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL C  95 " --> pdb=" O   MET C  91 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   SER C  96 " --> pdb=" O   SER C  92 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL C 103 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 134
      removed outlier: 3.917A  pdb=" N   GLU C 126 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   ASN C 127 " --> pdb=" O   SER C 123 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA C 130 " --> pdb=" O   GLU C 126 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU C 134 " --> pdb=" O   ALA C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 176
      removed outlier: 3.773A  pdb=" N   SER C 140 " --> pdb=" O   GLY C 136 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU C 147 " --> pdb=" O   THR C 143 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   CYS C 148 " --> pdb=" O   GLU C 144 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   ALA C 149 " --> pdb=" O   ARG C 145 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   LEU C 150 " --> pdb=" O   LYS C 146 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LYS C 175 " --> pdb=" O   MET C 171 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   THR C 176 " --> pdb=" O   GLN C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 186
    Processing helix  chain 'C' and resid 186 through 225
      removed outlier: 4.051A  pdb=" N   TYR C 190 " --> pdb=" O   TYR C 186 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE C 191 " --> pdb=" O   ALA C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 341
      removed outlier: 3.646A  pdb=" N   GLY C 292 " --> pdb=" O   CYS C 288 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   LEU C 314 " --> pdb=" O   ASP C 310 " (cutoff:3.500A)
      Proline residue:  C 315  - end of helix
      Proline residue:  C 331  - end of helix
    Processing helix  chain 'C' and resid 344 through 390
      Proline residue:  C 368  - end of helix
    Processing helix  chain 'C' and resid 394 through 410
      removed outlier: 4.122A  pdb=" N   SER C 398 " --> pdb=" O   GLY C 394 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG C 399 " --> pdb=" O   VAL C 395 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   LEU C 400 " --> pdb=" O   LEU C 396 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 415 through 419
    Processing helix  chain 'C' and resid 423 through 446
      removed outlier: 3.708A  pdb=" N   MET C 427 " --> pdb=" O   ASP C 423 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL C 428 " --> pdb=" O   ARG C 424 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 32
      removed outlier: 3.817A  pdb=" N   PHE D  24 " --> pdb=" O   GLY D  20 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   LEU D  26 " --> pdb=" O   HIS D  22 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LYS D  27 " --> pdb=" O   ALA D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 79
      removed outlier: 3.533A  pdb=" N   TYR D  57 " --> pdb=" O   GLY D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 112
      removed outlier: 4.100A  pdb=" N   VAL D  94 " --> pdb=" O   ARG D  90 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL D  95 " --> pdb=" O   MET D  91 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   SER D  96 " --> pdb=" O   SER D  92 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 134
      removed outlier: 3.916A  pdb=" N   GLU D 126 " --> pdb=" O   LEU D 122 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   ASN D 127 " --> pdb=" O   SER D 123 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA D 130 " --> pdb=" O   GLU D 126 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU D 134 " --> pdb=" O   ALA D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 136 through 176
      removed outlier: 3.774A  pdb=" N   SER D 140 " --> pdb=" O   GLY D 136 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU D 147 " --> pdb=" O   THR D 143 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   CYS D 148 " --> pdb=" O   GLU D 144 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   ALA D 149 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   LEU D 150 " --> pdb=" O   LYS D 146 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS D 175 " --> pdb=" O   MET D 171 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   THR D 176 " --> pdb=" O   GLN D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 186
    Processing helix  chain 'D' and resid 186 through 225
      removed outlier: 4.052A  pdb=" N   TYR D 190 " --> pdb=" O   TYR D 186 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE D 191 " --> pdb=" O   ALA D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 341
      removed outlier: 3.646A  pdb=" N   GLY D 292 " --> pdb=" O   CYS D 288 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   LEU D 314 " --> pdb=" O   ASP D 310 " (cutoff:3.500A)
      Proline residue:  D 315  - end of helix
      Proline residue:  D 331  - end of helix
    Processing helix  chain 'D' and resid 344 through 390
      Proline residue:  D 368  - end of helix
    Processing helix  chain 'D' and resid 394 through 410
      removed outlier: 4.121A  pdb=" N   SER D 398 " --> pdb=" O   GLY D 394 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG D 399 " --> pdb=" O   VAL D 395 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   LEU D 400 " --> pdb=" O   LEU D 396 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 415 through 419
    Processing helix  chain 'D' and resid 423 through 446
      removed outlier: 3.708A  pdb=" N   MET D 427 " --> pdb=" O   ASP D 423 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL D 428 " --> pdb=" O   ARG D 424 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18
      removed outlier: 4.267A  pdb=" N   CYS A  16 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR A  49 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 18
      removed outlier: 4.268A  pdb=" N   CYS B  16 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR B  49 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 16 through 18
      removed outlier: 4.268A  pdb=" N   CYS C  16 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   THR C  49 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 16 through 18
      removed outlier: 4.269A  pdb=" N   CYS D  16 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR D  49 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)

    984 hydrogen bonds defined for protein.
