Starting phenix.real_space_refine
on Wed Sep 25 14:55:05 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/09_2024/7k9l_22754.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/09_2024/7k9l_22754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/09_2024/7k9l_22754.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/09_2024/7k9l_22754.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/09_2024/7k9l_22754.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/09_2024/7k9l_22754.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    1980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.42, per 1000 atoms: 0.52
  Number of scatterers: 10472
  At special positions: 0
  Unit cell: (97.37, 80.99, 106.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1980      8.00
     N    1860      7.00
     C    6588      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: 2.49
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      56.0% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 35 through 47
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.592A  pdb=" N   LEU B  83 " --> pdb=" O   PHE B  79 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   TYR B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 79 through 84'
    Processing helix  chain 'B' and resid 92 through 100
      removed outlier: 3.866A  pdb=" N   LYS B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 181
      removed outlier: 3.870A  pdb=" N   ASN B 180 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 219
      removed outlier: 3.620A  pdb=" N   CYS B 201 " --> pdb=" O   ASP B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 244 through 258
    Processing helix  chain 'B' and resid 275 through 288
      removed outlier: 4.094A  pdb=" N   SER B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 3.738A  pdb=" N   GLN B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY B 314 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 340
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 35 through 47
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.593A  pdb=" N   LEU A  83 " --> pdb=" O   PHE A  79 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TYR A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 79 through 84'
    Processing helix  chain 'A' and resid 92 through 100
      removed outlier: 3.865A  pdb=" N   LYS A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 181
      removed outlier: 3.870A  pdb=" N   ASN A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 219
      removed outlier: 3.619A  pdb=" N   CYS A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 244 through 258
    Processing helix  chain 'A' and resid 275 through 288
      removed outlier: 4.093A  pdb=" N   SER A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 314
      removed outlier: 3.740A  pdb=" N   GLN A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   ALA A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 319 through 340
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 35 through 47
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 79 through 84
      removed outlier: 3.593A  pdb=" N   LEU C  83 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TYR C  84 " --> pdb=" O   HIS C  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 79 through 84'
    Processing helix  chain 'C' and resid 92 through 100
      removed outlier: 3.867A  pdb=" N   LYS C 100 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 181
      removed outlier: 3.870A  pdb=" N   ASN C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 219
      removed outlier: 3.620A  pdb=" N   CYS C 201 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 244 through 258
    Processing helix  chain 'C' and resid 275 through 288
      removed outlier: 4.093A  pdb=" N   SER C 280 " --> pdb=" O   GLU C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 3.738A  pdb=" N   GLN C 306 " --> pdb=" O   GLY C 302 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY C 314 " --> pdb=" O   LEU C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 319 through 340
    Processing helix  chain 'D' and resid 8 through 23
    Processing helix  chain 'D' and resid 35 through 47
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 70
    Processing helix  chain 'D' and resid 79 through 84
      removed outlier: 3.593A  pdb=" N   LEU D  83 " --> pdb=" O   PHE D  79 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TYR D  84 " --> pdb=" O   HIS D  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 79 through 84'
    Processing helix  chain 'D' and resid 92 through 100
      removed outlier: 3.866A  pdb=" N   LYS D 100 " --> pdb=" O   VAL D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 181
      removed outlier: 3.870A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 219
      removed outlier: 3.621A  pdb=" N   CYS D 201 " --> pdb=" O   ASP D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 244 through 258
    Processing helix  chain 'D' and resid 275 through 288
      removed outlier: 4.094A  pdb=" N   SER D 280 " --> pdb=" O   GLU D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 3.739A  pdb=" N   GLN D 306 " --> pdb=" O   GLY D 302 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   ALA D 309 " --> pdb=" O   LEU D 305 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY D 314 " --> pdb=" O   LEU D 310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 319 through 340
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 32
      removed outlier: 6.147A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   ILE B  77 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU B  30 " --> pdb=" O   ILE B  77 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLY B  74 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   GLY B 105 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU B  78 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE B 106 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B 187 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA B  31 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32
      removed outlier: 6.147A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ILE A  77 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU A  30 " --> pdb=" O   ILE A  77 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLY A  74 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   GLY A 105 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   LYS A 107 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU A  78 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU A 187 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A  31 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32
      removed outlier: 6.148A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  75 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ILE C  77 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU C  30 " --> pdb=" O   ILE C  77 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLY C  74 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   GLY C 105 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   LYS C 107 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU C  78 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   VAL C 104 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   ALA C 145 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE C 106 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU C 187 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA C  31 " --> pdb=" O   TYR C 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
      removed outlier: 6.148A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ILE D  77 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU D  30 " --> pdb=" O   ILE D  77 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLY D  74 " --> pdb=" O   VAL D 103 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   GLY D 105 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D 105 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   LYS D 107 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU D  78 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   VAL D 104 " --> pdb=" O   ASP D 143 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   ALA D 145 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE D 106 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU D 187 " --> pdb=" O   TRP D 147 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA D  31 " --> pdb=" O   TYR D 301 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    564 hydrogen bonds defined for protein.
