Starting phenix.real_space_refine
on Sat Oct 11 05:11:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uvu_42629/10_2025/8uvu_42629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uvu_42629/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uvu_42629/10_2025/8uvu_42629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uvu_42629/10_2025/8uvu_42629.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uvu_42629/10_2025/8uvu_42629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uvu_42629/10_2025/8uvu_42629.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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:
    B, C, 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: 2.62, per 1000 atoms: 0.22
  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: 1.27
  Conformation dependent library (CDL) restraints added in 650.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.41
  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: 2.19

  Time building geometry restraints manager: 1.57 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             5.380
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.790
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.260
-------------------------------------------------------------------------------
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= 0.150
  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 : 8.73
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (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
 ARG   0.005   0.000   ARG A 306 
 TYR   0.019   0.001   TYR D 124 
 PHE   0.014   0.001   PHE C 189 
 TRP   0.008   0.001   TRP A 193 
 HIS   0.002   0.000   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (12208)
  covalent geometry    : angle       0.60096 (16584)
  hydrogen bonds       : bond        0.11868 (  984)
  hydrogen bonds       : angle       4.14452 ( 2916)

*********************** 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  : 0.468 
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: 0.7040
  time to fit residues: 167.7265
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  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.150783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.120780 restraints weight = 15042.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.94
r_work: 0.3143 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2911
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12208  Z= 0.195
  Angle     :  0.595   6.761  16584  Z= 0.307
  Chirality :  0.039   0.133   2052
  Planarity :  0.004   0.035   1992
  Dihedral  :  4.169  20.858   1856
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  8.11 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.22), residues: 1500
  helix:  2.31 (0.14), residues: 1224
  sheet: -4.46 (0.55), residues: 44
  loop : -3.20 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 211 
 TYR   0.019   0.002   TYR C 124 
 PHE   0.014   0.001   PHE A 203 
 TRP   0.008   0.002   TRP D 193 
 HIS   0.004   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (12208)
  covalent geometry    : angle       0.59507 (16584)
  hydrogen bonds       : bond        0.04809 (  984)
  hydrogen bonds       : angle       3.53753 ( 2916)

*********************** 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
  220 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 193
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A  389 LEU cc_start: 0.8459 (mt) cc_final: 0.8123 (mt)
REVERT: B  121 MET cc_start: 0.8741 (tmm) cc_final: 0.8467 (tmt)
REVERT: B  389 LEU cc_start: 0.8453 (mt) cc_final: 0.8116 (mt)
REVERT: C  179 GLN cc_start: 0.7922 (pm20) cc_final: 0.7628 (pm20)
REVERT: C  389 LEU cc_start: 0.8476 (mt) cc_final: 0.8147 (mt)
REVERT: D  389 LEU cc_start: 0.8481 (mt) cc_final: 0.8149 (mt)
  outliers start: 27
  outliers final: 12
  residues processed: 211
  average time/residue: 0.6422
  time to fit residues: 146.1367
Evaluate side-chains
  195 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 183
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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 53 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 147 optimal weight:    0.9990
   chunk 115 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3738 r_free = 0.3738 target = 0.149241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.118838 restraints weight = 15946.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.02
r_work: 0.3128 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12208  Z= 0.169
  Angle     :  0.582   7.159  16584  Z= 0.298
  Chirality :  0.038   0.130   2052
  Planarity :  0.004   0.038   1992
  Dihedral  :  4.178  18.559   1856
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.58 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.22), residues: 1500
  helix:  2.33 (0.14), residues: 1224
  sheet: -4.33 (0.55), residues: 44
  loop : -3.27 (0.35), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 117 
 TYR   0.020   0.002   TYR A 124 
 PHE   0.015   0.001   PHE D 205 
 TRP   0.004   0.001   TRP D 193 
 HIS   0.003   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (12208)
  covalent geometry    : angle       0.58205 (16584)
  hydrogen bonds       : bond        0.04647 (  984)
  hydrogen bonds       : angle       3.45762 ( 2916)

