Starting phenix.real_space_refine
on Thu Feb  5 11:01:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k2o_61997/02_2026/9k2o_61997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k2o_61997/02_2026/9k2o_61997.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k2o_61997/02_2026/9k2o_61997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k2o_61997/02_2026/9k2o_61997.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k2o_61997/02_2026/9k2o_61997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k2o_61997/02_2026/9k2o_61997.cif"
  }
  resolution = 3.4
  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=   0.008 sd=   0.072
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     104      5.16       5
     C   10536      2.51       5
     N    2840      2.21       5
     O    3128      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16608
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2076
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 11, 'TRANS': 246}
          Chain breaks: 2
  Restraints were copied for chains:
    B, C, D, E, F, G, H
  Time building chain proxies: 1.75, per 1000 atoms: 0.11
  Number of scatterers: 16608
  At special positions: 0
  Unit cell: (193.88, 73.36, 149.34, 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     104     16.00
     O    3128      8.00
     N    2840      7.00
     C   10536      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS A  49 " distance=2.48
    Simple disulfide: pdb=" SG  CYS A 229 " - pdb=" SG  CYS B 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  36 " - pdb=" SG  CYS B  49 " distance=2.48
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  49 " distance=2.48
    Simple disulfide: pdb=" SG  CYS D  36 " - pdb=" SG  CYS D  49 " distance=2.48
    Simple disulfide: pdb=" SG  CYS E  36 " - pdb=" SG  CYS E  49 " distance=2.48
    Simple disulfide: pdb=" SG  CYS F  36 " - pdb=" SG  CYS F  49 " distance=2.48
    Simple disulfide: pdb=" SG  CYS G  36 " - pdb=" SG  CYS G  49 " distance=2.48
    Simple disulfide: pdb=" SG  CYS H  36 " - pdb=" SG  CYS H  49 " distance=2.48
    Simple disulfide: pdb=" SG  CYS C 229 " - pdb=" SG  CYS D 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 229 " - pdb=" SG  CYS F 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 229 " - pdb=" SG  CYS H 229 " distance=2.05

  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: 1.21
  Conformation dependent library (CDL) restraints added in 756.9 milliseconds
  

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3936

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 24 sheets defined
      39.1% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 22
      removed outlier: 3.910A  pdb=" N   SER A  22 " --> pdb=" O   ILE A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 41
    Processing helix  chain 'A' and resid 49 through 56
    Processing helix  chain 'A' and resid 88 through 91
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 107 through 110
    Processing helix  chain 'A' and resid 111 through 123
    Processing helix  chain 'A' and resid 124 through 136
      removed outlier: 3.525A  pdb=" N   LYS A 136 " --> pdb=" O   CYS A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 162
      removed outlier: 3.853A  pdb=" N   ASN A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLN A 146 " --> pdb=" O   THR A 142 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   ARG A 147 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 198
    Processing helix  chain 'A' and resid 201 through 212
    Processing helix  chain 'B' and resid 18 through 22
      removed outlier: 3.910A  pdb=" N   SER B  22 " --> pdb=" O   ILE B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 41
    Processing helix  chain 'B' and resid 49 through 56
    Processing helix  chain 'B' and resid 88 through 91
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 107 through 110
    Processing helix  chain 'B' and resid 111 through 123
    Processing helix  chain 'B' and resid 124 through 136
      removed outlier: 3.526A  pdb=" N   LYS B 136 " --> pdb=" O   CYS B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 162
      removed outlier: 3.853A  pdb=" N   ASN B 144 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLN B 146 " --> pdb=" O   THR B 142 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   ARG B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR B 162 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 198
    Processing helix  chain 'B' and resid 201 through 212
    Processing helix  chain 'C' and resid 18 through 22
      removed outlier: 3.910A  pdb=" N   SER C  22 " --> pdb=" O   ILE C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 41
    Processing helix  chain 'C' and resid 49 through 56
    Processing helix  chain 'C' and resid 88 through 91
    Processing helix  chain 'C' and resid 101 through 106
    Processing helix  chain 'C' and resid 107 through 110
    Processing helix  chain 'C' and resid 111 through 123
    Processing helix  chain 'C' and resid 124 through 136
      removed outlier: 3.525A  pdb=" N   LYS C 136 " --> pdb=" O   CYS C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 162
      removed outlier: 3.852A  pdb=" N   ASN C 144 " --> pdb=" O   GLY C 140 " (cutoff:3.500A)
