Starting phenix.real_space_refine
on Sat Aug 23 09:37:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ypo_34010/08_2025/7ypo_34010.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ypo_34010/08_2025/7ypo_34010.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ypo_34010/08_2025/7ypo_34010.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ypo_34010/08_2025/7ypo_34010.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ypo_34010/08_2025/7ypo_34010.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ypo_34010/08_2025/7ypo_34010.cif"
  }
  resolution = 3.5
  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=   0.002 sd=   0.111
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      28      5.49       5
     S      48      5.16       5
     C    7084      2.51       5
     N    1892      2.21       5
     O    2272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11324
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2684
          Classifications: {'peptide': 327}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 324}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2684
          Classifications: {'peptide': 327}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 324}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2684
          Classifications: {'peptide': 327}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 324}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2684
          Classifications: {'peptide': 327}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 324}
          Chain breaks: 1
    Chain: "Q"
      Number of atoms: 588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 588
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
  Time building chain proxies: 3.36, per 1000 atoms: 0.30
  Number of scatterers: 11324
  At special positions: 0
  Unit cell: (114, 109.25, 125.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P      28     15.00
     O    2272      8.00
     N    1892      7.00
     C    7084      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 600.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2536

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 24 sheets defined
      18.3% alpha, 41.9% beta
      0 base pairs and 15 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 88 through 95
    Processing helix  chain 'A' and resid 135 through 141
    Processing helix  chain 'A' and resid 188 through 196
    Processing helix  chain 'A' and resid 203 through 213
    Processing helix  chain 'A' and resid 319 through 343
      removed outlier: 3.543A  pdb=" N   ASP A 324 " --> pdb=" O   LYS A 320 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASN A 338 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   SER A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 95
    Processing helix  chain 'B' and resid 135 through 141
    Processing helix  chain 'B' and resid 188 through 196
    Processing helix  chain 'B' and resid 203 through 213
    Processing helix  chain 'B' and resid 319 through 343
      removed outlier: 3.542A  pdb=" N   ASP B 324 " --> pdb=" O   LYS B 320 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASN B 338 " --> pdb=" O   LEU B 334 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   SER B 339 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 95
    Processing helix  chain 'C' and resid 135 through 141
    Processing helix  chain 'C' and resid 188 through 196
    Processing helix  chain 'C' and resid 203 through 213
    Processing helix  chain 'C' and resid 319 through 343
      removed outlier: 3.542A  pdb=" N   ASP C 324 " --> pdb=" O   LYS C 320 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ASN C 338 " --> pdb=" O   LEU C 334 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   SER C 339 " --> pdb=" O   SER C 335 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 95
    Processing helix  chain 'D' and resid 135 through 141
    Processing helix  chain 'D' and resid 188 through 196
    Processing helix  chain 'D' and resid 203 through 213
    Processing helix  chain 'D' and resid 319 through 343
      removed outlier: 3.542A  pdb=" N   ASP D 324 " --> pdb=" O   LYS D 320 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASN D 338 " --> pdb=" O   LEU D 334 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   SER D 339 " --> pdb=" O   SER D 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 87
      removed outlier: 4.247A  pdb=" N   TYR A  72 " --> pdb=" O   GLY A  87 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   GLU A  69 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   SER A  65 " --> pdb=" O   GLU A  69 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   TYR A  71 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR A  63 " --> pdb=" O   TYR A  71 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU A  73 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   LYS A  61 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   LYS A  75 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLU A 102 " --> pdb=" O   TYR A 117 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   TYR A 117 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL A 104 " --> pdb=" O   LYS A 115 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134
      removed outlier: 6.392A  pdb=" N   VAL A 133 " --> pdb=" O   GLU A 172 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134
      removed outlier: 6.392A  pdb=" N   VAL A 133 " --> pdb=" O   GLU A 172 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LYS A 164 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   GLY A 153 " --> pdb=" O   LYS A 164 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   VAL A 166 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   LEU A 170 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   LEU A 147 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
      removed outlier: 11.540A  pdb=" N   GLU A 172 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
      removed outlier: 14.796A  pdb=" N   SER A 145 " --> pdb=" O   GLU A 172 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   LYS A 144 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE A 224 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
      removed outlier: 10.189A  pdb=" N   ASN A 241 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228
    Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 277
      removed outlier: 5.717A  pdb=" N   VAL A 353 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   ILE A 364 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 288
    Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 87
