Starting phenix.real_space_refine
on Wed Aug  5 09:53:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oq7_70742/08_2026/9oq7_70742.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oq7_70742/08_2026/9oq7_70742.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oq7_70742/08_2026/9oq7_70742.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oq7_70742/08_2026/9oq7_70742.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oq7_70742/08_2026/9oq7_70742.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oq7_70742/08_2026/9oq7_70742.cif"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      3      5.21       5
     S      48      5.16       5
     C    5748      2.51       5
     N    1437      2.21       5
     O    1764      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9006
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2855
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 365, 2796
          Classifications: {'peptide': 365}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348}
      Conformer: "B"
        Number of residues, atoms: 365, 2796
          Classifications: {'peptide': 365}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348}
          bond proxies already assigned to first conformer: 2791
    Chain: "B"
      Number of atoms: 2855
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 365, 2796
          Classifications: {'peptide': 365}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348}
      Conformer: "B"
        Number of residues, atoms: 365, 2796
          Classifications: {'peptide': 365}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348}
          bond proxies already assigned to first conformer: 2791
    Chain: "G"
      Number of atoms: 2855
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 365, 2796
          Classifications: {'peptide': 365}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348}
      Conformer: "B"
        Number of residues, atoms: 365, 2796
          Classifications: {'peptide': 365}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348}
          bond proxies already assigned to first conformer: 2791
    Chain: "A"
      Number of atoms: 135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 135
          Unusual residues: {' MG': 1, 'DAO': 2, 'FO4': 1, 'NAG': 1, 'PEX': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 135
          Unusual residues: {' MG': 1, 'DAO': 2, 'FO4': 1, 'NAG': 1, 'PEX': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "G"
      Number of atoms: 135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 135
          Unusual residues: {' MG': 1, 'DAO': 2, 'FO4': 1, 'NAG': 1, 'PEX': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "G"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" N  AASN A  57 " occ=0.15
      ... (14 atoms not shown)
      pdb=" ND2BASN A  57 " occ=0.85
    residue:
      pdb=" N  APHE A 110 " occ=0.57
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 110 " occ=0.43
    residue:
      pdb=" N  ALYS A 227 " occ=0.74
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 227 " occ=0.26
    residue:
      pdb=" N  ATRP A 246 " occ=0.47
      ... (26 atoms not shown)
      pdb=" CH2BTRP A 246 " occ=0.53
    residue:
      pdb=" N  AARG A 255 " occ=0.53
      ... (20 atoms not shown)
      pdb=" NH2BARG A 255 " occ=0.47
    residue:
      pdb=" N  ASER A 271 " occ=0.44
      ... (10 atoms not shown)
      pdb=" OG BSER A 271 " occ=0.56
    residue:
      pdb=" N  AASN B  57 " occ=0.15
      ... (14 atoms not shown)
      pdb=" ND2BASN B  57 " occ=0.85
    residue:
      pdb=" N  APHE B 110 " occ=0.57
      ... (20 atoms not shown)
      pdb=" CZ BPHE B 110 " occ=0.43
    residue:
      pdb=" N  ALYS B 227 " occ=0.74
      ... (16 atoms not shown)
      pdb=" NZ BLYS B 227 " occ=0.26
    residue:
      pdb=" N  ATRP B 246 " occ=0.47
      ... (26 atoms not shown)
      pdb=" CH2BTRP B 246 " occ=0.53
    residue:
      pdb=" N  AARG B 255 " occ=0.53
      ... (20 atoms not shown)
      pdb=" NH2BARG B 255 " occ=0.47
    residue:
      pdb=" N  ASER B 271 " occ=0.44
      ... (10 atoms not shown)
      pdb=" OG BSER B 271 " occ=0.56
    ... (remaining 6 not shown)
  Time building chain proxies: 3.14, per 1000 atoms: 0.35
  Number of scatterers: 9006
  At special positions: 0
  Unit cell: (79.846, 78.767, 106.821, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P       6     15.00
     Mg      3     11.99
     O    1764      8.00
     N    1437      7.00
     C    5748      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: 0.45
  Conformation dependent library (CDL) restraints added in 363.3 milliseconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2070

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 15 sheets defined
      4.4% alpha, 58.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 12
      removed outlier: 4.614A  pdb=" N   MET A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 36
      removed outlier: 3.925A  pdb=" N   ALA A  35 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A  36 " --> pdb=" O   TRP A  32 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 31 through 36'