      removed outlier: 4.979A  pdb=" N   GLN C 146 " --> pdb=" O   THR C 142 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   ARG C 147 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR C 162 " --> pdb=" O   SER C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 198
    Processing helix  chain 'C' and resid 201 through 212
    Processing helix  chain 'D' and resid 18 through 22
      removed outlier: 3.909A  pdb=" N   SER D  22 " --> pdb=" O   ILE D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 41
    Processing helix  chain 'D' and resid 49 through 56
    Processing helix  chain 'D' and resid 88 through 91
    Processing helix  chain 'D' and resid 101 through 106
    Processing helix  chain 'D' and resid 107 through 110
    Processing helix  chain 'D' and resid 111 through 123
    Processing helix  chain 'D' and resid 124 through 136
      removed outlier: 3.525A  pdb=" N   LYS D 136 " --> pdb=" O   CYS D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 162
      removed outlier: 3.853A  pdb=" N   ASN D 144 " --> pdb=" O   GLY D 140 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLN D 146 " --> pdb=" O   THR D 142 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   ARG D 147 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR D 162 " --> pdb=" O   SER D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 191 through 198
    Processing helix  chain 'D' and resid 201 through 212
    Processing helix  chain 'E' and resid 18 through 22
      removed outlier: 3.909A  pdb=" N   SER E  22 " --> pdb=" O   ILE E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 41
    Processing helix  chain 'E' and resid 49 through 56
    Processing helix  chain 'E' and resid 88 through 91
    Processing helix  chain 'E' and resid 101 through 106
    Processing helix  chain 'E' and resid 107 through 110
    Processing helix  chain 'E' and resid 111 through 123
    Processing helix  chain 'E' and resid 124 through 136
      removed outlier: 3.526A  pdb=" N   LYS E 136 " --> pdb=" O   CYS E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 140 through 162
      removed outlier: 3.852A  pdb=" N   ASN E 144 " --> pdb=" O   GLY E 140 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLN E 146 " --> pdb=" O   THR E 142 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   ARG E 147 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR E 162 " --> pdb=" O   SER E 158 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 191 through 198
    Processing helix  chain 'E' and resid 201 through 212
    Processing helix  chain 'F' and resid 18 through 22
      removed outlier: 3.909A  pdb=" N   SER F  22 " --> pdb=" O   ILE F  19 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 37 through 41
    Processing helix  chain 'F' and resid 49 through 56
    Processing helix  chain 'F' and resid 88 through 91
    Processing helix  chain 'F' and resid 101 through 106
    Processing helix  chain 'F' and resid 107 through 110
    Processing helix  chain 'F' and resid 111 through 123
    Processing helix  chain 'F' and resid 124 through 136
      removed outlier: 3.526A  pdb=" N   LYS F 136 " --> pdb=" O   CYS F 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 140 through 162
      removed outlier: 3.853A  pdb=" N   ASN F 144 " --> pdb=" O   GLY F 140 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLN F 146 " --> pdb=" O   THR F 142 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   ARG F 147 " --> pdb=" O   SER F 143 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR F 162 " --> pdb=" O   SER F 158 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 191 through 198
    Processing helix  chain 'F' and resid 201 through 212
    Processing helix  chain 'G' and resid 18 through 22
      removed outlier: 3.910A  pdb=" N   SER G  22 " --> pdb=" O   ILE G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 37 through 41
    Processing helix  chain 'G' and resid 49 through 56
    Processing helix  chain 'G' and resid 88 through 91
    Processing helix  chain 'G' and resid 101 through 106
    Processing helix  chain 'G' and resid 107 through 110
    Processing helix  chain 'G' and resid 111 through 123
    Processing helix  chain 'G' and resid 124 through 136
      removed outlier: 3.526A  pdb=" N   LYS G 136 " --> pdb=" O   CYS G 132 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 140 through 162
      removed outlier: 3.853A  pdb=" N   ASN G 144 " --> pdb=" O   GLY G 140 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLN G 146 " --> pdb=" O   THR G 142 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   ARG G 147 " --> pdb=" O   SER G 143 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR G 162 " --> pdb=" O   SER G 158 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 191 through 198
    Processing helix  chain 'G' and resid 201 through 212
    Processing helix  chain 'H' and resid 18 through 22
      removed outlier: 3.910A  pdb=" N   SER H  22 " --> pdb=" O   ILE H  19 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 41
    Processing helix  chain 'H' and resid 49 through 56
    Processing helix  chain 'H' and resid 88 through 91
    Processing helix  chain 'H' and resid 101 through 106
    Processing helix  chain 'H' and resid 107 through 110
    Processing helix  chain 'H' and resid 111 through 123
    Processing helix  chain 'H' and resid 124 through 136