      removed outlier: 4.247A  pdb=" N   TYR B  72 " --> pdb=" O   GLY B  87 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLU B  69 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   SER B  65 " --> pdb=" O   GLU B  69 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   TYR B  71 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR B  63 " --> pdb=" O   TYR B  71 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU B  73 " --> pdb=" O   LYS B  61 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   LYS B  61 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   LYS B  75 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLU B 102 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   TYR B 117 " --> pdb=" O   GLU B 102 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL B 104 " --> pdb=" O   LYS B 115 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 134
      removed outlier: 6.392A  pdb=" N   VAL B 133 " --> pdb=" O   GLU B 172 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 134
      removed outlier: 6.392A  pdb=" N   VAL B 133 " --> pdb=" O   GLU B 172 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LYS B 164 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   GLY B 153 " --> pdb=" O   LYS B 164 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   VAL B 166 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   LEU B 170 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   LEU B 147 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
      removed outlier: 11.540A  pdb=" N   GLU B 172 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
      removed outlier: 14.796A  pdb=" N   SER B 145 " --> pdb=" O   GLU B 172 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   LYS B 144 " --> pdb=" O   ARG B 223 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ILE B 224 " --> pdb=" O   ASN B 241 " (cutoff:3.500A)
      removed outlier: 10.190A  pdb=" N   ASN B 241 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 227 through 228
    Processing sheet with id=AB2, first strand: chain 'B' and resid 272 through 277
      removed outlier: 5.716A  pdb=" N   VAL B 353 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   ILE B 364 " --> pdb=" O   VAL B 353 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 282 through 288
    Processing sheet with id=AB4, first strand: chain 'C' and resid 81 through 87
      removed outlier: 4.246A  pdb=" N   TYR C  72 " --> pdb=" O   GLY C  87 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLU C  69 " --> pdb=" O   SER C  65 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   SER C  65 " --> pdb=" O   GLU C  69 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   TYR C  71 " --> pdb=" O   THR C  63 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR C  63 " --> pdb=" O   TYR C  71 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU C  73 " --> pdb=" O   LYS C  61 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   LYS C  61 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   LYS C  75 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLU C 102 " --> pdb=" O   TYR C 117 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   TYR C 117 " --> pdb=" O   GLU C 102 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL C 104 " --> pdb=" O   LYS C 115 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 133 through 134
      removed outlier: 6.392A  pdb=" N   VAL C 133 " --> pdb=" O   GLU C 172 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 133 through 134
      removed outlier: 6.392A  pdb=" N   VAL C 133 " --> pdb=" O   GLU C 172 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LYS C 164 " --> pdb=" O   GLY C 153 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   GLY C 153 " --> pdb=" O   LYS C 164 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL C 166 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   LEU C 170 " --> pdb=" O   LEU C 147 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   LEU C 147 " --> pdb=" O   LEU C 170 " (cutoff:3.500A)
      removed outlier: 11.540A  pdb=" N   GLU C 172 " --> pdb=" O   SER C 145 " (cutoff:3.500A)
      removed outlier: 14.796A  pdb=" N   SER C 145 " --> pdb=" O   GLU C 172 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   LYS C 144 " --> pdb=" O   ARG C 223 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ILE C 224 " --> pdb=" O   ASN C 241 " (cutoff:3.500A)
      removed outlier: 10.190A  pdb=" N   ASN C 241 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 228
    Processing sheet with id=AB8, first strand: chain 'C' and resid 272 through 277
      removed outlier: 5.716A  pdb=" N   VAL C 353 " --> pdb=" O   ILE C 364 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   ILE C 364 " --> pdb=" O   VAL C 353 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 282 through 288
    Processing sheet with id=AC1, first strand: chain 'D' and resid 81 through 87
      removed outlier: 4.246A  pdb=" N   TYR D  72 " --> pdb=" O   GLY D  87 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   GLU D  69 " --> pdb=" O   SER D  65 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   SER D  65 " --> pdb=" O   GLU D  69 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   TYR D  71 " --> pdb=" O   THR D  63 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR D  63 " --> pdb=" O   TYR D  71 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU D  73 " --> pdb=" O   LYS D  61 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   LYS D  61 " --> pdb=" O   LEU D  73 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   LYS D  75 " --> pdb=" O   LEU D  59 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLU D 102 " --> pdb=" O   TYR D 117 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TYR D 117 " --> pdb=" O   GLU D 102 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL D 104 " --> pdb=" O   LYS D 115 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 133 through 134
      removed outlier: 6.392A  pdb=" N   VAL D 133 " --> pdb=" O   GLU D 172 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 133 through 134
      removed outlier: 6.392A  pdb=" N   VAL D 133 " --> pdb=" O   GLU D 172 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LYS D 164 " --> pdb=" O   GLY D 153 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   GLY D 153 " --> pdb=" O   LYS D 164 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   VAL D 166 " --> pdb=" O   LEU D 151 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   LEU D 170 " --> pdb=" O   LEU D 147 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   LEU D 147 " --> pdb=" O   LEU D 170 " (cutoff:3.500A)
      removed outlier: 11.540A  pdb=" N   GLU D 172 " --> pdb=" O   SER D 145 " (cutoff:3.500A)
      removed outlier: 14.796A  pdb=" N   SER D 145 " --> pdb=" O   GLU D 172 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   LYS D 144 " --> pdb=" O   ARG D 223 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ILE D 224 " --> pdb=" O   ASN D 241 " (cutoff:3.500A)
      removed outlier: 10.190A  pdb=" N   ASN D 241 " --> pdb=" O   ILE D 224 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 227 through 228
    Processing sheet with id=AC5, first strand: chain 'D' and resid 272 through 277
      removed outlier: 5.717A  pdb=" N   VAL D 353 " --> pdb=" O   ILE D 364 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   ILE D 364 " --> pdb=" O   VAL D 353 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 282 through 288

    416 hydrogen bonds defined for protein.