    Processing helix  chain 'A' and resid 128 through 131
    Processing helix  chain 'B' and resid 7 through 12
      removed outlier: 4.614A  pdb=" N   MET B  12 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 36
      removed outlier: 3.924A  pdb=" N   ALA B  35 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B  36 " --> pdb=" O   TRP B  32 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 31 through 36'
    Processing helix  chain 'B' and resid 128 through 131
    Processing helix  chain 'G' and resid 7 through 12
      removed outlier: 4.614A  pdb=" N   MET G  12 " --> pdb=" O   GLU G   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 31 through 36
      removed outlier: 3.925A  pdb=" N   ALA G  35 " --> pdb=" O   THR G  31 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE G  36 " --> pdb=" O   TRP G  32 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 31 through 36'
    Processing helix  chain 'G' and resid 128 through 131
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 55
      removed outlier: 4.240A  pdb=" N   LYS A 322 " --> pdb=" O   ASP A  55 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA A 270 " --> pdb=" O   SER A 325 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA A 186 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   ALA A 175 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   PHE A 188 " --> pdb=" O   ARG A 173 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   ARG A 173 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   TYR A 190 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   GLY A 171 " --> pdb=" O   TYR A 190 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   GLN A 192 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   SER A 169 " --> pdb=" O   GLN A 192 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLY A 121 " --> pdb=" O   THR A 162 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL A 157 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL A 202 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   GLU A 159 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LEU A 200 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TYR A 161 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55
      removed outlier: 4.240A  pdb=" N   LYS A 322 " --> pdb=" O   ASP A  55 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA A 270 " --> pdb=" O   SER A 325 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 356 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ARG A 355 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   LEU A  38 " --> pdb=" O   ASN A 105 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ASN A 105 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   LEU A  40 " --> pdb=" O   ALA A 103 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA A 103 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   TYR A  42 " --> pdb=" O   TYR A 101 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   TYR A 101 " --> pdb=" O   TYR A  42 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   GLY A  44 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   ALA A  99 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   PHE A  46 " --> pdb=" O   THR A  97 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   THR A  97 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   PHE A  48 " --> pdb=" O   MET A  95 " (cutoff:3.500A)
      removed outlier: 5.707A  pdb=" N   MET A  95 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ALA A  93 " --> pdb=" O   ARG A  50 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLY A 121 " --> pdb=" O   THR A 162 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL A 157 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL A 202 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   GLU A 159 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LEU A 200 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TYR A 161 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 63
    Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 152
      removed outlier: 6.597A  pdb=" N   VAL A 133 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   VAL A 316 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ILE A 277 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 216
    Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 55
      removed outlier: 4.240A  pdb=" N   LYS B 322 " --> pdb=" O   ASP B  55 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA B 270 " --> pdb=" O   SER B 325 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA B 186 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   ALA B 175 " --> pdb=" O   ALA B 186 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   PHE B 188 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   ARG B 173 " --> pdb=" O   PHE B 188 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   TYR B 190 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   GLY B 171 " --> pdb=" O   TYR B 190 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   GLN B 192 " --> pdb=" O   SER B 169 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   SER B 169 " --> pdb=" O   GLN B 192 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLY B 121 " --> pdb=" O   THR B 162 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   VAL B 157 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL B 202 " --> pdb=" O   VAL B 157 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   GLU B 159 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LEU B 200 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TYR B 161 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 55