      removed outlier: 3.526A  pdb=" N   LYS H 136 " --> pdb=" O   CYS H 132 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 140 through 162
      removed outlier: 3.853A  pdb=" N   ASN H 144 " --> pdb=" O   GLY H 140 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLN H 146 " --> pdb=" O   THR H 142 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   ARG H 147 " --> pdb=" O   SER H 143 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR H 162 " --> pdb=" O   SER H 158 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 191 through 198
    Processing helix  chain 'H' and resid 201 through 212
    Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 66
      removed outlier: 4.015A  pdb=" N   PHE A  74 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96
      removed outlier: 6.707A  pdb=" N   LEU A 239 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 179
      removed outlier: 6.875A  pdb=" N   TYR A 216 " --> pdb=" O   GLN A 302 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   ILE A 304 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN A 218 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 66
      removed outlier: 4.014A  pdb=" N   PHE B  74 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 96
      removed outlier: 6.707A  pdb=" N   LEU B 239 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 177 through 179
      removed outlier: 6.876A  pdb=" N   TYR B 216 " --> pdb=" O   GLN B 302 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ILE B 304 " --> pdb=" O   TYR B 216 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLN B 218 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 66
      removed outlier: 4.016A  pdb=" N   PHE C  74 " --> pdb=" O   ILE C  66 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 96
      removed outlier: 6.707A  pdb=" N   LEU C 239 " --> pdb=" O   LEU C  94 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 177 through 179
      removed outlier: 6.874A  pdb=" N   TYR C 216 " --> pdb=" O   GLN C 302 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ILE C 304 " --> pdb=" O   TYR C 216 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN C 218 " --> pdb=" O   ILE C 304 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 59 through 66
      removed outlier: 4.015A  pdb=" N   PHE D  74 " --> pdb=" O   ILE D  66 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 93 through 96
      removed outlier: 6.707A  pdb=" N   LEU D 239 " --> pdb=" O   LEU D  94 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 177 through 179
      removed outlier: 6.875A  pdb=" N   TYR D 216 " --> pdb=" O   GLN D 302 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ILE D 304 " --> pdb=" O   TYR D 216 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN D 218 " --> pdb=" O   ILE D 304 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 59 through 66
      removed outlier: 4.016A  pdb=" N   PHE E  74 " --> pdb=" O   ILE E  66 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 93 through 96
      removed outlier: 6.707A  pdb=" N   LEU E 239 " --> pdb=" O   LEU E  94 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 177 through 179
      removed outlier: 6.875A  pdb=" N   TYR E 216 " --> pdb=" O   GLN E 302 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ILE E 304 " --> pdb=" O   TYR E 216 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLN E 218 " --> pdb=" O   ILE E 304 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 59 through 66
      removed outlier: 4.015A  pdb=" N   PHE F  74 " --> pdb=" O   ILE F  66 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 93 through 96
      removed outlier: 6.708A  pdb=" N   LEU F 239 " --> pdb=" O   LEU F  94 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 177 through 179
      removed outlier: 6.874A  pdb=" N   TYR F 216 " --> pdb=" O   GLN F 302 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ILE F 304 " --> pdb=" O   TYR F 216 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN F 218 " --> pdb=" O   ILE F 304 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 59 through 66
      removed outlier: 4.015A  pdb=" N   PHE G  74 " --> pdb=" O   ILE G  66 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 93 through 96
      removed outlier: 6.707A  pdb=" N   LEU G 239 " --> pdb=" O   LEU G  94 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 177 through 179
      removed outlier: 6.875A  pdb=" N   TYR G 216 " --> pdb=" O   GLN G 302 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ILE G 304 " --> pdb=" O   TYR G 216 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN G 218 " --> pdb=" O   ILE G 304 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'H' and resid 59 through 66
      removed outlier: 4.014A  pdb=" N   PHE H  74 " --> pdb=" O   ILE H  66 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 93 through 96
      removed outlier: 6.708A  pdb=" N   LEU H 239 " --> pdb=" O   LEU H  94 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 177 through 179
      removed outlier: 6.875A  pdb=" N   TYR H 216 " --> pdb=" O   GLN H 302 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   ILE H 304 " --> pdb=" O   TYR H 216 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN H 218 " --> pdb=" O   ILE H 304 " (cutoff:3.500A)

    600 hydrogen bonds defined for protein.