    1188 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      15 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3607
        1.34 -     1.46: 2568
        1.46 -     1.57: 5273
        1.57 -     1.69: 55
        1.69 -     1.81: 76
  Bond restraints: 11579
  Sorted by residual:
  bond pdb=" CZ  ARG C 313 "
       pdb=" NH2 ARG C 313 "
    ideal  model  delta    sigma   weight residual
    1.330  1.317  0.013 1.30e-02 5.92e+03 1.03e+00
  bond pdb=" CZ  ARG D 313 "
       pdb=" NH2 ARG D 313 "
    ideal  model  delta    sigma   weight residual
    1.330  1.317  0.013 1.30e-02 5.92e+03 1.03e+00
  bond pdb=" CZ  ARG B 313 "
       pdb=" NH2 ARG B 313 "
    ideal  model  delta    sigma   weight residual
    1.330  1.317  0.013 1.30e-02 5.92e+03 1.01e+00
  bond pdb=" C4'  DA Q  26 "
       pdb=" O4'  DA Q  26 "
    ideal  model  delta    sigma   weight residual
    1.450  1.430  0.020 2.00e-02 2.50e+03 9.93e-01
  bond pdb=" CZ  ARG A 313 "
       pdb=" NH2 ARG A 313 "
    ideal  model  delta    sigma   weight residual
    1.330  1.318  0.012 1.30e-02 5.92e+03 9.02e-01
  ... (remaining 11574 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 14956
        1.21 -     2.42: 668
        2.42 -     3.63: 100
        3.63 -     4.83: 16
        4.83 -     6.04: 4
  Bond angle restraints: 15744
  Sorted by residual:
  angle pdb=" C   ARG B 109 "
        pdb=" N   LYS B 110 "
        pdb=" CA  LYS B 110 "
      ideal   model   delta    sigma   weight residual
     121.54  127.58   -6.04 1.91e+00 2.74e-01 1.00e+01
  angle pdb=" C   ARG A 109 "
        pdb=" N   LYS A 110 "
        pdb=" CA  LYS A 110 "
      ideal   model   delta    sigma   weight residual
     121.54  127.56   -6.02 1.91e+00 2.74e-01 9.92e+00
  angle pdb=" C   ARG D 109 "
        pdb=" N   LYS D 110 "
        pdb=" CA  LYS D 110 "
      ideal   model   delta    sigma   weight residual
     121.54  127.55   -6.01 1.91e+00 2.74e-01 9.90e+00
  angle pdb=" C   ARG C 109 "
        pdb=" N   LYS C 110 "
        pdb=" CA  LYS C 110 "
      ideal   model   delta    sigma   weight residual
     121.54  127.55   -6.01 1.91e+00 2.74e-01 9.89e+00
  angle pdb=" C   ILE B  66 "
        pdb=" N   ASN B  67 "
        pdb=" CA  ASN B  67 "
      ideal   model   delta    sigma   weight residual
     122.82  126.13   -3.31 1.42e+00 4.96e-01 5.42e+00
  ... (remaining 15739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.29: 6569
       28.29 -    56.59: 406
       56.59 -    84.88: 25
       84.88 -   113.17: 4
      113.17 -   141.46: 1
  Dihedral angle restraints: 7005
    sinusoidal: 3077
      harmonic: 3928
  Sorted by residual:
  dihedral pdb=" C4'  DA Q  17 "
           pdb=" C3'  DA Q  17 "
           pdb=" O3'  DA Q  17 "
           pdb=" P    DA Q  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   78.54  141.46     1      3.50e+01 8.16e-04 1.40e+01
  dihedral pdb=" CA  ASN D 303 "
           pdb=" C   ASN D 303 "
           pdb=" N   GLU D 304 "
           pdb=" CA  GLU D 304 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  ASN C 303 "
           pdb=" C   ASN C 303 "
           pdb=" N   GLU C 304 "
           pdb=" CA  GLU C 304 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.40  -17.60     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 7002 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1053
       0.029 -    0.059: 426
       0.059 -    0.088: 167
       0.088 -    0.117: 99
       0.117 -    0.147: 27
  Chirality restraints: 1772
  Sorted by residual:
  chirality pdb=" CA  ILE B  83 "
            pdb=" N   ILE B  83 "
            pdb=" C   ILE B  83 "
            pdb=" CB  ILE B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.38e-01
  chirality pdb=" CA  ILE A  83 "
            pdb=" N   ILE A  83 "
            pdb=" C   ILE A  83 "
            pdb=" CB  ILE A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CA  ILE D  83 "
            pdb=" N   ILE D  83 "
            pdb=" C   ILE D  83 "
            pdb=" CB  ILE D  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  ... (remaining 1769 not shown)

  Planarity restraints: 1908
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 152 "   -0.007 2.00e-02 2.50e+03   6.35e-03 8.06e-01
        pdb=" CG  TYR B 152 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 152 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 152 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 152 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 152 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 152 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 152 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 152 "   -0.007 2.00e-02 2.50e+03   6.15e-03 7.58e-01
        pdb=" CG  TYR A 152 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 152 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 152 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 152 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 152 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 152 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 152 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 152 "    0.007 2.00e-02 2.50e+03   6.09e-03 7.42e-01