*********************** 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
  208 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 180
  time to evaluate  : 0.495 
Fit side-chains
REVERT: A  389 LEU cc_start: 0.8393 (mt) cc_final: 0.8061 (mt)
REVERT: B  121 MET cc_start: 0.8734 (tmm) cc_final: 0.8470 (tmt)
REVERT: B  125 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.7107 (mmm)
REVERT: B  389 LEU cc_start: 0.8384 (mt) cc_final: 0.8051 (mt)
REVERT: C  179 GLN cc_start: 0.7771 (pm20) cc_final: 0.7474 (pm20)
REVERT: C  389 LEU cc_start: 0.8399 (mt) cc_final: 0.8070 (mt)
REVERT: D  389 LEU cc_start: 0.8396 (mt) cc_final: 0.8062 (mt)
  outliers start: 28
  outliers final: 16
  residues processed: 200
  average time/residue: 0.6548
  time to fit residues: 140.7539
Evaluate side-chains
  194 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 177
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
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  125 MET
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 35 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 117 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 124 optimal weight:    0.4980
   chunk 49 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0000
   chunk 142 optimal weight:    0.6980
   overall best weight:    0.5184

-------------------------------------------------------------------------------
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
C 222 ASN
D 222 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.149161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.118581 restraints weight = 16121.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.08
r_work: 0.3171 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1437

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= 0.142
  Angle     :  0.549   7.432  16584  Z= 0.283
  Chirality :  0.037   0.122   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.123  18.890   1856
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.70 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.21), residues: 1500
  helix:  2.40 (0.14), residues: 1232
  sheet:  None (None), residues: 0
  loop : -2.98 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 405 
 TYR   0.019   0.001   TYR A 124 
 PHE   0.014   0.001   PHE B 205 
 TRP   0.005   0.001   TRP B 354 
 HIS   0.003   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (12208)
  covalent geometry    : angle       0.54862 (16584)
  hydrogen bonds       : bond        0.04345 (  984)
  hydrogen bonds       : angle       3.35489 ( 2916)

*********************** 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
  210 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 181
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A  129 VAL cc_start: 0.7587 (t) cc_final: 0.7057 (m)
REVERT: A  179 GLN cc_start: 0.7955 (pm20) cc_final: 0.7598 (pm20)
REVERT: A  365 VAL cc_start: 0.8545 (t) cc_final: 0.8207 (t)
REVERT: A  389 LEU cc_start: 0.8328 (mt) cc_final: 0.7968 (mt)
REVERT: B  121 MET cc_start: 0.8706 (tmm) cc_final: 0.8479 (tmt)
REVERT: B  125 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6987 (mmm)
REVERT: B  129 VAL cc_start: 0.7588 (t) cc_final: 0.7053 (m)
REVERT: B  179 GLN cc_start: 0.7953 (pm20) cc_final: 0.7594 (pm20)
REVERT: B  365 VAL cc_start: 0.8545 (t) cc_final: 0.8205 (t)
REVERT: B  389 LEU cc_start: 0.8317 (mt) cc_final: 0.7959 (mt)
REVERT: C  129 VAL cc_start: 0.7580 (t) cc_final: 0.7058 (m)
REVERT: C  365 VAL cc_start: 0.8545 (t) cc_final: 0.8210 (t)
REVERT: C  389 LEU cc_start: 0.8330 (mt) cc_final: 0.8014 (mt)
REVERT: D  129 VAL cc_start: 0.7597 (t) cc_final: 0.7057 (m)
REVERT: D  179 GLN cc_start: 0.7946 (pm20) cc_final: 0.7587 (pm20)
REVERT: D  365 VAL cc_start: 0.8545 (t) cc_final: 0.8206 (t)
REVERT: D  389 LEU cc_start: 0.8332 (mt) cc_final: 0.8014 (mt)
  outliers start: 29
  outliers final: 20
  residues processed: 205
  average time/residue: 0.6360
  time to fit residues: 140.2117
Evaluate side-chains
  202 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
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  128 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0570
   chunk 86 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 23 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    0.1980
   chunk 41 optimal weight:    0.0870
   chunk 129 optimal weight:    0.5980
   overall best weight:    0.2476