      removed outlier: 4.240A  pdb=" N   LYS B 322 " --> pdb=" O   ASP B  55 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA B 270 " --> pdb=" O   SER B 325 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA B 356 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   LEU B  38 " --> pdb=" O   ASN B 105 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ASN B 105 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   LEU B  40 " --> pdb=" O   ALA B 103 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA B 103 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   TYR B  42 " --> pdb=" O   TYR B 101 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   TYR B 101 " --> pdb=" O   TYR B  42 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   GLY B  44 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   ALA B  99 " --> pdb=" O   GLY B  44 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   PHE B  46 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   THR B  97 " --> pdb=" O   PHE B  46 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   PHE B  48 " --> pdb=" O   MET B  95 " (cutoff:3.500A)
      removed outlier: 5.707A  pdb=" N   MET B  95 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ALA B  93 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLY B 121 " --> pdb=" O   THR B 162 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   VAL B 157 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL B 202 " --> pdb=" O   VAL B 157 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   GLU B 159 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LEU B 200 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TYR B 161 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 59 through 63
    Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 152
      removed outlier: 6.598A  pdb=" N   VAL B 133 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   VAL B 316 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ILE B 277 " --> pdb=" O   LEU B 320 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 215 through 216
    Processing sheet with id=AB2, first strand: chain 'G' and resid 52 through 55
      removed outlier: 4.240A  pdb=" N   LYS G 322 " --> pdb=" O   ASP G  55 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA G 270 " --> pdb=" O   SER G 325 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA G 186 " --> pdb=" O   ALA G 175 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   ALA G 175 " --> pdb=" O   ALA G 186 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   PHE G 188 " --> pdb=" O   ARG G 173 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   ARG G 173 " --> pdb=" O   PHE G 188 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   TYR G 190 " --> pdb=" O   GLY G 171 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   GLY G 171 " --> pdb=" O   TYR G 190 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   GLN G 192 " --> pdb=" O   SER G 169 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   SER G 169 " --> pdb=" O   GLN G 192 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLY G 121 " --> pdb=" O   THR G 162 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL G 157 " --> pdb=" O   VAL G 202 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL G 202 " --> pdb=" O   VAL G 157 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   GLU G 159 " --> pdb=" O   LEU G 200 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU G 200 " --> pdb=" O   GLU G 159 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TYR G 161 " --> pdb=" O   GLU G 198 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 52 through 55
      removed outlier: 4.240A  pdb=" N   LYS G 322 " --> pdb=" O   ASP G  55 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA G 270 " --> pdb=" O   SER G 325 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA G 356 " --> pdb=" O   ARG G 350 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ARG G 355 " --> pdb=" O   PHE G  48 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   LEU G  38 " --> pdb=" O   ASN G 105 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ASN G 105 " --> pdb=" O   LEU G  38 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   LEU G  40 " --> pdb=" O   ALA G 103 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ALA G 103 " --> pdb=" O   LEU G  40 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   TYR G  42 " --> pdb=" O   TYR G 101 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   TYR G 101 " --> pdb=" O   TYR G  42 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   GLY G  44 " --> pdb=" O   ALA G  99 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   ALA G  99 " --> pdb=" O   GLY G  44 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   PHE G  46 " --> pdb=" O   THR G  97 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   THR G  97 " --> pdb=" O   PHE G  46 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   PHE G  48 " --> pdb=" O   MET G  95 " (cutoff:3.500A)