    1632 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.13

  Time building geometry restraints manager: 2.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3395
        1.34 -     1.45: 1572
        1.45 -     1.57: 5645
        1.57 -     1.69: 4
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" C   HIS A 220 "
       pdb=" N   ILE A 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.305  0.029 1.29e-02 6.01e+03 5.11e+00
  bond pdb=" C   HIS C 220 "
       pdb=" N   ILE C 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.305  0.029 1.29e-02 6.01e+03 4.88e+00
  bond pdb=" C   HIS B 220 "
       pdb=" N   ILE B 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.306  0.028 1.29e-02 6.01e+03 4.79e+00
  bond pdb=" C   HIS D 220 "
       pdb=" N   ILE D 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.306  0.028 1.29e-02 6.01e+03 4.67e+00
  bond pdb=" CB  GLU B  52 "
       pdb=" CG  GLU B  52 "
    ideal  model  delta    sigma   weight residual
    1.520  1.580 -0.060 3.00e-02 1.11e+03 4.05e+00
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.58: 14241
        3.58 -     7.16: 191
        7.16 -    10.74: 20
       10.74 -    14.32: 4
       14.32 -    17.90: 8
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" CA  LEU A 320 "
        pdb=" CB  LEU A 320 "
        pdb=" CG  LEU A 320 "
      ideal   model   delta    sigma   weight residual
     116.30  134.20  -17.90 3.50e+00 8.16e-02 2.62e+01
  angle pdb=" CA  LEU B 320 "
        pdb=" CB  LEU B 320 "
        pdb=" CG  LEU B 320 "
      ideal   model   delta    sigma   weight residual
     116.30  134.20  -17.90 3.50e+00 8.16e-02 2.62e+01
  angle pdb=" CA  LEU C 320 "
        pdb=" CB  LEU C 320 "
        pdb=" CG  LEU C 320 "
      ideal   model   delta    sigma   weight residual
     116.30  134.19  -17.89 3.50e+00 8.16e-02 2.61e+01
  angle pdb=" CA  LEU D 320 "
        pdb=" CB  LEU D 320 "
        pdb=" CG  LEU D 320 "
      ideal   model   delta    sigma   weight residual
     116.30  134.18  -17.88 3.50e+00 8.16e-02 2.61e+01
  angle pdb=" CA  LEU A  78 "
        pdb=" CB  LEU A  78 "
        pdb=" CG  LEU A  78 "
      ideal   model   delta    sigma   weight residual
     116.30  132.68  -16.38 3.50e+00 8.16e-02 2.19e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 5843
       17.34 -    34.68: 485
       34.68 -    52.03: 112
       52.03 -    69.37: 48
       69.37 -    86.71: 16
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  ASN A 319 "
           pdb=" C   ASN A 319 "
           pdb=" N   LEU A 320 "
           pdb=" CA  LEU A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.93  -29.07     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  ASN B 319 "
           pdb=" C   ASN B 319 "
           pdb=" N   LEU B 320 "
           pdb=" CA  LEU B 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.94  -29.06     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  ASN D 319 "
           pdb=" C   ASN D 319 "
           pdb=" N   LEU D 320 "
           pdb=" CA  LEU D 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.94  -29.06     0      5.00e+00 4.00e-02 3.38e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1372
       0.080 -    0.159: 223
       0.159 -    0.239: 35
       0.239 -    0.318: 10
       0.318 -    0.398: 4
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CB  THR C 205 "
            pdb=" CA  THR C 205 "
            pdb=" OG1 THR C 205 "
            pdb=" CG2 THR C 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.15    0.40 2.00e-01 2.50e+01 3.96e+00
  chirality pdb=" CB  THR D 205 "
            pdb=" CA  THR D 205 "
            pdb=" OG1 THR D 205 "
            pdb=" CG2 THR D 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.15    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CB  THR B 205 "
            pdb=" CA  THR B 205 "
            pdb=" OG1 THR B 205 "
            pdb=" CG2 THR B 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.16    0.40 2.00e-01 2.50e+01 3.92e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 329 "    0.016 2.00e-02 2.50e+03   3.14e-02 9.84e+00
        pdb=" C   LYS B 329 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   LYS B 329 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ARG B 330 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 329 "    0.016 2.00e-02 2.50e+03   3.14e-02 9.83e+00
        pdb=" C   LYS C 329 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   LYS C 329 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ARG C 330 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 329 "   -0.016 2.00e-02 2.50e+03   3.13e-02 9.80e+00
        pdb=" C   LYS D 329 "    0.054 2.00e-02 2.50e+03
        pdb=" O   LYS D 329 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ARG D 330 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2647
        2.78 -     3.31: 10217
        3.31 -     3.84: 18354
        3.84 -     4.37: 20655
        4.37 -     4.90: 34745
  Nonbonded interactions: 86618
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 269 "
            pdb=" OG  SER B 300 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   PHE D 269 "
            pdb=" OG  SER D 300 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   PHE C 269 "
            pdb=" OG  SER C 300 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   PHE A 269 "
            pdb=" OG  SER A 300 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   GLN A  60 "
            pdb=" OG1 THR A  64 "
     model   vdw
     2.272 3.040
  ... (remaining 86613 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
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}
Set refine NCS operators
  NCS operators will be refined.