    2916 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: 3.47

  Time building geometry restraints manager: 3.57 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: 3716
        1.34 -     1.46: 2834
        1.46 -     1.58: 5478
        1.58 -     1.70: 0
        1.70 -     1.82: 180
  Bond restraints: 12208
  Sorted by residual:
  bond pdb=" C2 BFRU B 502 "
       pdb=" O2 BFRU B 502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.426 -0.038 2.00e-02 2.50e+03 3.66e+00
  bond pdb=" C2 BFRU A 502 "
       pdb=" O2 BFRU A 502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.426 -0.038 2.00e-02 2.50e+03 3.57e+00
  bond pdb=" C2 BFRU C 502 "
       pdb=" O2 BFRU C 502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.426 -0.038 2.00e-02 2.50e+03 3.56e+00
  bond pdb=" C2 BFRU D 502 "
       pdb=" O2 BFRU D 502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.425 -0.037 2.00e-02 2.50e+03 3.49e+00
  bond pdb=" C2 ABDF A 501 "
       pdb=" O2 ABDF A 501 "
    ideal  model  delta    sigma   weight residual
    1.390  1.425 -0.035 2.00e-02 2.50e+03 3.07e+00
  ... (remaining 12203 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 16272
        1.84 -     3.67: 230
        3.67 -     5.51: 62
        5.51 -     7.35: 16
        7.35 -     9.18: 4
  Bond angle restraints: 16584
  Sorted by residual:
  angle pdb=" N   ALA B  23 "
        pdb=" CA  ALA B  23 "
        pdb=" C   ALA B  23 "
      ideal   model   delta    sigma   weight residual
     114.62  108.80    5.82 1.14e+00 7.69e-01 2.61e+01
  angle pdb=" N   ALA A  23 "
        pdb=" CA  ALA A  23 "
        pdb=" C   ALA A  23 "
      ideal   model   delta    sigma   weight residual
     114.62  108.83    5.79 1.14e+00 7.69e-01 2.58e+01
  angle pdb=" N   ALA D  23 "
        pdb=" CA  ALA D  23 "
        pdb=" C   ALA D  23 "
      ideal   model   delta    sigma   weight residual
     114.62  108.83    5.79 1.14e+00 7.69e-01 2.58e+01
  angle pdb=" N   ALA C  23 "
        pdb=" CA  ALA C  23 "
        pdb=" C   ALA C  23 "
      ideal   model   delta    sigma   weight residual
     114.62  108.86    5.76 1.14e+00 7.69e-01 2.55e+01
  angle pdb=" CA  ALA A  23 "
        pdb=" C   ALA A  23 "
        pdb=" N   PHE A  24 "
      ideal   model   delta    sigma   weight residual
     119.71  116.12    3.59 1.17e+00 7.31e-01 9.41e+00
  ... (remaining 16579 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 6640
       17.96 -    35.91: 599
       35.91 -    53.87: 145
       53.87 -    71.82: 32
       71.82 -    89.78: 8
  Dihedral angle restraints: 7424
    sinusoidal: 3000
      harmonic: 4424
  Sorted by residual:
  dihedral pdb=" CA  LYS D  52 "
           pdb=" C   LYS D  52 "
           pdb=" N   GLY D  53 "
           pdb=" CA  GLY D  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.65  -16.35     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  LYS A  52 "
           pdb=" C   LYS A  52 "
           pdb=" N   GLY A  53 "
           pdb=" CA  GLY A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.67  -16.33     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  LYS C  52 "
           pdb=" C   LYS C  52 "
           pdb=" N   GLY C  53 "
           pdb=" CA  GLY C  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.68  -16.32     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 7421 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1846
       0.062 -    0.124: 186
       0.124 -    0.186: 8
       0.186 -    0.248: 8
       0.248 -    0.309: 4
  Chirality restraints: 2052
  Sorted by residual:
  chirality pdb=" C3 BFRU A 502 "
            pdb=" C2 BFRU A 502 "
            pdb=" C4 BFRU A 502 "
            pdb=" O3 BFRU A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.78   -0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" C3 BFRU C 502 "
            pdb=" C2 BFRU C 502 "
            pdb=" C4 BFRU C 502 "
            pdb=" O3 BFRU C 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.78   -0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" C3 BFRU B 502 "
            pdb=" C2 BFRU B 502 "
            pdb=" C4 BFRU B 502 "
            pdb=" O3 BFRU B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.78   -0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 2049 not shown)