      removed outlier: 5.707A  pdb=" N   MET G  95 " --> pdb=" O   PHE G  48 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ALA G  93 " --> pdb=" O   ARG G  50 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLY G 121 " --> pdb=" O   THR G 162 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL G 157 " --> pdb=" O   VAL G 202 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL G 202 " --> pdb=" O   VAL G 157 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   GLU G 159 " --> pdb=" O   LEU G 200 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU G 200 " --> pdb=" O   GLU G 159 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TYR G 161 " --> pdb=" O   GLU G 198 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 59 through 63
    Processing sheet with id=AB5, first strand: chain 'G' and resid 151 through 152
      removed outlier: 6.598A  pdb=" N   VAL G 133 " --> pdb=" O   VAL G 316 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   VAL G 316 " --> pdb=" O   VAL G 133 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ILE G 277 " --> pdb=" O   LEU G 320 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'G' and resid 215 through 216

    429 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1482
        1.31 -     1.43: 2406
        1.43 -     1.56: 5136
        1.56 -     1.69: 72
        1.69 -     1.81: 75
  Bond restraints: 9171
  Sorted by residual:
  bond pdb=" C1  FO4 G 402 "
       pdb=" C2  FO4 G 402 "
    ideal  model  delta    sigma   weight residual
    1.328  1.565 -0.237 2.00e-02 2.50e+03 1.41e+02
  bond pdb=" C1  FO4 A 405 "
       pdb=" C2  FO4 A 405 "
    ideal  model  delta    sigma   weight residual
    1.328  1.565 -0.237 2.00e-02 2.50e+03 1.41e+02
  bond pdb=" C1  FO4 B 405 "
       pdb=" C2  FO4 B 405 "
    ideal  model  delta    sigma   weight residual
    1.328  1.565 -0.237 2.00e-02 2.50e+03 1.40e+02
  bond pdb=" C31 FO4 B 405 "
       pdb=" C32 FO4 B 405 "
    ideal  model  delta    sigma   weight residual
    1.333  1.557 -0.224 2.00e-02 2.50e+03 1.25e+02
  bond pdb=" C31 FO4 A 405 "
       pdb=" C32 FO4 A 405 "
    ideal  model  delta    sigma   weight residual
    1.333  1.557 -0.224 2.00e-02 2.50e+03 1.25e+02
  ... (remaining 9166 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.43: 12250
        3.43 -     6.86: 155
        6.86 -    10.30: 9
       10.30 -    13.73: 9
       13.73 -    17.16: 9
  Bond angle restraints: 12432
  Sorted by residual:
  angle pdb=" C30 FO4 B 405 "
        pdb=" C31 FO4 B 405 "
        pdb=" C32 FO4 B 405 "
      ideal   model   delta    sigma   weight residual
     126.80  109.64   17.16 3.00e+00 1.11e-01 3.27e+01
  angle pdb=" C30 FO4 G 402 "
        pdb=" C31 FO4 G 402 "
        pdb=" C32 FO4 G 402 "
      ideal   model   delta    sigma   weight residual
     126.80  109.67   17.13 3.00e+00 1.11e-01 3.26e+01
  angle pdb=" C30 FO4 A 405 "
        pdb=" C31 FO4 A 405 "
        pdb=" C32 FO4 A 405 "
      ideal   model   delta    sigma   weight residual
     126.80  109.67   17.13 3.00e+00 1.11e-01 3.26e+01
  angle pdb=" C31 FO4 B 405 "
        pdb=" C32 FO4 B 405 "
        pdb=" C33 FO4 B 405 "
      ideal   model   delta    sigma   weight residual
     126.49  111.30   15.19 3.00e+00 1.11e-01 2.56e+01
  angle pdb=" C31 FO4 A 405 "
        pdb=" C32 FO4 A 405 "
        pdb=" C33 FO4 A 405 "
      ideal   model   delta    sigma   weight residual
     126.49  111.31   15.18 3.00e+00 1.11e-01 2.56e+01
  ... (remaining 12427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.54: 5283
       29.54 -    59.08: 204
       59.08 -    88.62: 42
       88.62 -   118.17: 30
      118.17 -   147.71: 9
  Dihedral angle restraints: 5568
    sinusoidal: 2334
      harmonic: 3234
  Sorted by residual:
  dihedral pdb=" C33 FO4 B 405 "
           pdb=" C34 FO4 B 405 "
           pdb=" C35 FO4 B 405 "
           pdb=" C36 FO4 B 405 "
      ideal   model   delta sinusoidal    sigma   weight residual
      61.82 -150.47 -147.71     1      3.00e+01 1.11e-03 1.97e+01
  dihedral pdb=" C33 FO4 G 402 "
           pdb=" C34 FO4 G 402 "
           pdb=" C35 FO4 G 402 "
           pdb=" C36 FO4 G 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
      61.82 -150.48 -147.70     1      3.00e+01 1.11e-03 1.97e+01
  dihedral pdb=" C33 FO4 A 405 "
           pdb=" C34 FO4 A 405 "
           pdb=" C35 FO4 A 405 "
           pdb=" C36 FO4 A 405 "
      ideal   model   delta sinusoidal    sigma   weight residual
      61.82 -150.49 -147.69     1      3.00e+01 1.11e-03 1.97e+01
  ... (remaining 5565 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 633
       0.036 -    0.071: 429
       0.071 -    0.107: 243
       0.107 -    0.143: 51
       0.143 -    0.178: 6
  Chirality restraints: 1362
  Sorted by residual:
  chirality pdb=" CG  LEU A 203 "
            pdb=" CB  LEU A 203 "
            pdb=" CD1 LEU A 203 "