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:             1.640
  Set stop_for_unknowns flag:              0.010
  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:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     24.690
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
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      :  0.007   0.065  10672  Z= 0.482
  Angle     :  1.189  17.902  14464  Z= 0.639
  Chirality :  0.066   0.398   1644
  Planarity :  0.008   0.048   1880
  Dihedral  : 15.276  86.709   3984
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 10.79 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.19), residues: 1364
  helix: -0.95 (0.16), residues: 652
  sheet: -2.05 (0.33), residues: 196
  loop : -1.22 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A 295 
 HIS   0.007   0.002   HIS B 219 
 PHE   0.013   0.003   PHE C  93 
 TYR   0.021   0.004   TYR B  58 
 ARG   0.009   0.001   ARG D  42 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8999 (mttt) cc_final: 0.8664 (mmtp)
REVERT: A   21 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8633 (mtp85)
REVERT: A   61 LEU cc_start: 0.8986 (mt) cc_final: 0.8585 (mt)
REVERT: A   81 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8786 (pp20)
REVERT: A   89 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6445 (p0)
REVERT: A  104 VAL cc_start: 0.8846 (t) cc_final: 0.8534 (t)
REVERT: A  113 VAL cc_start: 0.9303 (t) cc_final: 0.8977 (t)
REVERT: A  115 LEU cc_start: 0.9133 (mt) cc_final: 0.8883 (mm)
REVERT: A  122 THR cc_start: 0.8325 (t) cc_final: 0.7883 (t)
REVERT: A  144 PHE cc_start: 0.8375 (p90) cc_final: 0.8166 (p90)
REVERT: A  149 CYS cc_start: 0.8233 (p) cc_final: 0.7731 (t)
REVERT: A  152 LYS cc_start: 0.8278 (pttp) cc_final: 0.7948 (pttp)
REVERT: A  178 GLN cc_start: 0.9144 (mt0) cc_final: 0.8876 (mt0)
REVERT: A  191 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8884 (tp)
REVERT: A  199 LYS cc_start: 0.9384 (mtmm) cc_final: 0.8929 (mmmt)
REVERT: A  203 TYR cc_start: 0.8758 (t80) cc_final: 0.8533 (t80)
REVERT: A  242 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8628 (tttm)
REVERT: A  247 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8740 (mt-10)
REVERT: A  254 THR cc_start: 0.8950 (p) cc_final: 0.8730 (t)
REVERT: A  282 ASN cc_start: 0.9117 (m-40) cc_final: 0.8915 (m-40)
REVERT: A  284 ASN cc_start: 0.8287 (t0) cc_final: 0.7532 (t0)
REVERT: A  291 LEU cc_start: 0.8450 (mt) cc_final: 0.8099 (tp)
REVERT: A  292 LEU cc_start: 0.8655 (mm) cc_final: 0.8436 (mm)
REVERT: A  305 LEU cc_start: 0.9363 (tp) cc_final: 0.9052 (tp)
REVERT: A  310 LEU cc_start: 0.9112 (tp) cc_final: 0.8849 (mt)
REVERT: A  313 TRP cc_start: 0.7413 (t60) cc_final: 0.6422 (t60)
  outliers start: 11
  outliers final: 3
  residues processed: 158
  average time/residue: 0.1717
  time to fit residues: 30.8488
Evaluate side-chains
  116 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0870
   chunk 123 optimal weight:    3.9990
   overall best weight:    3.8166
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D  60 GLN
D 119 ASN
D 125 GLN
D 237 HIS
D 284 ASN
D 287 ASN
** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 324 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  10672  Z= 0.359
  Angle     :  0.755   7.537  14464  Z= 0.398
  Chirality :  0.045   0.150   1644
  Planarity :  0.009   0.134   1880
  Dihedral  :  5.657  24.908   1472
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  5.76 %
    Favored  : 92.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.21), residues: 1364
  helix:  0.64 (0.18), residues: 688
  sheet: -1.57 (0.32), residues: 220
  loop : -0.45 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP D 295 
 HIS   0.009   0.002   HIS A 219 
 PHE   0.023   0.003   PHE A  93 
 TYR   0.013   0.002   TYR B 327 
 ARG   0.006   0.001   ARG A 257 

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    7 LEU cc_start: 0.9054 (mt) cc_final: 0.8431 (mt)
REVERT: D   14 GLU cc_start: 0.8905 (mp0) cc_final: 0.8642 (mm-30)
REVERT: D   61 LEU cc_start: 0.8842 (mt) cc_final: 0.8095 (mp)
REVERT: D   72 CYS cc_start: 0.9035 (m) cc_final: 0.8828 (m)
REVERT: D  104 VAL cc_start: 0.8751 (t) cc_final: 0.8433 (t)
REVERT: D  128 ASP cc_start: 0.7302 (m-30) cc_final: 0.7038 (p0)