        pdb=" CG  TYR D 152 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 152 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 152 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 152 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 152 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 152 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D 152 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1905 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 172
        2.65 -     3.21: 10736
        3.21 -     3.78: 16580
        3.78 -     4.34: 23545
        4.34 -     4.90: 38894
  Nonbonded interactions: 89927
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 188 "
            pdb=" N   PHE D 189 "
     model   vdw
     2.091 3.120
  nonbonded pdb=" OD1 ASP C 188 "
            pdb=" N   PHE C 189 "
     model   vdw
     2.091 3.120
  nonbonded pdb=" OD1 ASP B 188 "
            pdb=" N   PHE B 189 "
     model   vdw
     2.091 3.120
  nonbonded pdb=" OD1 ASP A 188 "
            pdb=" N   PHE A 189 "
     model   vdw
     2.091 3.120
  nonbonded pdb=" NE2 GLN A 119 "
            pdb=" O   CYS A 120 "
     model   vdw
     2.241 3.120
  ... (remaining 89922 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.390
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  11579  Z= 0.172
  Angle     :  0.586   6.042  15744  Z= 0.343
  Chirality :  0.044   0.147   1772
  Planarity :  0.002   0.016   1908
  Dihedral  : 16.334 141.464   4469
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.23), residues: 1292
  helix:  0.22 (0.32), residues: 248
  sheet: -1.46 (0.21), residues: 504
  loop : -1.43 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 223 
 TYR   0.016   0.001   TYR B 152 
 PHE   0.014   0.001   PHE A 295 
 HIS   0.007   0.002   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (11579)
  covalent geometry    : angle       0.58634 (15744)
  hydrogen bonds       : bond        0.11464 (  416)
  hydrogen bonds       : angle       7.40723 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 TYR cc_start: 0.7437 (t80) cc_final: 0.6962 (t80)
REVERT: D   64 MET cc_start: 0.7941 (ptp) cc_final: 0.7729 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.0886
  time to fit residues: 32.8254
Evaluate side-chains
  179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    6.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 129 optimal weight:    5.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A  68 ASN
A 119 GLN
B  68 ASN
B 119 GLN
B 229 ASN
** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
C  91 GLN
C 119 GLN
C 232 ASN
C 270 ASN
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  68 ASN
** D  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 119 GLN
D 232 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.178726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.141659 restraints weight = 13179.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.141760 restraints weight = 12946.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.143362 restraints weight = 12313.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.143901 restraints weight = 9773.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.144834 restraints weight = 9431.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11579  Z= 0.201
  Angle     :  0.602   5.595  15744  Z= 0.344
  Chirality :  0.046   0.168   1772
  Planarity :  0.003   0.034   1908
  Dihedral  : 14.357 139.120   1825
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.77 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.23), residues: 1292
  helix:  0.45 (0.32), residues: 252
  sheet: -1.55 (0.21), residues: 528
  loop : -1.29 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 286 
 TYR   0.021   0.001   TYR D 299 
 PHE   0.021   0.002   PHE A 135 
 HIS   0.006   0.001   HIS D 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (11579)
  covalent geometry    : angle       0.60239 (15744)
  hydrogen bonds       : bond        0.03922 (  416)
  hydrogen bonds       : angle       6.16654 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  299 TYR cc_start: 0.8295 (p90) cc_final: 0.8090 (p90)
REVERT: A  313 ARG cc_start: 0.7291 (mtt90) cc_final: 0.7035 (mtt-85)
REVERT: A  377 GLU cc_start: 0.7981 (tp30) cc_final: 0.7727 (tp30)
REVERT: C   55 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8501 (tttt)
REVERT: C   72 TYR cc_start: 0.7727 (m-10) cc_final: 0.7514 (m-10)
REVERT: C  190 LYS cc_start: 0.8006 (ptpp) cc_final: 0.7747 (ptpp)
REVERT: C  349 ASP cc_start: 0.7461 (m-30) cc_final: 0.7206 (m-30)
REVERT: D   68 ASN cc_start: 0.7162 (m110) cc_final: 0.6916 (m110)
REVERT: D  190 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7610 (ptpp)
  outliers start: 18
  outliers final: 13
  residues processed: 212
  average time/residue: 0.0974
  time to fit residues: 30.7227
Evaluate side-chains
  183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  373 ASP
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   90 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 121 optimal weight:    0.8980
   chunk 71 optimal weight:    9.9990
   chunk 62 optimal weight:    0.1980
   chunk 0 optimal weight:   30.0000
   chunk 75 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A 316 ASN
B 229 ASN