            pdb=" CD2 LEU A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CG  LEU B 203 "
            pdb=" CB  LEU B 203 "
            pdb=" CD1 LEU B 203 "
            pdb=" CD2 LEU B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.83e-01
  chirality pdb=" CG  LEU G 203 "
            pdb=" CB  LEU G 203 "
            pdb=" CD1 LEU G 203 "
            pdb=" CD2 LEU G 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.60e-01
  ... (remaining 1359 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C30 FO4 B 405 "    0.156 2.00e-02 2.50e+03   2.98e-01 8.91e+02
        pdb=" C31 FO4 B 405 "   -0.385 2.00e-02 2.50e+03
        pdb=" C32 FO4 B 405 "    0.395 2.00e-02 2.50e+03
        pdb=" C33 FO4 B 405 "   -0.166 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C30 FO4 G 402 "   -0.156 2.00e-02 2.50e+03   2.98e-01 8.90e+02
        pdb=" C31 FO4 G 402 "    0.385 2.00e-02 2.50e+03
        pdb=" C32 FO4 G 402 "   -0.395 2.00e-02 2.50e+03
        pdb=" C33 FO4 G 402 "    0.166 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C30 FO4 A 405 "   -0.156 2.00e-02 2.50e+03   2.98e-01 8.90e+02
        pdb=" C31 FO4 A 405 "    0.385 2.00e-02 2.50e+03
        pdb=" C32 FO4 A 405 "   -0.395 2.00e-02 2.50e+03
        pdb=" C33 FO4 A 405 "    0.166 2.00e-02 2.50e+03
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 97
        2.64 -     3.21: 7543
        3.21 -     3.77: 13122
        3.77 -     4.34: 19207
        4.34 -     4.90: 33853
  Nonbonded interactions: 73822
  Sorted by model distance:
  nonbonded pdb="MG    MG B 406 "
            pdb=" O   HOH A 511 "
     model   vdw
     2.078 2.170
  nonbonded pdb="MG    MG B 406 "
            pdb=" O   HOH B 505 "
     model   vdw
     2.079 2.170
  nonbonded pdb="MG    MG G 406 "
            pdb=" O   HOH G 506 "
     model   vdw
     2.079 2.170
  nonbonded pdb="MG    MG A 406 "
            pdb=" O   HOH A 505 "
     model   vdw
     2.079 2.170
  nonbonded pdb="MG    MG A 406 "
            pdb=" O   HOH A 506 "
     model   vdw
     2.079 2.170
  ... (remaining 73817 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 56 or resid 58 through 109 or resid 111 through  \ 
226 or resid 228 through 245 or resid 247 through 254 or resid 256 through 270 o \ 
r resid 272 through 365 or resid 404 or resid 406))
  selection = (chain 'B' and (resid 1 through 56 or resid 58 through 109 or resid 111 through  \ 
226 or resid 228 through 245 or resid 247 through 254 or resid 256 through 270 o \ 
r resid 272 through 365 or resid 404 or resid 406))
  selection = (chain 'G' and (resid 1 through 56 or resid 58 through 109 or resid 111 through  \ 
226 or resid 228 through 245 or resid 247 through 254 or resid 256 through 270 o \ 
r resid 272 through 365 or resid 404 or resid 406))
}

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=0.15 max=1.00 mean=0.98
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:             3.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.610
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  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:7.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
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      :  0.013   0.237   9171  Z= 0.785
  Angle     :  1.166  17.159  12432  Z= 0.644
  Chirality :  0.055   0.178   1362
  Planarity :  0.018   0.298   1584
  Dihedral  : 19.305 147.708   3498
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.31 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.24), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.08 (0.23), residues: 522
  loop : -1.06 (0.22), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  81 
 TYR   0.012   0.002   TYR G 343 
 PHE   0.018   0.003   PHE A 259 
 TRP   0.014   0.002   TRP B  18 
 HIS   0.003   0.002   HIS B 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01278 /  0.79 ( 9171)
  covalent geometry    : angle       1.16629 /  0.64 (12432)
  hydrogen bonds       : bond        0.11087 /  7.80 (  381)
  hydrogen bonds       : angle       7.01088 /  4.92 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.209 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.4773
  time to fit residues: 26.3927
Evaluate side-chains
  38 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0570
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.1980
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.5698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 247 GLN
B 247 GLN
G 247 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.098193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.078524 restraints weight = 95759.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 4.85
r_work: 0.2905 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.2951
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9171  Z= 0.144
  Angle     :  0.637   6.580  12432  Z= 0.329
  Chirality :  0.045   0.170   1362
  Planarity :  0.004   0.045   1584
  Dihedral  : 18.348 144.284   1587
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  1.65 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  2.87 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.19 (0.22), residues: 534