    1560 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.28

  Time building geometry restraints manager: 1.66 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: 5494
        1.34 -     1.46: 2682
        1.46 -     1.57: 8640
        1.57 -     1.69: 0
        1.69 -     1.81: 144
  Bond restraints: 16960
  Sorted by residual:
  bond pdb=" C   PRO D  38 "
       pdb=" N   ASP D  39 "
    ideal  model  delta    sigma   weight residual
    1.334  1.320  0.014 1.38e-02 5.25e+03 1.06e+00
  bond pdb=" C   GLN C 115 "
       pdb=" N   LEU C 116 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.013 1.31e-02 5.83e+03 9.85e-01
  bond pdb=" C   PRO G  38 "
       pdb=" N   ASP G  39 "
    ideal  model  delta    sigma   weight residual
    1.334  1.321  0.013 1.38e-02 5.25e+03 8.81e-01
  bond pdb=" CA  ASP C 245 "
       pdb=" CB  ASP C 245 "
    ideal  model  delta    sigma   weight residual
    1.530  1.546 -0.016 1.69e-02 3.50e+03 8.65e-01
  bond pdb=" CA  ASP A 245 "
       pdb=" CB  ASP A 245 "
    ideal  model  delta    sigma   weight residual
    1.530  1.546 -0.016 1.69e-02 3.50e+03 8.58e-01
  ... (remaining 16955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 21922
        1.25 -     2.50: 836
        2.50 -     3.76: 186
        3.76 -     5.01: 24
        5.01 -     6.26: 24
  Bond angle restraints: 22992
  Sorted by residual:
  angle pdb=" C   ASP A  27 "
        pdb=" N   ALA A  28 "
        pdb=" CA  ALA A  28 "
      ideal   model   delta    sigma   weight residual
     121.54  127.80   -6.26 1.91e+00 2.74e-01 1.07e+01
  angle pdb=" C   ASP B  27 "
        pdb=" N   ALA B  28 "
        pdb=" CA  ALA B  28 "
      ideal   model   delta    sigma   weight residual
     121.54  127.80   -6.26 1.91e+00 2.74e-01 1.07e+01
  angle pdb=" C   ASP C  27 "
        pdb=" N   ALA C  28 "
        pdb=" CA  ALA C  28 "
      ideal   model   delta    sigma   weight residual
     121.54  127.78   -6.24 1.91e+00 2.74e-01 1.07e+01
  angle pdb=" C   ASP E  27 "
        pdb=" N   ALA E  28 "
        pdb=" CA  ALA E  28 "
      ideal   model   delta    sigma   weight residual
     121.54  127.78   -6.24 1.91e+00 2.74e-01 1.07e+01
  angle pdb=" C   PRO G 244 "
        pdb=" N   ASP G 245 "
        pdb=" CA  ASP G 245 "
      ideal   model   delta    sigma   weight residual
     121.54  127.78   -6.24 1.91e+00 2.74e-01 1.07e+01
  ... (remaining 22987 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.04: 8468
       12.04 -    24.08: 1054
       24.08 -    36.11: 517
       36.11 -    48.15: 128
       48.15 -    60.19: 29
  Dihedral angle restraints: 10196
    sinusoidal: 4116
      harmonic: 6080
  Sorted by residual:
  dihedral pdb=" CB  CYS C 229 "
           pdb=" SG  CYS C 229 "
           pdb=" SG  CYS D 229 "
           pdb=" CB  CYS D 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.20   54.20     1      1.00e+01 1.00e-02 3.98e+01
  dihedral pdb=" CB  CYS E 229 "
           pdb=" SG  CYS E 229 "
           pdb=" SG  CYS F 229 "
           pdb=" CB  CYS F 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.15   54.15     1      1.00e+01 1.00e-02 3.98e+01
  dihedral pdb=" CB  CYS G 229 "
           pdb=" SG  CYS G 229 "
           pdb=" SG  CYS H 229 "
           pdb=" CB  CYS H 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.02   54.02     1      1.00e+01 1.00e-02 3.96e+01
  ... (remaining 10193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1344
       0.031 -    0.061: 813
       0.061 -    0.092: 281
       0.092 -    0.123: 88
       0.123 -    0.154: 26
  Chirality restraints: 2552
  Sorted by residual:
  chirality pdb=" CA  ASP A 245 "
            pdb=" N   ASP A 245 "
            pdb=" C   ASP A 245 "
            pdb=" CB  ASP A 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.90e-01
  chirality pdb=" CA  ASP D 245 "
            pdb=" N   ASP D 245 "
            pdb=" C   ASP D 245 "
            pdb=" CB  ASP D 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.85e-01
  chirality pdb=" CA  ASP H 245 "
            pdb=" N   ASP H 245 "
            pdb=" C   ASP H 245 "
            pdb=" CB  ASP H 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.82e-01