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.141019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.111616 restraints weight = 19330.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 1.89
r_work: 0.3114 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12208  Z= 0.113
  Angle     :  0.518   7.536  16584  Z= 0.269
  Chirality :  0.035   0.120   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  3.925  16.548   1856
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.53 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.21), residues: 1500
  helix:  2.57 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -2.91 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 178 
 TYR   0.019   0.001   TYR A 124 
 PHE   0.012   0.001   PHE A 205 
 TRP   0.006   0.001   TRP D 354 
 HIS   0.001   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (12208)
  covalent geometry    : angle       0.51788 (16584)
  hydrogen bonds       : bond        0.03849 (  984)
  hydrogen bonds       : angle       3.23043 ( 2916)

*********************** 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
  221 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 192
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A  125 MET cc_start: 0.7176 (mmm) cc_final: 0.6742 (mmt)
REVERT: A  365 VAL cc_start: 0.8467 (t) cc_final: 0.8059 (t)
REVERT: A  389 LEU cc_start: 0.8343 (mt) cc_final: 0.7994 (mt)
REVERT: B  129 VAL cc_start: 0.7656 (t) cc_final: 0.7138 (m)
REVERT: B  365 VAL cc_start: 0.8471 (t) cc_final: 0.8059 (t)
REVERT: B  389 LEU cc_start: 0.8319 (mt) cc_final: 0.7950 (mt)
REVERT: C  125 MET cc_start: 0.7179 (mmm) cc_final: 0.6749 (mmt)
REVERT: C  179 GLN cc_start: 0.7936 (pm20) cc_final: 0.7702 (pm20)
REVERT: C  365 VAL cc_start: 0.8470 (t) cc_final: 0.8067 (t)
REVERT: C  389 LEU cc_start: 0.8326 (mt) cc_final: 0.7977 (mt)
REVERT: D  125 MET cc_start: 0.7181 (mmm) cc_final: 0.6751 (mmt)
REVERT: D  365 VAL cc_start: 0.8468 (t) cc_final: 0.8064 (t)
REVERT: D  389 LEU cc_start: 0.8324 (mt) cc_final: 0.7973 (mt)
  outliers start: 29
  outliers final: 11
  residues processed: 216
  average time/residue: 0.6384
  time to fit residues: 148.8069
Evaluate side-chains
  190 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue  128 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 112 optimal weight:    0.1980
   chunk 100 optimal weight:    0.8980
   chunk 90 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 410 GLN
C 222 ASN
C 410 GLN
D 222 ASN
D 410 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.139429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.109754 restraints weight = 17949.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.88
r_work: 0.3088 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12208  Z= 0.143
  Angle     :  0.551   8.247  16584  Z= 0.281
  Chirality :  0.037   0.118   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  3.994  19.235   1856
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.61 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.21), residues: 1500
  helix:  2.53 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -2.90 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 405 
 TYR   0.019   0.001   TYR B 124 
 PHE   0.014   0.001   PHE D 205 
 TRP   0.004   0.001   TRP B 354 
 HIS   0.003   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (12208)
  covalent geometry    : angle       0.55095 (16584)
  hydrogen bonds       : bond        0.04124 (  984)
  hydrogen bonds       : angle       3.31209 ( 2916)

*********************** 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
  220 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 183
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A  365 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8199 (t)
REVERT: A  389 LEU cc_start: 0.8396 (mt) cc_final: 0.8079 (mt)
REVERT: B  365 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8194 (t)
REVERT: B  389 LEU cc_start: 0.8395 (mt) cc_final: 0.8080 (mt)
REVERT: C  365 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8204 (t)
REVERT: C  389 LEU cc_start: 0.8352 (mt) cc_final: 0.8044 (mt)
REVERT: D  365 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8202 (t)
REVERT: D  389 LEU cc_start: 0.8351 (mt) cc_final: 0.8040 (mt)
  outliers start: 37
  outliers final: 20
  residues processed: 211
  average time/residue: 0.6897
  time to fit residues: 156.2947
Evaluate side-chains
  194 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 170
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
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 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  103 VAL
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  365 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 116 optimal weight:    0.6980
   chunk 146 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 118 optimal weight:    0.1980
   chunk 133 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 143 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 410 GLN
C 222 ASN
C 410 GLN
D 222 ASN
D 410 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.144673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.111963 restraints weight = 21968.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.46
r_work: 0.3103 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1626