REVERT: D  138 LYS cc_start: 0.8424 (tptt) cc_final: 0.7941 (ttmt)
REVERT: D  178 GLN cc_start: 0.9175 (mt0) cc_final: 0.8874 (mt0)
REVERT: D  195 ASP cc_start: 0.8884 (p0) cc_final: 0.8000 (t0)
REVERT: D  214 LYS cc_start: 0.9302 (tmtt) cc_final: 0.9094 (tptp)
REVERT: D  248 ILE cc_start: 0.9462 (mt) cc_final: 0.9255 (tt)
REVERT: D  284 ASN cc_start: 0.8292 (t0) cc_final: 0.7585 (t0)
REVERT: D  305 LEU cc_start: 0.9464 (tp) cc_final: 0.9163 (tp)
REVERT: D  313 TRP cc_start: 0.7603 (t60) cc_final: 0.6388 (t60)
REVERT: D  326 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8754 (mm-30)
REVERT: D  329 LYS cc_start: 0.8794 (mttp) cc_final: 0.8279 (mttm)
REVERT: D  332 LEU cc_start: 0.8416 (tp) cc_final: 0.8174 (pp)
  outliers start: 4
  outliers final: 1
  residues processed: 131
  average time/residue: 0.1585
  time to fit residues: 24.0054
Evaluate side-chains
  87 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 102 optimal weight:    8.9990
   chunk 84 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 123 optimal weight:    4.9990
   chunk 133 optimal weight:    9.9990
   chunk 110 optimal weight:    0.2980
   chunk 122 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 99 optimal weight:    9.9990
   overall best weight:    3.1786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B  80 HIS
B 287 ASN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  10672  Z= 0.303
  Angle     :  0.692   7.694  14464  Z= 0.355
  Chirality :  0.043   0.139   1644
  Planarity :  0.005   0.055   1880
  Dihedral  :  5.226  17.672   1472
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 18.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.96 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.22), residues: 1364
  helix:  0.68 (0.18), residues: 688
  sheet: -1.14 (0.37), residues: 172
  loop : -0.55 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 295 
 HIS   0.008   0.001   HIS B 219 
 PHE   0.009   0.002   PHE C 299 
 TYR   0.011   0.002   TYR C 327 
 ARG   0.007   0.001   ARG C 257 

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 LEU cc_start: 0.8055 (tt) cc_final: 0.7812 (tp)
REVERT: B   61 LEU cc_start: 0.8937 (mt) cc_final: 0.8657 (mt)
REVERT: B   98 LYS cc_start: 0.8468 (tttt) cc_final: 0.8261 (tptm)
REVERT: B  128 ASP cc_start: 0.6754 (m-30) cc_final: 0.6044 (p0)
REVERT: B  138 LYS cc_start: 0.8455 (tptt) cc_final: 0.8027 (tttt)
REVERT: B  178 GLN cc_start: 0.8998 (mt0) cc_final: 0.8768 (mt0)
REVERT: B  195 ASP cc_start: 0.8935 (p0) cc_final: 0.8181 (t0)
REVERT: B  214 LYS cc_start: 0.9289 (tmtt) cc_final: 0.9078 (tptp)
REVERT: B  250 MET cc_start: 0.9276 (ttp) cc_final: 0.9073 (tmm)
REVERT: B  276 GLU cc_start: 0.7834 (pm20) cc_final: 0.7332 (pm20)
REVERT: B  282 ASN cc_start: 0.9236 (m-40) cc_final: 0.8903 (m-40)
REVERT: B  283 LEU cc_start: 0.9280 (tp) cc_final: 0.8965 (tp)
REVERT: B  284 ASN cc_start: 0.7933 (t0) cc_final: 0.7696 (m110)
REVERT: B  305 LEU cc_start: 0.9444 (tp) cc_final: 0.8850 (tp)
REVERT: B  332 LEU cc_start: 0.8356 (tp) cc_final: 0.8123 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1464
  time to fit residues: 20.6993
Evaluate side-chains
  91 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 83 optimal weight:    8.9990
   chunk 124 optimal weight:    0.0770
   chunk 131 optimal weight:    0.9980
   chunk 117 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 109 optimal weight:    0.0050
   overall best weight:    0.6154
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B  54 ASN
B 324 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.5085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10672  Z= 0.188
  Angle     :  0.621   7.375  14464  Z= 0.308
  Chirality :  0.043   0.159   1644
  Planarity :  0.005   0.056   1880
  Dihedral  :  4.725  17.653   1472
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.22), residues: 1364
  helix:  1.11 (0.18), residues: 704
  sheet: -1.25 (0.34), residues: 200
  loop : -0.40 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 295 
 HIS   0.004   0.001   HIS A 219 
 PHE   0.010   0.002   PHE A 144 
 TYR   0.010   0.001   TYR A 213 
 ARG   0.006   0.001   ARG C  42 

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 GLU cc_start: 0.9205 (pm20) cc_final: 0.8584 (mp0)
REVERT: B   11 GLN cc_start: 0.9575 (mt0) cc_final: 0.9298 (mt0)