  ... (remaining 2549 not shown)

  Planarity restraints: 3008
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 291 "    0.005 2.00e-02 2.50e+03   1.00e-02 1.00e+00
        pdb=" C   TYR C 291 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   TYR C 291 "    0.006 2.00e-02 2.50e+03
        pdb=" N   PRO C 292 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR H 291 "   -0.005 2.00e-02 2.50e+03   9.88e-03 9.77e-01
        pdb=" C   TYR H 291 "    0.017 2.00e-02 2.50e+03
        pdb=" O   TYR H 291 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   PRO H 292 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR G 291 "    0.005 2.00e-02 2.50e+03   9.83e-03 9.65e-01
        pdb=" C   TYR G 291 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   TYR G 291 "    0.006 2.00e-02 2.50e+03
        pdb=" N   PRO G 292 "    0.006 2.00e-02 2.50e+03
  ... (remaining 3005 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 2155
        2.75 -     3.29: 17847
        3.29 -     3.83: 27833
        3.83 -     4.36: 32160
        4.36 -     4.90: 55616
  Nonbonded interactions: 135611
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 107 "
            pdb=" NE2 GLN C 115 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OH  TYR A 101 "
            pdb=" OD1 ASN A 124 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OH  TYR F 101 "
            pdb=" OD1 ASN F 124 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OH  TYR E 101 "
            pdb=" OD1 ASN E 124 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OH  TYR C 101 "
            pdb=" OD1 ASN C 124 "
     model   vdw
     2.245 3.040
  ... (remaining 135606 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             17.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     11.480
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
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      :  0.010   0.448  16972  Z= 0.504
  Angle     :  0.685  15.877  23016  Z= 0.363
  Chirality :  0.044   0.154   2552
  Planarity :  0.003   0.026   3008
  Dihedral  : 13.305  60.188   6224
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.05 %
    Favored  : 99.95 %
  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 are not related in a simple way.
  whole: -0.51 (0.21), residues: 2016
  helix:  0.59 (0.23), residues: 560
  sheet: -2.28 (0.43), residues: 144
  loop : -0.48 (0.20), residues: 1312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  56 
 TYR   0.010   0.001   TYR C 294 
 PHE   0.012   0.001   PHE D 118 
 TRP   0.010   0.002   TRP F  46 
 HIS   0.007   0.002   HIS G  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (16960)
  covalent geometry    : angle       0.61045 (22992)
  SS BOND              : bond        0.36495 (   12)
  SS BOND              : angle       9.65064 (   24)
  hydrogen bonds       : bond        0.12062 (  600)
  hydrogen bonds       : angle       6.37846 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 409
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8019 (mp10)
REVERT: A  125 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7680 (tp30)
REVERT: B  157 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8349 (mmtt)
REVERT: B  161 ASP cc_start: 0.7360 (m-30) cc_final: 0.7153 (m-30)
REVERT: B  204 LEU cc_start: 0.8013 (mt) cc_final: 0.7621 (mt)
REVERT: C  110 MET cc_start: 0.7842 (mtt) cc_final: 0.7560 (mtt)
REVERT: C  114 GLU cc_start: 0.7892 (tt0) cc_final: 0.7580 (tt0)
REVERT: D   41 TYR cc_start: 0.7282 (m-10) cc_final: 0.7029 (m-80)
REVERT: D   62 MET cc_start: 0.7935 (mtt) cc_final: 0.7599 (mtt)
REVERT: D  116 LEU cc_start: 0.9007 (tp) cc_final: 0.8806 (tp)
REVERT: E   62 MET cc_start: 0.7743 (mtt) cc_final: 0.7365 (mtm)
REVERT: E  112 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7730 (mm-40)
REVERT: F  132 CYS cc_start: 0.7252 (m) cc_final: 0.6940 (p)
REVERT: G   43 ASP cc_start: 0.7697 (t70) cc_final: 0.7413 (t0)
REVERT: G  133 ASP cc_start: 0.6627 (p0) cc_final: 0.6163 (p0)
REVERT: G  200 TYR cc_start: 0.8326 (m-80) cc_final: 0.7997 (m-80)