** C  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 232 ASN
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.185305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.148647 restraints weight = 13109.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.149546 restraints weight = 11993.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.151082 restraints weight = 11460.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.151569 restraints weight = 9096.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.152013 restraints weight = 9252.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11579  Z= 0.113
  Angle     :  0.497   6.210  15744  Z= 0.287
  Chirality :  0.043   0.144   1772
  Planarity :  0.002   0.015   1908
  Dihedral  : 15.044 135.934   1825
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 15.16 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.23), residues: 1292
  helix:  0.88 (0.33), residues: 252
  sheet: -1.26 (0.21), residues: 536
  loop : -1.04 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 223 
 TYR   0.025   0.001   TYR D 256 
 PHE   0.021   0.001   PHE A 258 
 HIS   0.006   0.001   HIS C 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (11579)
  covalent geometry    : angle       0.49744 (15744)
  hydrogen bonds       : bond        0.03057 (  416)
  hydrogen bonds       : angle       5.45496 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 223
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLN cc_start: 0.7627 (tt0) cc_final: 0.7419 (tt0)
REVERT: A   72 TYR cc_start: 0.8108 (m-80) cc_final: 0.7900 (m-10)
REVERT: A  149 LYS cc_start: 0.8209 (tttp) cc_final: 0.7789 (tttp)
REVERT: A  377 GLU cc_start: 0.7909 (tp30) cc_final: 0.7645 (tp30)
REVERT: B  173 ASP cc_start: 0.7689 (p0) cc_final: 0.7462 (p0)
REVERT: B  377 GLU cc_start: 0.8120 (tp30) cc_final: 0.7798 (tp30)
REVERT: C  117 TYR cc_start: 0.8127 (p90) cc_final: 0.7864 (p90)
REVERT: C  349 ASP cc_start: 0.7452 (m-30) cc_final: 0.7172 (m-30)
  outliers start: 16
  outliers final: 8
  residues processed: 230
  average time/residue: 0.1027
  time to fit residues: 34.3282
Evaluate side-chains
  199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 191
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain C residue  253 MET
Chi-restraints excluded: chain D residue   62 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 52 optimal weight:   20.0000
   chunk 21 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 111 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A  79 ASN
A 316 ASN
B 228 HIS
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  68 ASN
** D  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 232 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.176472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.140069 restraints weight = 13338.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.139783 restraints weight = 14746.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.141488 restraints weight = 13710.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.142317 restraints weight = 10618.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.143264 restraints weight = 9957.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  11579  Z= 0.246
  Angle     :  0.613   8.633  15744  Z= 0.343
  Chirality :  0.045   0.167   1772
  Planarity :  0.003   0.025   1908
  Dihedral  : 15.180 139.033   1825
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.94 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.23), residues: 1292
  helix:  0.63 (0.31), residues: 248
  sheet: -1.46 (0.24), residues: 464
  loop : -1.08 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 313 
 TYR   0.017   0.002   TYR B 157 
 PHE   0.027   0.002   PHE B 295 
 HIS   0.005   0.001   HIS D 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 (11579)
  covalent geometry    : angle       0.61281 (15744)
  hydrogen bonds       : bond        0.03844 (  416)
  hydrogen bonds       : angle       5.87149 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 186
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 TYR cc_start: 0.7309 (t80) cc_final: 0.7093 (t80)
REVERT: A  157 TYR cc_start: 0.7346 (t80) cc_final: 0.7109 (t80)
REVERT: A  377 GLU cc_start: 0.7994 (tp30) cc_final: 0.7776 (tp30)
REVERT: C  156 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8242 (mm)
REVERT: C  232 ASN cc_start: 0.7791 (t0) cc_final: 0.7586 (p0)
REVERT: C  342 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7295 (tm-30)
REVERT: C  349 ASP cc_start: 0.7421 (m-30) cc_final: 0.7189 (m-30)
REVERT: D  190 LYS cc_start: 0.7890 (ptpp) cc_final: 0.7610 (ptpp)
  outliers start: 32
  outliers final: 20
  residues processed: 203
  average time/residue: 0.1016
  time to fit residues: 30.3307
Evaluate side-chains
  190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  228 HIS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue  156 ILE
Chi-restraints excluded: chain C residue  253 MET
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain C residue  339 SER
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  200 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 79 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 128 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0370
   chunk 66 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.7860

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A  67 ASN
A  79 ASN
A 316 ASN