REVERT: B   12 LYS cc_start: 0.9012 (mttt) cc_final: 0.8633 (mmtp)
REVERT: B   14 GLU cc_start: 0.9005 (mp0) cc_final: 0.8650 (mm-30)
REVERT: B   61 LEU cc_start: 0.8867 (mt) cc_final: 0.8217 (mt)
REVERT: B   81 GLU cc_start: 0.8947 (tp30) cc_final: 0.8689 (tm-30)
REVERT: B   99 SER cc_start: 0.8559 (p) cc_final: 0.8332 (p)
REVERT: B  138 LYS cc_start: 0.8428 (tptt) cc_final: 0.8055 (tttt)
REVERT: B  140 ASP cc_start: 0.8558 (m-30) cc_final: 0.8342 (m-30)
REVERT: B  144 PHE cc_start: 0.8445 (p90) cc_final: 0.8209 (p90)
REVERT: B  155 GLU cc_start: 0.8746 (mp0) cc_final: 0.8545 (mm-30)
REVERT: B  178 GLN cc_start: 0.8943 (mt0) cc_final: 0.8717 (mt0)
REVERT: B  195 ASP cc_start: 0.9015 (p0) cc_final: 0.8322 (t0)
REVERT: B  245 HIS cc_start: 0.8281 (m90) cc_final: 0.8009 (p-80)
REVERT: B  246 GLU cc_start: 0.9609 (mp0) cc_final: 0.9009 (mp0)
REVERT: B  250 MET cc_start: 0.9219 (ttp) cc_final: 0.8970 (tpp)
REVERT: B  276 GLU cc_start: 0.7922 (pm20) cc_final: 0.7501 (pm20)
REVERT: B  282 ASN cc_start: 0.9234 (m-40) cc_final: 0.8887 (m-40)
REVERT: B  283 LEU cc_start: 0.9300 (tp) cc_final: 0.9020 (tp)
REVERT: B  284 ASN cc_start: 0.8155 (t0) cc_final: 0.7936 (m110)
REVERT: B  305 LEU cc_start: 0.9409 (tp) cc_final: 0.9066 (tp)
REVERT: B  313 TRP cc_start: 0.7887 (t60) cc_final: 0.6827 (t60)
REVERT: B  325 GLU cc_start: 0.9073 (tp30) cc_final: 0.8788 (tp30)
REVERT: B  332 LEU cc_start: 0.8285 (tp) cc_final: 0.8027 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1495
  time to fit residues: 23.0024
Evaluate side-chains
  99 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 112 optimal weight:    0.0060
   chunk 90 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   chunk 117 optimal weight:   20.0000
   chunk 33 optimal weight:    7.9990
   chunk 44 optimal weight:    0.0270
   overall best weight:    0.9658
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
B  60 GLN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.5298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10672  Z= 0.190
  Angle     :  0.620   6.650  14464  Z= 0.310
  Chirality :  0.041   0.126   1644
  Planarity :  0.005   0.059   1880
  Dihedral  :  4.587  16.751   1472
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.60 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.22), residues: 1364
  helix:  1.30 (0.19), residues: 696
  sheet: -1.37 (0.33), residues: 200
  loop : -0.32 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 295 
 HIS   0.004   0.001   HIS B 219 
 PHE   0.011   0.002   PHE C 144 
 TYR   0.012   0.002   TYR A 137 
 ARG   0.007   0.001   ARG A  42 

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 GLU cc_start: 0.9034 (pm20) cc_final: 0.8833 (mp0)
REVERT: B   12 LYS cc_start: 0.9022 (mttt) cc_final: 0.8656 (mmtp)
REVERT: B   30 LEU cc_start: 0.7937 (tt) cc_final: 0.7678 (tp)
REVERT: B   61 LEU cc_start: 0.8758 (mt) cc_final: 0.8231 (mt)
REVERT: B   79 PHE cc_start: 0.8171 (t80) cc_final: 0.7926 (t80)
REVERT: B   81 GLU cc_start: 0.9092 (tp30) cc_final: 0.8628 (tm-30)
REVERT: B  138 LYS cc_start: 0.8438 (tptt) cc_final: 0.7879 (ttmt)
REVERT: B  140 ASP cc_start: 0.8576 (m-30) cc_final: 0.8300 (m-30)
REVERT: B  144 PHE cc_start: 0.8389 (p90) cc_final: 0.8180 (p90)
REVERT: B  178 GLN cc_start: 0.8888 (mt0) cc_final: 0.8678 (mt0)
REVERT: B  195 ASP cc_start: 0.9010 (p0) cc_final: 0.8286 (t0)
REVERT: B  245 HIS cc_start: 0.8398 (m90) cc_final: 0.8123 (p-80)
REVERT: B  246 GLU cc_start: 0.9619 (mp0) cc_final: 0.9087 (pm20)
REVERT: B  250 MET cc_start: 0.9192 (ttp) cc_final: 0.8968 (tpp)
REVERT: B  276 GLU cc_start: 0.7964 (pm20) cc_final: 0.7595 (pm20)
REVERT: B  282 ASN cc_start: 0.9175 (m-40) cc_final: 0.8828 (m-40)
REVERT: B  284 ASN cc_start: 0.8178 (t0) cc_final: 0.7641 (t0)
REVERT: B  293 LYS cc_start: 0.8908 (pptt) cc_final: 0.8681 (pptt)
REVERT: B  305 LEU cc_start: 0.9404 (tp) cc_final: 0.8760 (tp)
REVERT: B  313 TRP cc_start: 0.7824 (t60) cc_final: 0.7218 (t60)
REVERT: B  325 GLU cc_start: 0.9053 (tp30) cc_final: 0.8741 (tp30)
REVERT: B  332 LEU cc_start: 0.8303 (tp) cc_final: 0.8046 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1382
  time to fit residues: 19.9157
Evaluate side-chains
  94 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 131 optimal weight:    5.9990
   chunk 109 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 126 optimal weight:    0.7980