  loop : -0.89 (0.22), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 109 
 TYR   0.012   0.001   TYR A 343 
 PHE   0.013   0.001   PHE A 209 
 TRP   0.012   0.001   TRP G  18 
 HIS   0.004   0.001   HIS A 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.14 ( 9171)
  covalent geometry    : angle       0.63705 /  0.33 (12432)
  hydrogen bonds       : bond        0.03443 /  2.21 (  381)
  hydrogen bonds       : angle       5.48492 /  3.86 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.315 
Fit side-chains
REVERT: G  258 MET cc_start: 0.8420 (ptt) cc_final: 0.8154 (ptt)
REVERT: G  291 MET cc_start: 0.9101 (mtp) cc_final: 0.8786 (mtp)
  outliers start: 6
  outliers final: 3
  residues processed: 47
  average time/residue: 0.5052
  time to fit residues: 25.6749
Evaluate side-chains
  40 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   95 MET
Chi-restraints excluded: chain B residue  235 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.7980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.096194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.076591 restraints weight = 100378.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 4.85
r_work: 0.2873 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9171  Z= 0.174
  Angle     :  0.625   6.668  12432  Z= 0.329
  Chirality :  0.045   0.137   1362
  Planarity :  0.004   0.048   1584
  Dihedral  : 17.421 152.438   1587
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  4.53 %
    Favored  : 94.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.20 (0.22), residues: 534
  loop : -0.78 (0.22), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 350 
 TYR   0.012   0.001   TYR A 343 
 PHE   0.014   0.001   PHE A 209 
 TRP   0.010   0.001   TRP B  18 
 HIS   0.004   0.001   HIS A 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.17 ( 9171)
  covalent geometry    : angle       0.62521 /  0.33 (12432)
  hydrogen bonds       : bond        0.03564 /  2.31 (  381)
  hydrogen bonds       : angle       5.50532 /  3.88 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.215 
Fit side-chains
REVERT: G  258 MET cc_start: 0.8490 (ptt) cc_final: 0.8228 (ptt)
  outliers start: 8
  outliers final: 4
  residues processed: 45
  average time/residue: 0.5005
  time to fit residues: 24.3391
Evaluate side-chains
  42 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   95 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain G residue   95 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 87 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0070
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 104 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.5798

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.097506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.077779 restraints weight = 87581.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 4.69
r_work: 0.2788 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2943
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   9171  Z= 0.137
  Angle     :  0.577   5.546  12432  Z= 0.308
  Chirality :  0.044   0.136   1362
  Planarity :  0.004   0.047   1584
  Dihedral  : 16.912 149.887   1587
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  4.97 %
    Favored  : 94.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.27 (0.22), residues: 534
  loop : -0.69 (0.23), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 350 
 TYR   0.010   0.001   TYR B 343 
 PHE   0.013   0.001   PHE A 209 
 TRP   0.008   0.001   TRP G  18 
 HIS   0.004   0.001   HIS A 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 9171)
  covalent geometry    : angle       0.57680 /  0.31 (12432)
  hydrogen bonds       : bond        0.03304 /  2.13 (  381)
  hydrogen bonds       : angle       5.33550 /  3.77 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.231 
Fit side-chains
REVERT: G  258 MET cc_start: 0.8376 (ptt) cc_final: 0.8102 (ptt)
  outliers start: 6
  outliers final: 4
  residues processed: 39
  average time/residue: 0.5728
  time to fit residues: 24.0058
Evaluate side-chains
  41 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   95 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain G residue   95 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0970
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 102 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.5778

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.094920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.074921 restraints weight = 90974.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 4.89
r_work: 0.2742 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9171  Z= 0.136
  Angle     :  0.567   5.521  12432  Z= 0.303
  Chirality :  0.043   0.136   1362
  Planarity :  0.004   0.047   1584
  Dihedral  : 16.545 151.302   1587
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  5.63 %
    Favored  : 93.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.33 (0.22), residues: 534
  loop : -0.63 (0.23), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 350 
 TYR   0.010   0.001   TYR B 343 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.008   0.001   TRP B  18 