** C  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 232 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.184217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.148393 restraints weight = 12977.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147383 restraints weight = 12540.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.149287 restraints weight = 12070.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.149894 restraints weight = 9642.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.150491 restraints weight = 9824.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11579  Z= 0.111
  Angle     :  0.500   7.870  15744  Z= 0.283
  Chirality :  0.043   0.139   1772
  Planarity :  0.002   0.014   1908
  Dihedral  : 15.068 135.687   1825
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 18.95 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.23), residues: 1292
  helix:  1.02 (0.32), residues: 252
  sheet: -1.21 (0.23), residues: 476
  loop : -0.97 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 268 
 TYR   0.017   0.001   TYR D 299 
 PHE   0.020   0.001   PHE A 258 
 HIS   0.005   0.001   HIS C 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (11579)
  covalent geometry    : angle       0.50046 (15744)
  hydrogen bonds       : bond        0.03031 (  416)
  hydrogen bonds       : angle       5.25506 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 206
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7630 (pt0)
REVERT: A  209 ASP cc_start: 0.7106 (t0) cc_final: 0.6836 (t0)
REVERT: A  234 LYS cc_start: 0.8343 (mttm) cc_final: 0.8140 (mttm)
REVERT: C   72 TYR cc_start: 0.7556 (m-10) cc_final: 0.7311 (m-80)
REVERT: C  117 TYR cc_start: 0.8245 (p90) cc_final: 0.7962 (p90)
REVERT: C  232 ASN cc_start: 0.7781 (t0) cc_final: 0.7462 (p0)
REVERT: C  247 LEU cc_start: 0.7227 (tt) cc_final: 0.6973 (tt)
REVERT: D  331 ASP cc_start: 0.8366 (t0) cc_final: 0.8013 (t0)
  outliers start: 21
  outliers final: 10
  residues processed: 216
  average time/residue: 0.1026
  time to fit residues: 32.4317
Evaluate side-chains
  190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  186 MET
Chi-restraints excluded: chain B residue  228 HIS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  200 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 129 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 114 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A  79 ASN
A 316 ASN
B 228 HIS
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.167661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.129644 restraints weight = 13636.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.128752 restraints weight = 14777.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.130432 restraints weight = 13780.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.131271 restraints weight = 10924.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.132193 restraints weight = 10298.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11579  Z= 0.226
  Angle     :  0.592   6.870  15744  Z= 0.331
  Chirality :  0.044   0.168   1772
  Planarity :  0.003   0.022   1908
  Dihedral  : 15.248 139.082   1825
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.68 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.23), residues: 1292
  helix:  1.00 (0.32), residues: 248
  sheet: -1.52 (0.24), residues: 436
  loop : -0.91 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 286 
 TYR   0.018   0.002   TYR B 157 
 PHE   0.023   0.002   PHE B 295 
 HIS   0.005   0.001   HIS D 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 (11579)
  covalent geometry    : angle       0.59190 (15744)
  hydrogen bonds       : bond        0.03709 (  416)
  hydrogen bonds       : angle       5.66495 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 180
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 ASP cc_start: 0.7536 (t0) cc_final: 0.7332 (t0)
REVERT: B  106 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7162 (pp30)
REVERT: C  232 ASN cc_start: 0.7918 (t0) cc_final: 0.7524 (p0)
REVERT: D  106 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7505 (pp30)
  outliers start: 33
  outliers final: 18
  residues processed: 201
  average time/residue: 0.0994
  time to fit residues: 29.4840
Evaluate side-chains
  181 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  228 HIS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  339 SER
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  106 GLN
Chi-restraints excluded: chain D residue  200 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 119 optimal weight:    4.9990
   chunk 101 optimal weight:   10.0000
   chunk 92 optimal weight:    0.8980
   chunk 44 optimal weight:   20.0000
   chunk 98 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A  79 ASN
A 106 GLN
A 316 ASN
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.179938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.141763 restraints weight = 13235.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.142237 restraints weight = 12145.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.143786 restraints weight = 11349.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.144353 restraints weight = 9105.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.145258 restraints weight = 8847.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11579  Z= 0.136
  Angle     :  0.527   7.568  15744  Z= 0.296
  Chirality :  0.043   0.161   1772
  Planarity :  0.002   0.026   1908
  Dihedral  : 15.081 137.540   1825