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= 0.168
  Angle     :  0.589   7.530  16584  Z= 0.300
  Chirality :  0.039   0.143   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.187  18.249   1856
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 14.09 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.21), residues: 1500
  helix:  2.38 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -2.94 (0.32), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 405 
 TYR   0.019   0.002   TYR B 124 
 PHE   0.017   0.001   PHE A 205 
 TRP   0.004   0.001   TRP A 354 
 HIS   0.004   0.001   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (12208)
  covalent geometry    : angle       0.58929 (16584)
  hydrogen bonds       : bond        0.04525 (  984)
  hydrogen bonds       : angle       3.45092 ( 2916)

*********************** 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
  233 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 183
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  365 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8263 (t)
REVERT: A  389 LEU cc_start: 0.8348 (mt) cc_final: 0.8016 (mt)
REVERT: B  365 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8257 (t)
REVERT: B  389 LEU cc_start: 0.8347 (mt) cc_final: 0.8013 (mt)
REVERT: C  121 MET cc_start: 0.8406 (tmt) cc_final: 0.8092 (tmt)
REVERT: C  365 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8259 (t)
REVERT: C  389 LEU cc_start: 0.8292 (mt) cc_final: 0.7966 (mt)
REVERT: D  365 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8259 (t)
REVERT: D  389 LEU cc_start: 0.8284 (mt) cc_final: 0.7954 (mt)
  outliers start: 50
  outliers final: 23
  residues processed: 226
  average time/residue: 0.6803
  time to fit residues: 165.3160
Evaluate side-chains
  206 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 179
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
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 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  103 VAL
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  420 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 14 optimal weight:    0.4980
   chunk 81 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 135 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 124 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.145710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.113660 restraints weight = 20761.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.38
r_work: 0.3133 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1678

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= 0.157
  Angle     :  0.585   8.810  16584  Z= 0.297
  Chirality :  0.038   0.131   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.209  19.599   1856
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.44 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.21), residues: 1500
  helix:  2.35 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -2.91 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 145 
 TYR   0.019   0.001   TYR B 124 
 PHE   0.014   0.001   PHE A 203 
 TRP   0.005   0.001   TRP D 354 
 HIS   0.003   0.001   HIS C  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (12208)
  covalent geometry    : angle       0.58506 (16584)
  hydrogen bonds       : bond        0.04415 (  984)
  hydrogen bonds       : angle       3.44581 ( 2916)

*********************** 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
  211 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 173
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6909 (tp)
REVERT: A  365 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8261 (t)
REVERT: A  389 LEU cc_start: 0.8268 (mt) cc_final: 0.7950 (mt)
REVERT: B  151 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6903 (tp)
REVERT: B  365 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8255 (t)
REVERT: B  389 LEU cc_start: 0.8268 (mt) cc_final: 0.7949 (mt)
REVERT: C  365 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8261 (t)
REVERT: C  389 LEU cc_start: 0.8331 (mt) cc_final: 0.8007 (mt)
REVERT: D  151 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6918 (tp)
REVERT: D  365 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8265 (t)
REVERT: D  389 LEU cc_start: 0.8336 (mt) cc_final: 0.8009 (mt)
  outliers start: 38
  outliers final: 23
  residues processed: 203
  average time/residue: 0.6847
  time to fit residues: 149.4542
Evaluate side-chains
  202 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 172
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
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  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  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 124 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 109 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 106 optimal weight:    1.9990
   chunk 121 optimal weight:    0.5980
   chunk 140 optimal weight:    0.5980
   chunk 71 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 = 0.3645 r_free = 0.3645 target = 0.143072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.109313 restraints weight = 25969.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.67
r_work: 0.3106 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1744

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= 0.172
  Angle     :  0.604   9.174  16584  Z= 0.305
  Chirality :  0.039   0.135   2052
  Planarity :  0.004   0.037   1992
  Dihedral  :  4.281  18.717   1856
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.52 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.21), residues: 1500
  helix:  2.28 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -2.91 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 405 
 TYR   0.018   0.001   TYR B 124 
 PHE   0.015   0.001   PHE C 205 
 TRP   0.005   0.001   TRP A 354 
 HIS   0.004   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (12208)
  covalent geometry    : angle       0.60408 (16584)
  hydrogen bonds       : bond        0.04582 (  984)
  hydrogen bonds       : angle       3.47795 ( 2916)