 HIS   0.004   0.001   HIS G 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 9171)
  covalent geometry    : angle       0.56655 /  0.30 (12432)
  hydrogen bonds       : bond        0.03238 /  2.08 (  381)
  hydrogen bonds       : angle       5.23292 /  3.70 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   51 VAL cc_start: 0.8431 (t) cc_final: 0.8166 (m)
REVERT: G  258 MET cc_start: 0.8371 (ptt) cc_final: 0.8043 (ptt)
  outliers start: 5
  outliers final: 4
  residues processed: 46
  average time/residue: 0.4593
  time to fit residues: 22.9613
Evaluate side-chains
  41 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   95 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain G residue   95 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 106 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 104 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 46 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   overall best weight:    0.5780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.094630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.075601 restraints weight = 89443.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 4.71
r_work: 0.2725 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9171  Z= 0.135
  Angle     :  0.562   5.375  12432  Z= 0.302
  Chirality :  0.043   0.157   1362
  Planarity :  0.004   0.049   1584
  Dihedral  : 15.943 156.868   1587
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.47 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  5.96 %
    Favored  : 93.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.39 (0.22), residues: 534
  loop : -0.63 (0.23), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 350 
 TYR   0.009   0.001   TYR B 343 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.007   0.001   TRP G  18 
 HIS   0.004   0.001   HIS G 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 9171)
  covalent geometry    : angle       0.56247 /  0.30 (12432)
  hydrogen bonds       : bond        0.03207 /  2.07 (  381)
  hydrogen bonds       : angle       5.22291 /  3.70 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   51 VAL cc_start: 0.8411 (t) cc_final: 0.8179 (m)
REVERT: G  258 MET cc_start: 0.8348 (ptt) cc_final: 0.8020 (ptt)
  outliers start: 7
  outliers final: 4
  residues processed: 41
  average time/residue: 0.5270
  time to fit residues: 23.3582
Evaluate side-chains
  41 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   95 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain G residue   95 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.7582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.096782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.076409 restraints weight = 86231.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 4.81
r_work: 0.2872 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   9171  Z= 0.164
  Angle     :  0.581   5.506  12432  Z= 0.311
  Chirality :  0.044   0.145   1362
  Planarity :  0.004   0.049   1584
  Dihedral  : 15.694 163.597   1587
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  6.29 %
    Favored  : 93.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.39 (0.22), residues: 537
  loop : -0.69 (0.23), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 350 
 TYR   0.010   0.001   TYR B 343 
 PHE   0.015   0.001   PHE A  21 
 TRP   0.008   0.001   TRP B  18 
 HIS   0.004   0.001   HIS G 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.16 ( 9171)
  covalent geometry    : angle       0.58107 /  0.31 (12432)
  hydrogen bonds       : bond        0.03334 /  2.15 (  381)
  hydrogen bonds       : angle       5.33504 /  3.78 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.397 
Fit side-chains
REVERT: G  258 MET cc_start: 0.8379 (ptt) cc_final: 0.8104 (ptt)
  outliers start: 5
  outliers final: 4
  residues processed: 37
  average time/residue: 0.5694
  time to fit residues: 22.8256
Evaluate side-chains
  40 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   95 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain G residue   95 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.096460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.076503 restraints weight = 75484.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 4.56
r_work: 0.2866 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   9171  Z= 0.173
  Angle     :  0.588   5.628  12432  Z= 0.315
  Chirality :  0.044   0.143   1362
  Planarity :  0.004   0.050   1584
  Dihedral  : 15.814 177.544   1587
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  6.18 %
    Favored  : 93.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.37 (0.22), residues: 549
  loop : -0.73 (0.23), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  81 
 TYR   0.010   0.001   TYR B 343 
 PHE   0.013   0.001   PHE A 209 
 TRP   0.007   0.001   TRP A  18 
 HIS   0.004   0.001   HIS G 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.17 ( 9171)
  covalent geometry    : angle       0.58821 /  0.32 (12432)
  hydrogen bonds       : bond        0.03384 /  2.18 (  381)
  hydrogen bonds       : angle       5.39775 /  3.83 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.230 
Fit side-chains