  Planarity restraints: 1992
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 285 "   -0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO D 286 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO D 286 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D 286 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 285 "    0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO A 286 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 286 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 286 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 285 "   -0.023 5.00e-02 4.00e+02   3.46e-02 1.92e+00
        pdb=" N   PRO C 286 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO C 286 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 286 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1989 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2385
        2.78 -     3.31: 12351
        3.31 -     3.84: 20664
        3.84 -     4.37: 23759
        4.37 -     4.90: 42018
  Nonbonded interactions: 101177
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 218 "
            pdb=" OG1 THR A 379 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OD1 ASN B 218 "
            pdb=" OG1 THR B 379 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OD1 ASN D 218 "
            pdb=" OG1 THR D 379 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OD1 ASN C 218 "
            pdb=" OG1 THR C 379 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" N   GLN B 179 "
            pdb=" OE1 GLN B 179 "
     model   vdw
     2.256 3.120
  ... (remaining 101172 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 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:             4.630
  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:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     27.610
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12208  Z= 0.209
  Angle     :  0.601   9.182  16584  Z= 0.304
  Chirality :  0.041   0.309   2052
  Planarity :  0.004   0.035   1992
  Dihedral  : 14.700  89.777   4568
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.22), residues: 1500
  helix:  2.06 (0.14), residues: 1224
  sheet: -4.55 (0.58), residues: 44
  loop : -2.92 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 193 
 HIS   0.002   0.000   HIS D 307 
 PHE   0.014   0.001   PHE C 189 
 TYR   0.019   0.001   TYR D 124 
 ARG   0.005   0.000   ARG A 306 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 1.272 
Fit side-chains
REVERT: A  389 LEU cc_start: 0.8293 (mt) cc_final: 0.8018 (mt)
REVERT: B  121 MET cc_start: 0.8756 (tmm) cc_final: 0.8540 (tmt)
REVERT: B  389 LEU cc_start: 0.8310 (mt) cc_final: 0.8022 (mt)
REVERT: C  389 LEU cc_start: 0.8322 (mt) cc_final: 0.8045 (mt)
REVERT: D  389 LEU cc_start: 0.8328 (mt) cc_final: 0.8062 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 1.4411
  time to fit residues: 343.6591
Evaluate side-chains
  178 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 116 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 86 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 410 GLN
B 222 ASN
B 410 GLN
C 222 ASN
C 410 GLN
D 222 ASN
D 410 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.151449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.121316 restraints weight = 14942.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.99
r_work: 0.3147 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12208  Z= 0.281
  Angle     :  0.584   6.679  16584  Z= 0.301
  Chirality :  0.039   0.129   2052
  Planarity :  0.004   0.036   1992
  Dihedral  :  4.173  21.445   1856
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  8.41 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.22), residues: 1500
  helix:  2.36 (0.14), residues: 1224
  sheet: -4.46 (0.55), residues: 44
  loop : -3.15 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP D 193 
 HIS   0.004   0.001   HIS C 358 
 PHE   0.014   0.001   PHE A 203 
 TYR   0.018   0.002   TYR D 124 
 ARG   0.003   0.000   ARG B 211 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 1.395 
Fit side-chains
REVERT: A  179 GLN cc_start: 0.7901 (pm20) cc_final: 0.7610 (pm20)
REVERT: A  389 LEU cc_start: 0.8452 (mt) cc_final: 0.8137 (mt)