   overall best weight:    1.6784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.5517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10672  Z= 0.217
  Angle     :  0.628   7.234  14464  Z= 0.312
  Chirality :  0.041   0.125   1644
  Planarity :  0.005   0.049   1880
  Dihedral  :  4.580  16.254   1472
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.23), residues: 1364
  helix:  1.28 (0.19), residues: 696
  sheet: -1.29 (0.32), residues: 220
  loop : -0.30 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A 295 
 HIS   0.005   0.001   HIS A 219 
 PHE   0.009   0.002   PHE B 144 
 TYR   0.012   0.002   TYR C 213 
 ARG   0.007   0.000   ARG D  42 

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 LEU cc_start: 0.7906 (tt) cc_final: 0.7667 (tp)
REVERT: B  115 LEU cc_start: 0.7716 (mm) cc_final: 0.7429 (mm)
REVERT: B  128 ASP cc_start: 0.6142 (m-30) cc_final: 0.5276 (p0)
REVERT: B  140 ASP cc_start: 0.8548 (m-30) cc_final: 0.8316 (m-30)
REVERT: B  178 GLN cc_start: 0.8852 (mt0) cc_final: 0.8622 (mt0)
REVERT: B  195 ASP cc_start: 0.8973 (p0) cc_final: 0.8289 (t0)
REVERT: B  229 LYS cc_start: 0.7970 (tttm) cc_final: 0.7357 (tptt)
REVERT: B  237 HIS cc_start: 0.8541 (t70) cc_final: 0.8208 (t70)
REVERT: B  276 GLU cc_start: 0.8049 (pm20) cc_final: 0.7687 (pm20)
REVERT: B  282 ASN cc_start: 0.9134 (m-40) cc_final: 0.8810 (m-40)
REVERT: B  284 ASN cc_start: 0.8264 (t0) cc_final: 0.7683 (t0)
REVERT: B  313 TRP cc_start: 0.7939 (t60) cc_final: 0.7164 (t60)
REVERT: B  329 LYS cc_start: 0.8656 (mttp) cc_final: 0.8429 (mttt)
REVERT: B  332 LEU cc_start: 0.8296 (tp) cc_final: 0.8075 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1220
  time to fit residues: 16.8973
Evaluate side-chains
  79 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 14 optimal weight:    0.0010
   chunk 74 optimal weight:    0.4980
   chunk 96 optimal weight:    0.0770
   chunk 110 optimal weight:    0.3980
   chunk 73 optimal weight:    0.5980
   chunk 131 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.3144
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.5872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10672  Z= 0.172
  Angle     :  0.609   7.406  14464  Z= 0.297
  Chirality :  0.042   0.126   1644
  Planarity :  0.005   0.042   1880
  Dihedral  :  4.458  16.532   1472
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  1.44 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.23), residues: 1364
  helix:  1.39 (0.19), residues: 696
  sheet: -0.83 (0.31), residues: 220
  loop : -0.42 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP C 295 
 HIS   0.006   0.001   HIS B 219 
 PHE   0.017   0.002   PHE B  79 
 TYR   0.011   0.001   TYR A 137 
 ARG   0.007   0.000   ARG C  42 

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.8980 (mttt) cc_final: 0.8599 (mmtp)
REVERT: B   14 GLU cc_start: 0.8952 (mp0) cc_final: 0.8663 (mm-30)
REVERT: B   61 LEU cc_start: 0.8857 (mt) cc_final: 0.8438 (mt)
REVERT: B   72 CYS cc_start: 0.8991 (m) cc_final: 0.8735 (m)
REVERT: B   73 ILE cc_start: 0.9125 (mm) cc_final: 0.8909 (tp)
REVERT: B  115 LEU cc_start: 0.7707 (mm) cc_final: 0.7417 (mp)
REVERT: B  140 ASP cc_start: 0.8654 (m-30) cc_final: 0.8415 (m-30)
REVERT: B  195 ASP cc_start: 0.8942 (p0) cc_final: 0.8302 (t0)
REVERT: B  221 ILE cc_start: 0.9276 (tp) cc_final: 0.9056 (tp)
REVERT: B  229 LYS cc_start: 0.7835 (tttm) cc_final: 0.7214 (tptt)
REVERT: B  237 HIS cc_start: 0.8386 (t70) cc_final: 0.8053 (t70)
REVERT: B  250 MET cc_start: 0.9498 (tpp) cc_final: 0.9159 (tpp)
REVERT: B  269 PHE cc_start: 0.8103 (m-80) cc_final: 0.7895 (m-80)
REVERT: B  276 GLU cc_start: 0.8006 (pm20) cc_final: 0.7717 (pm20)
REVERT: B  282 ASN cc_start: 0.9055 (m-40) cc_final: 0.8809 (m-40)
REVERT: B  284 ASN cc_start: 0.8369 (t0) cc_final: 0.7871 (t0)
REVERT: B  305 LEU cc_start: 0.9337 (tp) cc_final: 0.8926 (tp)
REVERT: B  313 TRP cc_start: 0.7802 (t60) cc_final: 0.6741 (t60)
REVERT: B  332 LEU cc_start: 0.8300 (tp) cc_final: 0.8080 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1304
  time to fit residues: 18.7251
Evaluate side-chains
  90 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:    0.1980
   chunk 39 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 83 optimal weight:   20.0000