REVERT: G  258 MET cc_start: 0.8404 (ptt) cc_final: 0.8133 (ptt)
  outliers start: 5
  outliers final: 4
  residues processed: 37
  average time/residue: 0.5524
  time to fit residues: 22.0968
Evaluate side-chains
  39 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   95 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain G residue   95 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0870
   chunk 39 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.6758

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.097808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.077934 restraints weight = 101361.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 4.96
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   9171  Z= 0.149
  Angle     :  0.566   5.446  12432  Z= 0.305
  Chirality :  0.043   0.141   1362
  Planarity :  0.004   0.049   1584
  Dihedral  : 15.159 177.509   1587
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  6.40 %
    Favored  : 93.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.45 (0.22), residues: 534
  loop : -0.66 (0.23), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  81 
 TYR   0.008   0.001   TYR G 101 
 PHE   0.013   0.001   PHE A 209 
 TRP   0.007   0.001   TRP B  18 
 HIS   0.004   0.001   HIS G 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 ( 9171)
  covalent geometry    : angle       0.56615 /  0.30 (12432)
  hydrogen bonds       : bond        0.03248 /  2.09 (  381)
  hydrogen bonds       : angle       5.28625 /  3.74 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.347 
Fit side-chains
REVERT: G  258 MET cc_start: 0.7833 (ptt) cc_final: 0.7451 (ptt)
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 0.5543
  time to fit residues: 21.5384
Evaluate side-chains
  39 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   95 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain G residue   95 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0070
   chunk 107 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0470
   chunk 45 optimal weight:    0.8980
   chunk 57 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0270
   overall best weight:    0.2154

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.100609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.077853 restraints weight = 96664.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 4.97
r_work: 0.2898 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   9171  Z= 0.090
  Angle     :  0.518   5.335  12432  Z= 0.280
  Chirality :  0.042   0.138   1362
  Planarity :  0.004   0.048   1584
  Dihedral  : 13.748 158.317   1587
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.29 %
    Favored  : 93.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.58 (0.22), residues: 528
  loop : -0.62 (0.23), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.008   0.001   TYR G 101 
 PHE   0.011   0.001   PHE A  21 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.005   0.001   HIS G 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00199 /  0.09 ( 9171)
  covalent geometry    : angle       0.51793 /  0.28 (12432)
  hydrogen bonds       : bond        0.02882 /  1.85 (  381)
  hydrogen bonds       : angle       4.91924 /  3.48 ( 1182)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   51 VAL cc_start: 0.8482 (t) cc_final: 0.8224 (m)
REVERT: B   12 MET cc_start: 0.8939 (ptt) cc_final: 0.8699 (ptp)
REVERT: G   51 VAL cc_start: 0.8607 (t) cc_final: 0.8346 (m)
  outliers start: 6
  outliers final: 4
  residues processed: 50
  average time/residue: 0.4140
  time to fit residues: 22.6784
Evaluate side-chains
  46 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   95 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain G residue   95 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    0.0040
   chunk 29 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0000
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.4396

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.098877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.078979 restraints weight = 94299.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 4.79
r_work: 0.2875 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   9171  Z= 0.116
  Angle     :  0.538   5.293  12432  Z= 0.289
  Chirality :  0.043   0.138   1362
  Planarity :  0.004   0.049   1584
  Dihedral  : 13.562 154.729   1587
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.84 %
    Favored  : 92.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.23), residues: 1143
  helix:  None (None), residues: 0
  sheet:  0.65 (0.22), residues: 528
  loop : -0.60 (0.23), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  81 
 TYR   0.009   0.001   TYR B 101 
 PHE   0.011   0.001   PHE B 209 
 TRP   0.006   0.001   TRP A  18 
 HIS   0.005   0.001   HIS G 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 9171)
  covalent geometry    : angle       0.53836 /  0.29 (12432)
  hydrogen bonds       : bond        0.03043 /  1.95 (  381)
  hydrogen bonds       : angle       5.01773 /  3.56 ( 1182)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1972.12 seconds
wall clock time: 34 minutes 32.30 seconds (2072.30 seconds total)