REVERT: B  121 MET cc_start: 0.8758 (tmm) cc_final: 0.8502 (tmt)
REVERT: B  179 GLN cc_start: 0.7950 (pm20) cc_final: 0.7658 (pm20)
REVERT: B  389 LEU cc_start: 0.8452 (mt) cc_final: 0.8139 (mt)
REVERT: C  179 GLN cc_start: 0.7886 (pm20) cc_final: 0.7593 (pm20)
REVERT: C  389 LEU cc_start: 0.8509 (mt) cc_final: 0.8203 (mt)
REVERT: D  179 GLN cc_start: 0.7898 (pm20) cc_final: 0.7608 (pm20)
REVERT: D  389 LEU cc_start: 0.8514 (mt) cc_final: 0.8203 (mt)
  outliers start: 25
  outliers final: 12
  residues processed: 211
  average time/residue: 1.3909
  time to fit residues: 316.7902
Evaluate side-chains
  191 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 179
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  128 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 113 optimal weight:    0.0470
   chunk 35 optimal weight:    1.9990
   chunk 124 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 392 HIS
B 222 ASN
B 392 HIS
C 222 ASN
C 392 HIS
D 222 ASN
D 392 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.151020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.120888 restraints weight = 14904.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.00
r_work: 0.3129 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12208  Z= 0.228
  Angle     :  0.553   6.808  16584  Z= 0.285
  Chirality :  0.037   0.130   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.069  17.207   1856
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.89 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.22), residues: 1500
  helix:  2.40 (0.14), residues: 1232
  sheet:  None (None), residues: 0
  loop : -2.94 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 354 
 HIS   0.002   0.001   HIS A 392 
 PHE   0.014   0.001   PHE D 205 
 TYR   0.020   0.001   TYR A 124 
 ARG   0.002   0.000   ARG B 211 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 177
  time to evaluate  : 1.293 
Fit side-chains
REVERT: A  179 GLN cc_start: 0.7783 (pm20) cc_final: 0.7503 (pm20)
REVERT: A  389 LEU cc_start: 0.8413 (mt) cc_final: 0.8068 (mt)
REVERT: B  121 MET cc_start: 0.8718 (tmm) cc_final: 0.8494 (tmt)
REVERT: B  125 MET cc_start: 0.7311 (mmp) cc_final: 0.7089 (mmm)
REVERT: B  179 GLN cc_start: 0.7773 (pm20) cc_final: 0.7488 (pm20)
REVERT: B  389 LEU cc_start: 0.8406 (mt) cc_final: 0.8063 (mt)
REVERT: C  125 MET cc_start: 0.7353 (mmp) cc_final: 0.7087 (mmm)
REVERT: C  179 GLN cc_start: 0.7777 (pm20) cc_final: 0.7492 (pm20)
REVERT: C  389 LEU cc_start: 0.8412 (mt) cc_final: 0.8069 (mt)
REVERT: D  125 MET cc_start: 0.7347 (mmp) cc_final: 0.7095 (mmm)
REVERT: D  179 GLN cc_start: 0.7779 (pm20) cc_final: 0.7496 (pm20)
REVERT: D  389 LEU cc_start: 0.8414 (mt) cc_final: 0.8070 (mt)
  outliers start: 24
  outliers final: 16
  residues processed: 197
  average time/residue: 1.4833
  time to fit residues: 314.2459
Evaluate side-chains
  192 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 176
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  128 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 92 optimal weight:    0.4980
   chunk 140 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.1980
   chunk 36 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 145 optimal weight:    0.9980
   chunk 69 optimal weight:    0.1980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
B 222 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.152195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.121633 restraints weight = 16378.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.09
r_work: 0.3242 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12208  Z= 0.189
  Angle     :  0.521   5.246  16584  Z= 0.272
  Chirality :  0.036   0.119   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.019  18.290   1856
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.88 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.22), residues: 1500
  helix:  2.52 (0.14), residues: 1232
  sheet:  None (None), residues: 0
  loop : -2.97 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 354 
 HIS   0.003   0.001   HIS D  22 
 PHE   0.014   0.001   PHE B 205 
 TYR   0.018   0.001   TYR C 124 
 ARG   0.003   0.000   ARG B 405 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 190
  time to evaluate  : 1.399 