REVERT: G  297 LEU cc_start: 0.8655 (mm) cc_final: 0.8243 (mt)
REVERT: H   76 MET cc_start: 0.7551 (ptp) cc_final: 0.7315 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 409
  average time/residue: 0.1157
  time to fit residues: 69.5954
Evaluate side-chains
  268 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.0270
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN
B 123 ASN
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  81 HIS
C 115 GLN
C 123 ASN
D 123 ASN
** E  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  81 HIS
E 123 ASN
F 123 ASN
H 123 ASN
H 228 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.127942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.104005 restraints weight = 35093.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 3.48
r_work: 0.3509 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16972  Z= 0.150
  Angle     :  0.618   6.335  23016  Z= 0.330
  Chirality :  0.045   0.182   2552
  Planarity :  0.004   0.038   3008
  Dihedral  :  4.677  19.196   2264
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.17 %
    Favored  : 88.74 %
  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 are not related in a simple way.
  whole: -0.57 (0.20), residues: 2016
  helix:  0.17 (0.20), residues: 608
  sheet: -2.23 (0.45), residues: 144
  loop : -0.35 (0.21), residues: 1264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  92 
 TYR   0.021   0.002   TYR H 153 
 PHE   0.011   0.001   PHE C  26 
 TRP   0.015   0.002   TRP D  46 
 HIS   0.012   0.002   HIS E  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (16960)
  covalent geometry    : angle       0.61718 (22992)
  SS BOND              : bond        0.00427 (   12)
  SS BOND              : angle       1.00044 (   24)
  hydrogen bonds       : bond        0.02774 (  600)
  hydrogen bonds       : angle       5.56966 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 299
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7838 (tp30)
REVERT: B   43 ASP cc_start: 0.8483 (t0) cc_final: 0.8196 (t0)
REVERT: B  157 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8555 (mmtt)
REVERT: B  161 ASP cc_start: 0.7827 (m-30) cc_final: 0.7626 (m-30)
REVERT: B  224 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8503 (mt)
REVERT: B  290 GLU cc_start: 0.7744 (tp30) cc_final: 0.7517 (tp30)
REVERT: C  111 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7945 (ttm)
REVERT: C  114 GLU cc_start: 0.8662 (tt0) cc_final: 0.8118 (tt0)
REVERT: D   59 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8025 (mtt)
REVERT: D   62 MET cc_start: 0.8139 (mtt) cc_final: 0.7730 (mtt)
REVERT: D  110 MET cc_start: 0.7984 (mtt) cc_final: 0.7272 (mtm)
REVERT: D  204 LEU cc_start: 0.8552 (mt) cc_final: 0.8346 (mt)
REVERT: D  301 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.6279 (m-80)
REVERT: E   62 MET cc_start: 0.8237 (mtt) cc_final: 0.7848 (mtm)
REVERT: E  110 MET cc_start: 0.8339 (mtm) cc_final: 0.8129 (mtm)
REVERT: E  112 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7871 (mm-40)
REVERT: E  146 GLN cc_start: 0.8827 (tp40) cc_final: 0.8166 (pm20)
REVERT: F   43 ASP cc_start: 0.8569 (t0) cc_final: 0.8367 (m-30)
REVERT: F  132 CYS cc_start: 0.7403 (m) cc_final: 0.6951 (p)
REVERT: F  141 PHE cc_start: 0.6142 (t80) cc_final: 0.5395 (t80)
REVERT: F  216 TYR cc_start: 0.8935 (m-80) cc_final: 0.8504 (m-80)
REVERT: F  253 ILE cc_start: 0.8600 (mt) cc_final: 0.8364 (mm)
REVERT: G   43 ASP cc_start: 0.8383 (t70) cc_final: 0.8121 (t0)
REVERT: G  110 MET cc_start: 0.8522 (mtt) cc_final: 0.8120 (mtm)
REVERT: G  297 LEU cc_start: 0.8985 (mm) cc_final: 0.8540 (mt)
REVERT: H  120 LEU cc_start: 0.9093 (mt) cc_final: 0.8880 (mt)
REVERT: H  222 GLU cc_start: 0.8131 (pp20) cc_final: 0.7784 (pp20)
  outliers start: 20
  outliers final: 9
  residues processed: 311
  average time/residue: 0.1141
  time to fit residues: 53.4622
Evaluate side-chains
  270 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 257
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  150 HIS
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  301 TYR
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain G residue  104 VAL