   chunk 89 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0570
   chunk 12 optimal weight:    0.0770
   chunk 103 optimal weight:    6.9990
   chunk 119 optimal weight:    0.9990
   chunk 125 optimal weight:    4.9990
   chunk 114 optimal weight:    0.0770
   overall best weight:    0.2214
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 178 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.6087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10672  Z= 0.188
  Angle     :  0.648   8.083  14464  Z= 0.318
  Chirality :  0.043   0.129   1644
  Planarity :  0.004   0.040   1880
  Dihedral  :  4.376  16.426   1472
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.22), residues: 1364
  helix:  1.26 (0.19), residues: 700
  sheet: -1.01 (0.30), residues: 220
  loop : -0.66 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP D 295 
 HIS   0.004   0.001   HIS B 219 
 PHE   0.018   0.003   PHE D  79 
 TYR   0.010   0.001   TYR A 213 
 ARG   0.006   0.000   ARG C  42 

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.8961 (mttt) cc_final: 0.8675 (mmtp)
REVERT: B   61 LEU cc_start: 0.8838 (mt) cc_final: 0.8448 (mt)
REVERT: B   72 CYS cc_start: 0.8985 (m) cc_final: 0.8750 (m)
REVERT: B   81 GLU cc_start: 0.9131 (tp30) cc_final: 0.8726 (pp20)
REVERT: B  178 GLN cc_start: 0.8692 (mt0) cc_final: 0.8474 (mt0)
REVERT: B  195 ASP cc_start: 0.8959 (p0) cc_final: 0.8315 (t0)
REVERT: B  237 HIS cc_start: 0.8393 (t70) cc_final: 0.8074 (t70)
REVERT: B  245 HIS cc_start: 0.8568 (m170) cc_final: 0.8263 (p90)
REVERT: B  250 MET cc_start: 0.9449 (tpp) cc_final: 0.9091 (tpp)
REVERT: B  269 PHE cc_start: 0.8100 (m-80) cc_final: 0.7819 (m-80)
REVERT: B  276 GLU cc_start: 0.7966 (pm20) cc_final: 0.7712 (pm20)
REVERT: B  282 ASN cc_start: 0.9152 (m-40) cc_final: 0.8721 (m-40)
REVERT: B  284 ASN cc_start: 0.8543 (t0) cc_final: 0.8020 (t0)
REVERT: B  293 LYS cc_start: 0.8806 (pptt) cc_final: 0.8495 (pptt)
REVERT: B  305 LEU cc_start: 0.9347 (tp) cc_final: 0.8993 (tp)
REVERT: B  313 TRP cc_start: 0.7938 (t60) cc_final: 0.6796 (t60)
REVERT: B  325 GLU cc_start: 0.9104 (tp30) cc_final: 0.8836 (tp30)
REVERT: B  329 LYS cc_start: 0.9055 (ptmt) cc_final: 0.8430 (ptpt)
REVERT: B  332 LEU cc_start: 0.8308 (tp) cc_final: 0.8075 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1226
  time to fit residues: 18.6418
Evaluate side-chains
  83 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 125 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 95 optimal weight:    0.0570
   chunk 37 optimal weight:    9.9990
   chunk 110 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 121 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 129 optimal weight:    0.0170
   overall best weight:    0.6140
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 219 HIS
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.6243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10672  Z= 0.201
  Angle     :  0.669   7.892  14464  Z= 0.329
  Chirality :  0.042   0.128   1644
  Planarity :  0.005   0.042   1880
  Dihedral  :  4.286  15.348   1472
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.22), residues: 1364
  helix:  1.20 (0.19), residues: 696
  sheet: -1.21 (0.29), residues: 220
  loop : -0.62 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP C 295 
 HIS   0.006   0.001   HIS B 219 
 PHE   0.026   0.003   PHE A  79 
 TYR   0.019   0.001   TYR C 327 
 ARG   0.002   0.000   ARG C 172 

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   14 GLU cc_start: 0.8803 (mp0) cc_final: 0.8542 (mp0)
REVERT: B   30 LEU cc_start: 0.7989 (tt) cc_final: 0.7650 (tp)
REVERT: B   50 ASN cc_start: 0.7905 (p0) cc_final: 0.7514 (t0)
REVERT: B   61 LEU cc_start: 0.8773 (mt) cc_final: 0.8445 (mt)
REVERT: B   81 GLU cc_start: 0.9093 (tp30) cc_final: 0.8722 (pp20)
REVERT: B  140 ASP cc_start: 0.8650 (m-30) cc_final: 0.8437 (m-30)
REVERT: B  195 ASP cc_start: 0.9007 (p0) cc_final: 0.8315 (t0)
REVERT: B  250 MET cc_start: 0.9413 (tpp) cc_final: 0.9068 (tpp)
REVERT: B  269 PHE cc_start: 0.8121 (m-80) cc_final: 0.7864 (m-80)
REVERT: B  282 ASN cc_start: 0.9097 (m-40) cc_final: 0.8718 (m-40)
REVERT: B  284 ASN cc_start: 0.8537 (t0) cc_final: 0.7999 (t0)
REVERT: B  293 LYS cc_start: 0.8813 (pptt) cc_final: 0.8474 (pptt)
REVERT: B  305 LEU cc_start: 0.9331 (tp) cc_final: 0.9051 (tp)