Fit side-chains
REVERT: A  129 VAL cc_start: 0.7564 (t) cc_final: 0.7038 (m)
REVERT: A  365 VAL cc_start: 0.8371 (t) cc_final: 0.7973 (t)
REVERT: A  389 LEU cc_start: 0.8357 (mt) cc_final: 0.8022 (mt)
REVERT: B  121 MET cc_start: 0.8771 (tmm) cc_final: 0.8536 (tmt)
REVERT: B  125 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6880 (mmm)
REVERT: B  129 VAL cc_start: 0.7569 (t) cc_final: 0.7043 (m)
REVERT: B  365 VAL cc_start: 0.8367 (t) cc_final: 0.7972 (t)
REVERT: B  389 LEU cc_start: 0.8348 (mt) cc_final: 0.8013 (mt)
REVERT: C  129 VAL cc_start: 0.7545 (t) cc_final: 0.7029 (m)
REVERT: C  365 VAL cc_start: 0.8370 (t) cc_final: 0.7981 (t)
REVERT: C  389 LEU cc_start: 0.8318 (mt) cc_final: 0.7979 (mt)
REVERT: D  125 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6835 (mmm)
REVERT: D  129 VAL cc_start: 0.7557 (t) cc_final: 0.7036 (m)
REVERT: D  365 VAL cc_start: 0.8366 (t) cc_final: 0.7972 (t)
REVERT: D  389 LEU cc_start: 0.8324 (mt) cc_final: 0.7982 (mt)
  outliers start: 33
  outliers final: 20
  residues processed: 214
  average time/residue: 1.3107
  time to fit residues: 303.5336
Evaluate side-chains
  204 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 182
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  125 MET
Chi-restraints excluded: chain D residue  128 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 71 optimal weight:    0.3980
   chunk 100 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 108 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
B 222 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.149536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.119379 restraints weight = 15142.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.98
r_work: 0.3173 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2894
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12208  Z= 0.247
  Angle     :  0.571   7.370  16584  Z= 0.292
  Chirality :  0.037   0.125   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.105  17.553   1856
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.62 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.21), residues: 1500
  helix:  2.43 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -2.98 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 354 
 HIS   0.003   0.001   HIS A  22 
 PHE   0.016   0.001   PHE B 205 
 TYR   0.019   0.001   TYR C 124 
 ARG   0.003   0.000   ARG B 405 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 177
  time to evaluate  : 1.295 
Fit side-chains
REVERT: A  365 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8185 (t)
REVERT: A  389 LEU cc_start: 0.8477 (mt) cc_final: 0.8136 (mt)
REVERT: B  121 MET cc_start: 0.8740 (tmm) cc_final: 0.8489 (tmt)
REVERT: B  365 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8187 (t)
REVERT: B  389 LEU cc_start: 0.8469 (mt) cc_final: 0.8129 (mt)
REVERT: C  125 MET cc_start: 0.7116 (mmm) cc_final: 0.6681 (mmt)
REVERT: C  365 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8228 (t)
REVERT: C  389 LEU cc_start: 0.8464 (mt) cc_final: 0.8168 (mt)
REVERT: D  125 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6870 (mmm)
REVERT: D  129 VAL cc_start: 0.7608 (t) cc_final: 0.7073 (m)
REVERT: D  365 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8223 (t)
REVERT: D  389 LEU cc_start: 0.8478 (mt) cc_final: 0.8181 (mt)
  outliers start: 38
  outliers final: 20
  residues processed: 202
  average time/residue: 1.3686
  time to fit residues: 298.4418
Evaluate side-chains
  203 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  125 MET
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  365 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 145 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0670
   chunk 14 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
B 222 ASN
B 410 GLN
C 410 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.143876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.112114 restraints weight = 18135.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.22
r_work: 0.3124 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12208  Z= 0.238
  Angle     :  0.561   6.623  16584  Z= 0.288
  Chirality :  0.037   0.124   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.133  19.270   1856