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 19.60 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.23), residues: 1292
  helix:  1.17 (0.33), residues: 252
  sheet: -1.21 (0.23), residues: 476
  loop : -0.93 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 313 
 TYR   0.015   0.001   TYR D 299 
 PHE   0.017   0.001   PHE A 258 
 HIS   0.005   0.001   HIS C 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11579)
  covalent geometry    : angle       0.52673 (15744)
  hydrogen bonds       : bond        0.03200 (  416)
  hydrogen bonds       : angle       5.36342 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 184
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  106 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7075 (pp30)
REVERT: C   72 TYR cc_start: 0.7646 (m-10) cc_final: 0.7388 (m-80)
REVERT: C  117 TYR cc_start: 0.8397 (p90) cc_final: 0.8160 (p90)
REVERT: C  232 ASN cc_start: 0.7861 (t0) cc_final: 0.7448 (p0)
REVERT: C  349 ASP cc_start: 0.7492 (m-30) cc_final: 0.7202 (m-30)
REVERT: D  106 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7877 (pt0)
  outliers start: 29
  outliers final: 19
  residues processed: 202
  average time/residue: 0.0905
  time to fit residues: 27.7818
Evaluate side-chains
  187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  228 HIS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  106 GLN
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  339 SER
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue  106 GLN
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  273 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 125 optimal weight:    4.9990
   chunk 52 optimal weight:   20.0000
   chunk 27 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 95 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A 106 GLN
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 316 ASN
** B  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 HIS
C  67 ASN
** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.163528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.125292 restraints weight = 13722.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.124998 restraints weight = 15596.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.126573 restraints weight = 14237.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.127793 restraints weight = 11154.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.128553 restraints weight = 10368.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.064  11579  Z= 0.364
  Angle     :  0.733   8.488  15744  Z= 0.401
  Chirality :  0.048   0.175   1772
  Planarity :  0.004   0.039   1908
  Dihedral  : 15.441 142.338   1825
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.68 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.23), residues: 1292
  helix:  0.63 (0.31), residues: 248
  sheet: -1.47 (0.24), residues: 464
  loop : -1.19 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 286 
 TYR   0.020   0.002   TYR B 157 
 PHE   0.032   0.002   PHE D 295 
 HIS   0.005   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00854 (11579)
  covalent geometry    : angle       0.73293 (15744)
  hydrogen bonds       : bond        0.04517 (  416)
  hydrogen bonds       : angle       6.21578 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 161
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7049 (tt0)
REVERT: C  156 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8295 (mm)
REVERT: C  232 ASN cc_start: 0.7965 (t0) cc_final: 0.7609 (p0)
REVERT: C  349 ASP cc_start: 0.7598 (m-30) cc_final: 0.7277 (m-30)
REVERT: D  106 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7962 (pt0)
  outliers start: 39
  outliers final: 25
  residues processed: 188
  average time/residue: 0.0918
  time to fit residues: 26.2334
Evaluate side-chains
  179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  228 HIS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  156 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain C residue  339 SER
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  106 GLN
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  273 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 128 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   chunk 44 optimal weight:    8.9990
   chunk 84 optimal weight:    6.9990
   chunk 114 optimal weight:    3.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A 106 GLN
** B  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 106 GLN
C  67 ASN
** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.172121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.132982 restraints weight = 13311.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.131720 restraints weight = 13815.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.133622 restraints weight = 12874.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.135970 restraints weight = 10081.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.136626 restraints weight = 9359.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  11579  Z= 0.259
  Angle     :  0.652   7.772  15744  Z= 0.362
  Chirality :  0.046   0.163   1772
  Planarity :  0.003   0.035   1908
  Dihedral  : 15.369 141.256   1825
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.69 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.23), residues: 1292