*********************** 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
  220 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 177
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6839 (tp)
REVERT: A  365 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8303 (t)
REVERT: A  389 LEU cc_start: 0.8330 (mt) cc_final: 0.8072 (mt)
REVERT: B  151 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6832 (tp)
REVERT: B  365 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8303 (t)
REVERT: B  389 LEU cc_start: 0.8321 (mt) cc_final: 0.8063 (mt)
REVERT: C  151 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6826 (tp)
REVERT: C  365 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8302 (t)
REVERT: C  389 LEU cc_start: 0.8391 (mt) cc_final: 0.8116 (mt)
REVERT: D  151 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6844 (tp)
REVERT: D  365 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8304 (t)
REVERT: D  387 MET cc_start: 0.9159 (mtm) cc_final: 0.8955 (mtm)
REVERT: D  389 LEU cc_start: 0.8315 (mt) cc_final: 0.8058 (mt)
  outliers start: 43
  outliers final: 23
  residues processed: 212
  average time/residue: 0.6684
  time to fit residues: 151.9650
Evaluate side-chains
  204 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 173
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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  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 108 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 142 optimal weight:    0.3980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.148712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.117785 restraints weight = 18045.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.17
r_work: 0.3108 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12208  Z= 0.148
  Angle     :  0.590   8.974  16584  Z= 0.298
  Chirality :  0.038   0.127   2052
  Planarity :  0.004   0.038   1992
  Dihedral  :  4.220  19.233   1856
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.58 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.21), residues: 1500
  helix:  2.36 (0.14), residues: 1236
  sheet:  None (None), residues: 0
  loop : -2.90 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 145 
 TYR   0.018   0.001   TYR B 124 
 PHE   0.014   0.001   PHE C 205 
 TRP   0.007   0.001   TRP B 193 
 HIS   0.003   0.000   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12208)
  covalent geometry    : angle       0.59044 (16584)
  hydrogen bonds       : bond        0.04351 (  984)
  hydrogen bonds       : angle       3.43722 ( 2916)

********************** 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
  207 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6966 (tp)
REVERT: A  213 ARG cc_start: 0.8459 (mpt180) cc_final: 0.8239 (mpt180)
REVERT: A  365 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8359 (t)
REVERT: A  389 LEU cc_start: 0.8371 (mt) cc_final: 0.8057 (mt)
REVERT: B  151 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6963 (tp)
REVERT: B  365 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8358 (t)
REVERT: B  389 LEU cc_start: 0.8360 (mt) cc_final: 0.8047 (mt)
REVERT: C  151 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6929 (tp)
REVERT: C  365 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8362 (t)
REVERT: C  389 LEU cc_start: 0.8373 (mt) cc_final: 0.8061 (mt)
REVERT: D  151 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6970 (tp)
REVERT: D  213 ARG cc_start: 0.8456 (mpt180) cc_final: 0.8231 (mpt180)
REVERT: D  365 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8356 (t)
REVERT: D  389 LEU cc_start: 0.8329 (mt) cc_final: 0.8077 (mt)
  outliers start: 33
  outliers final: 23
  residues processed: 203
  average time/residue: 0.7231
  time to fit residues: 156.9893
Evaluate side-chains
  205 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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  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 66 optimal weight:    0.5980
   chunk 136 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 144 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3716 r_free = 0.3716 target = 0.147855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.114887 restraints weight = 25357.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.58
r_work: 0.3132 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1794

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= 0.167
  Angle     :  0.615   8.949  16584  Z= 0.309
  Chirality :  0.039   0.173   2052
  Planarity :  0.004   0.038   1992
  Dihedral  :  4.278  18.612   1856
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.22), residues: 1500
  helix:  2.30 (0.14), residues: 1236
  sheet: -4.49 (0.49), residues: 52
  loop : -3.01 (0.37), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 145 
 TYR   0.019   0.001   TYR B 124 
 PHE   0.015   0.001   PHE C 205 
 TRP   0.005   0.001   TRP B 193 
 HIS   0.003   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12208)
  covalent geometry    : angle       0.61491 (16584)
  hydrogen bonds       : bond        0.04536 (  984)
  hydrogen bonds       : angle       3.48454 ( 2916)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4473.66 seconds
wall clock time: 79 minutes 26.03 seconds (4766.03 seconds total)