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.29 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.21), residues: 1500
  helix:  2.45 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -3.04 (0.32), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 354 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.016   0.001   PHE B 205 
 TYR   0.019   0.001   TYR D 124 
 ARG   0.003   0.000   ARG B 405 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 176
  time to evaluate  : 1.316 
Fit side-chains
REVERT: A  389 LEU cc_start: 0.8345 (mt) cc_final: 0.8018 (mt)
REVERT: B  121 MET cc_start: 0.8704 (tmm) cc_final: 0.8438 (tmt)
REVERT: B  389 LEU cc_start: 0.8428 (mt) cc_final: 0.8115 (mt)
REVERT: C  389 LEU cc_start: 0.8421 (mt) cc_final: 0.8079 (mt)
REVERT: D  389 LEU cc_start: 0.8432 (mt) cc_final: 0.8091 (mt)
  outliers start: 33
  outliers final: 20
  residues processed: 200
  average time/residue: 1.5127
  time to fit residues: 325.1680
Evaluate side-chains
  192 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 172
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  128 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 16 optimal weight:    0.0010
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 134 optimal weight:    0.6980
   chunk 147 optimal weight:    0.7980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 410 GLN
B 222 ASN
B 410 GLN
C 222 ASN
C 410 GLN
D 222 ASN
D 410 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.144311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.110236 restraints weight = 24740.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.72
r_work: 0.3055 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12208  Z= 0.221
  Angle     :  0.572   8.786  16584  Z= 0.290
  Chirality :  0.037   0.121   2052
  Planarity :  0.004   0.038   1992
  Dihedral  :  4.120  18.131   1856
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.30 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.21), residues: 1500
  helix:  2.45 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -3.02 (0.32), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 354 
 HIS   0.003   0.001   HIS D  22 
 PHE   0.016   0.001   PHE B 205 
 TYR   0.020   0.001   TYR D 124 
 ARG   0.002   0.000   ARG B 405 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 182
  time to evaluate  : 1.402 
Fit side-chains
REVERT: A  365 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8247 (t)
REVERT: A  389 LEU cc_start: 0.8272 (mt) cc_final: 0.7924 (mt)
REVERT: B  121 MET cc_start: 0.8611 (tmm) cc_final: 0.8367 (tmt)
REVERT: B  365 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8201 (t)
REVERT: B  389 LEU cc_start: 0.8230 (mt) cc_final: 0.7884 (mt)
REVERT: C  365 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8214 (t)
REVERT: C  389 LEU cc_start: 0.8227 (mt) cc_final: 0.7882 (mt)
REVERT: D  121 MET cc_start: 0.8299 (tmt) cc_final: 0.8066 (tmt)
REVERT: D  365 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8204 (t)
REVERT: D  389 LEU cc_start: 0.8243 (mt) cc_final: 0.7901 (mt)
  outliers start: 48
  outliers final: 22
  residues processed: 220
  average time/residue: 1.4040
  time to fit residues: 332.7922
Evaluate side-chains
  198 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 172
  time to evaluate  : 2.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  420 CYS
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  420 CYS
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  365 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 111 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 144 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 410 GLN
B 222 ASN
B 410 GLN
C 222 ASN
C 410 GLN
D 222 ASN
D 410 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.142475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.111170 restraints weight = 16565.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.14
r_work: 0.3134 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2867
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12208  Z= 0.283
  Angle     :  0.603   8.982  16584  Z= 0.306
  Chirality :  0.038   0.135   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.248  19.789   1856