REVERT: B  313 TRP cc_start: 0.7744 (t60) cc_final: 0.6870 (t60)
REVERT: B  325 GLU cc_start: 0.9073 (tp30) cc_final: 0.8811 (tp30)
REVERT: B  329 LYS cc_start: 0.8975 (ptmt) cc_final: 0.8363 (ptpt)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1366
  time to fit residues: 19.3801
Evaluate side-chains
  87 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:    0.0770
   chunk 61 optimal weight:    0.3980
   chunk 89 optimal weight:    4.9990
   chunk 135 optimal weight:    6.9990
   chunk 124 optimal weight:    0.0070
   chunk 107 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 66 optimal weight:    8.9990
   chunk 85 optimal weight:    0.8980
   chunk 114 optimal weight:    0.6980
   overall best weight:    0.3956
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 178 GLN
B 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.6385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10672  Z= 0.203
  Angle     :  0.679   7.729  14464  Z= 0.337
  Chirality :  0.043   0.126   1644
  Planarity :  0.005   0.039   1880
  Dihedral  :  4.340  15.556   1472
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.00 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.22), residues: 1364
  helix:  1.15 (0.19), residues: 700
  sheet: -1.27 (0.29), residues: 220
  loop : -0.68 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP C 295 
 HIS   0.006   0.001   HIS B 219 
 PHE   0.025   0.003   PHE D  79 
 TYR   0.020   0.002   TYR C 327 
 ARG   0.004   0.000   ARG D  42 

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   14 GLU cc_start: 0.8766 (mp0) cc_final: 0.8507 (mp0)
REVERT: B   30 LEU cc_start: 0.7769 (tt) cc_final: 0.7408 (tp)
REVERT: B   61 LEU cc_start: 0.8747 (mt) cc_final: 0.8374 (mt)
REVERT: B   81 GLU cc_start: 0.9022 (tp30) cc_final: 0.8717 (pp20)
REVERT: B  165 GLU cc_start: 0.8299 (tt0) cc_final: 0.7839 (tt0)
REVERT: B  195 ASP cc_start: 0.8994 (p0) cc_final: 0.8335 (t0)
REVERT: B  237 HIS cc_start: 0.8475 (t70) cc_final: 0.8121 (t70)
REVERT: B  250 MET cc_start: 0.9395 (tpp) cc_final: 0.9050 (tpp)
REVERT: B  269 PHE cc_start: 0.7981 (m-80) cc_final: 0.7697 (m-80)
REVERT: B  282 ASN cc_start: 0.9100 (m-40) cc_final: 0.8684 (m-40)
REVERT: B  284 ASN cc_start: 0.8548 (t0) cc_final: 0.8026 (t0)
REVERT: B  303 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8139 (tpp80)
REVERT: B  305 LEU cc_start: 0.9361 (tp) cc_final: 0.8991 (tp)
REVERT: B  313 TRP cc_start: 0.7869 (t60) cc_final: 0.6797 (t60)
REVERT: B  325 GLU cc_start: 0.9056 (tp30) cc_final: 0.8760 (tp30)
REVERT: B  329 LYS cc_start: 0.8875 (ptmt) cc_final: 0.8279 (ptmt)
  outliers start: 1
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1440
  time to fit residues: 21.3473
Evaluate side-chains
  89 residues out of total 278 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 99 optimal weight:    0.0040
   chunk 15 optimal weight:   20.0000
   chunk 29 optimal weight:    3.9990
   chunk 108 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 110 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 94 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    2.6000
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 282 ASN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.106016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.083380 restraints weight = 5664.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.086974 restraints weight = 3750.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.089639 restraints weight = 2660.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.6275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10672  Z= 0.282
  Angle     :  0.741   8.058  14464  Z= 0.370
  Chirality :  0.044   0.127   1644
  Planarity :  0.005   0.043   1880
  Dihedral  :  4.524  16.515   1472
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 17.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.22), residues: 1364
  helix:  1.01 (0.19), residues: 700
  sheet: -1.14 (0.34), residues: 180
  loop : -0.76 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.004   TRP C 295 
 HIS   0.007   0.001   HIS C 219 
 PHE   0.022   0.002   PHE A  79 
 TYR   0.023   0.002   TYR B 327 
 ARG   0.002   0.000   ARG A  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1732.89 seconds
wall clock time: 32 minutes 1.61 seconds (1921.61 seconds total)