  helix:  0.79 (0.32), residues: 248
  sheet: -1.66 (0.25), residues: 420
  loop : -1.24 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 313 
 TYR   0.018   0.002   TYR B 157 
 PHE   0.024   0.002   PHE A 135 
 HIS   0.004   0.001   HIS D 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 (11579)
  covalent geometry    : angle       0.65219 (15744)
  hydrogen bonds       : bond        0.04007 (  416)
  hydrogen bonds       : angle       6.00829 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  232 ASN cc_start: 0.7790 (t0) cc_final: 0.7533 (p0)
REVERT: C  246 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7192 (mtm-85)
REVERT: C  349 ASP cc_start: 0.7523 (m-30) cc_final: 0.7221 (m-30)
REVERT: D  106 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7972 (pt0)
  outliers start: 31
  outliers final: 23
  residues processed: 166
  average time/residue: 0.0961
  time to fit residues: 23.9745
Evaluate side-chains
  167 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  246 ARG
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain C residue  339 SER
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  106 GLN
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  273 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 121 optimal weight:    5.9990
   chunk 120 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A 106 GLN
** B  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 106 GLN
B 228 HIS
C  67 ASN
** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.177269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.138787 restraints weight = 13248.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.138157 restraints weight = 12137.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.140000 restraints weight = 11756.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.140705 restraints weight = 9350.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.141336 restraints weight = 9287.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.3230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11579  Z= 0.127
  Angle     :  0.551   7.958  15744  Z= 0.309
  Chirality :  0.044   0.158   1772
  Planarity :  0.003   0.051   1908
  Dihedral  : 15.119 138.412   1825
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 22.18 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.23), residues: 1292
  helix:  1.19 (0.33), residues: 248
  sheet: -1.21 (0.24), residues: 476
  loop : -0.98 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 313 
 TYR   0.022   0.001   TYR A 107 
 PHE   0.018   0.001   PHE A 135 
 HIS   0.006   0.001   HIS C 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11579)
  covalent geometry    : angle       0.55107 (15744)
  hydrogen bonds       : bond        0.03281 (  416)
  hydrogen bonds       : angle       5.47327 ( 1188)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  257 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6607 (mp0)
REVERT: B   69 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6766 (tt0)
REVERT: C  232 ASN cc_start: 0.7874 (t0) cc_final: 0.7502 (p0)
REVERT: D  106 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7656 (pt0)
  outliers start: 21
  outliers final: 17
  residues processed: 198
  average time/residue: 0.0986
  time to fit residues: 28.9825
Evaluate side-chains
  186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  228 HIS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  106 GLN
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  273 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 53 optimal weight:    0.4980
   chunk 77 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 84 optimal weight:    8.9990
   chunk 120 optimal weight:    6.9990
   chunk 76 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 108 optimal weight:    9.9990
   overall best weight:    3.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
B 106 GLN
** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.180350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.140977 restraints weight = 13204.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.140602 restraints weight = 11934.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.142491 restraints weight = 11478.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.143190 restraints weight = 9143.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.143714 restraints weight = 9094.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.250  11579  Z= 0.362
  Angle     :  1.138  59.187  15744  Z= 0.740
  Chirality :  0.052   0.831   1772
  Planarity :  0.007   0.186   1908
  Dihedral  : 15.137 138.446   1825
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.94 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.24), residues: 1292
  helix:  1.18 (0.33), residues: 248
  sheet: -1.22 (0.24), residues: 476
  loop : -0.97 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 313 
 TYR   0.020   0.001   TYR A 107 
 PHE   0.020   0.001   PHE A 135 
 HIS   0.150   0.009   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 (11579)
  covalent geometry    : angle       1.13819 (15744)
  hydrogen bonds       : bond        0.03352 (  416)
  hydrogen bonds       : angle       5.47437 ( 1188)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1741.97 seconds
wall clock time: 31 minutes 20.45 seconds (1880.45 seconds total)