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.91 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.22), residues: 1500
  helix:  2.32 (0.14), residues: 1236
  sheet: -4.69 (0.48), residues: 52
  loop : -3.08 (0.36), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 354 
 HIS   0.004   0.001   HIS D  22 
 PHE   0.014   0.001   PHE D 203 
 TYR   0.019   0.001   TYR C 124 
 ARG   0.003   0.000   ARG D 405 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 181
  time to evaluate  : 1.366 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6793 (tp)
REVERT: A  365 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8290 (t)
REVERT: A  389 LEU cc_start: 0.8353 (mt) cc_final: 0.8034 (mt)
REVERT: B  121 MET cc_start: 0.8715 (tmm) cc_final: 0.8462 (tmt)
REVERT: B  151 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6779 (tp)
REVERT: B  365 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8290 (t)
REVERT: B  389 LEU cc_start: 0.8353 (mt) cc_final: 0.8037 (mt)
REVERT: C  151 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6786 (tp)
REVERT: C  365 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8293 (t)
REVERT: C  389 LEU cc_start: 0.8360 (mt) cc_final: 0.8041 (mt)
REVERT: D  151 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6798 (tp)
REVERT: D  365 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8290 (t)
REVERT: D  389 LEU cc_start: 0.8358 (mt) cc_final: 0.8038 (mt)
  outliers start: 48
  outliers final: 24
  residues processed: 219
  average time/residue: 1.3159
  time to fit residues: 311.2814
Evaluate side-chains
  210 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  420 CYS
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  420 CYS
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  420 CYS
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  420 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 102 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 22 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 142 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 136 optimal weight:    0.6980
   chunk 144 optimal weight:    0.4980
   chunk 108 optimal weight:    0.3980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 410 GLN
B 222 ASN
B 410 GLN
C 222 ASN
C 410 GLN
D 222 ASN
D 410 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.145398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.112287 restraints weight = 22875.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.52
r_work: 0.3139 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12208  Z= 0.215
  Angle     :  0.574   8.478  16584  Z= 0.291
  Chirality :  0.037   0.122   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.168  18.159   1856
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 16.82 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.21), residues: 1500
  helix:  2.40 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -3.00 (0.32), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 193 
 HIS   0.002   0.000   HIS C  22 
 PHE   0.014   0.001   PHE C 205 
 TYR   0.019   0.001   TYR D 124 
 ARG   0.003   0.000   ARG D 145 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 185
  time to evaluate  : 1.363 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6922 (tp)
REVERT: A  365 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8282 (t)
REVERT: A  389 LEU cc_start: 0.8261 (mt) cc_final: 0.7972 (mt)
REVERT: B  121 MET cc_start: 0.8631 (tmm) cc_final: 0.8385 (tmt)
REVERT: B  151 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6913 (tp)
REVERT: B  365 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8246 (t)
REVERT: B  389 LEU cc_start: 0.8282 (mt) cc_final: 0.8016 (mt)
REVERT: C  151 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6917 (tp)
REVERT: C  365 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8252 (t)
REVERT: C  389 LEU cc_start: 0.8275 (mt) cc_final: 0.8009 (mt)
REVERT: D  151 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6919 (tp)
REVERT: D  365 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8249 (t)
REVERT: D  389 LEU cc_start: 0.8247 (mt) cc_final: 0.7982 (mt)
  outliers start: 42
  outliers final: 23
  residues processed: 217
  average time/residue: 1.4152
  time to fit residues: 330.2545
Evaluate side-chains
  210 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 179
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  420 CYS
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  420 CYS
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  420 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 116 optimal weight:    0.8980
   chunk 126 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 143 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 410 GLN
B 222 ASN
B 410 GLN
C 222 ASN
C 410 GLN
D 222 ASN
D 410 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.146568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.112949 restraints weight = 25936.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.64
r_work: 0.3080 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12208  Z= 0.269
  Angle     :  0.606   8.492  16584  Z= 0.307
  Chirality :  0.038   0.131   2052
  Planarity :  0.004   0.038   1992
  Dihedral  :  4.266  19.308   1856
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.27 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.22), residues: 1500
  helix:  2.31 (0.14), residues: 1236
  sheet: -4.66 (0.48), residues: 52
  loop : -3.03 (0.37), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 193 
 HIS   0.003   0.001   HIS D  22 
 PHE   0.015   0.001   PHE B 205 
 TYR   0.018   0.001   TYR D 124 
 ARG   0.003   0.000   ARG B 211 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 178
  time to evaluate  : 1.350 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6837 (tp)
REVERT: A  365 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8319 (t)
REVERT: A  389 LEU cc_start: 0.8354 (mt) cc_final: 0.8100 (mt)
REVERT: B  121 MET cc_start: 0.8696 (tmm) cc_final: 0.8449 (tmt)
REVERT: B  151 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6834 (tp)
REVERT: B  365 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8318 (t)
REVERT: B  389 LEU cc_start: 0.8372 (mt) cc_final: 0.8088 (mt)
REVERT: C  151 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6831 (tp)
REVERT: C  365 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8326 (t)
REVERT: C  389 LEU cc_start: 0.8376 (mt) cc_final: 0.8090 (mt)
REVERT: D  151 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6853 (tp)
REVERT: D  365 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8322 (t)
REVERT: D  389 LEU cc_start: 0.8380 (mt) cc_final: 0.8135 (mt)
  outliers start: 39
  outliers final: 24
  residues processed: 208
  average time/residue: 1.4132
  time to fit residues: 316.6086
Evaluate side-chains
  206 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 174
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  420 CYS
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  420 CYS
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  420 CYS
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  420 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 125 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0980
   chunk 26 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9990
   chunk 132 optimal weight:    0.2980
   chunk 62 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 410 GLN
B 222 ASN
B 410 GLN
C 222 ASN
C 410 GLN
D 222 ASN
D 410 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.116835 restraints weight = 24988.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.63
r_work: 0.3109 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3085
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3085
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12208  Z= 0.202
  Angle     :  0.580   8.155  16584  Z= 0.294
  Chirality :  0.036   0.123   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.148  18.021   1856
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.80 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.21), residues: 1500
  helix:  2.42 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -2.96 (0.32), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 193 
 HIS   0.002   0.000   HIS D  22 
 PHE   0.014   0.001   PHE D 205 
 TYR   0.019   0.001   TYR D 124 
 ARG   0.003   0.000   ARG C 145 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8649.90 seconds
wall clock time: 159 minutes 13.09 seconds (9553.09 seconds total)