Chi-restraints excluded: chain G residue  152 VAL
Chi-restraints excluded: chain H residue   26 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 5 optimal weight:    0.0060
   chunk 50 optimal weight:    4.9990
   chunk 165 optimal weight:    0.0060
   chunk 52 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 173 optimal weight:    2.9990
   chunk 174 optimal weight:    1.9990
   chunk 162 optimal weight:    0.6980
   chunk 142 optimal weight:    3.9990
   chunk 194 optimal weight:    0.0040
   overall best weight:    0.3024

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

Flipped N/Q/H residues before XYZ refinement:
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 166 ASN
B 195 GLN
C  81 HIS
E  81 HIS
G  81 HIS
H  81 HIS
H 146 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.128463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.104739 restraints weight = 35575.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 3.59
r_work: 0.3527 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  16972  Z= 0.114
  Angle     :  0.591  14.888  23016  Z= 0.314
  Chirality :  0.044   0.163   2552
  Planarity :  0.003   0.020   3008
  Dihedral  :  4.498  33.620   2264
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.23 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.20), residues: 2016
  helix:  0.26 (0.20), residues: 616
  sheet: -2.15 (0.45), residues: 144
  loop : -0.27 (0.20), residues: 1256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  92 
 TYR   0.022   0.001   TYR G 294 
 PHE   0.009   0.001   PHE C  26 
 TRP   0.018   0.003   TRP D  46 
 HIS   0.006   0.001   HIS E  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (16960)
  covalent geometry    : angle       0.58911 (22992)
  SS BOND              : bond        0.00742 (   12)
  SS BOND              : angle       1.65996 (   24)
  hydrogen bonds       : bond        0.02606 (  600)
  hydrogen bonds       : angle       5.33349 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 290
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7828 (tp30)
REVERT: A  222 GLU cc_start: 0.8151 (pp20) cc_final: 0.7718 (pp20)
REVERT: A  301 TYR cc_start: 0.8011 (t80) cc_final: 0.7669 (t80)
REVERT: B  115 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8783 (mp10)
REVERT: B  157 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8487 (mmtt)
REVERT: C   91 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8526 (tppt)
REVERT: C  110 MET cc_start: 0.8236 (mtt) cc_final: 0.6968 (mtt)
REVERT: C  111 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7676 (mtp)
REVERT: C  114 GLU cc_start: 0.8666 (tt0) cc_final: 0.8139 (tt0)
REVERT: D   62 MET cc_start: 0.8353 (mtt) cc_final: 0.8100 (mtt)
REVERT: D  204 LEU cc_start: 0.8543 (mt) cc_final: 0.8288 (mt)
REVERT: D  301 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.6228 (m-80)
REVERT: E   62 MET cc_start: 0.8556 (mtt) cc_final: 0.8210 (mtm)
REVERT: E  146 GLN cc_start: 0.8808 (tp40) cc_final: 0.8110 (pm20)
REVERT: F  132 CYS cc_start: 0.7242 (m) cc_final: 0.6875 (p)
REVERT: F  216 TYR cc_start: 0.8894 (m-80) cc_final: 0.8518 (m-80)
REVERT: G   43 ASP cc_start: 0.8375 (t70) cc_final: 0.8097 (t0)
REVERT: G  195 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8162 (mm-40)
REVERT: G  297 LEU cc_start: 0.8836 (mm) cc_final: 0.8424 (mt)
  outliers start: 28
  outliers final: 17
  residues processed: 306
  average time/residue: 0.1181
  time to fit residues: 54.5327
Evaluate side-chains
  263 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 243
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue  115 GLN
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain C residue   55 LYS
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  301 TYR
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  295 VAL
Chi-restraints excluded: chain F residue   56 ARG
Chi-restraints excluded: chain H residue   26 PHE
Chi-restraints excluded: chain H residue  134 ASN
Chi-restraints excluded: chain H residue  150 HIS
Chi-restraints excluded: chain H residue  295 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   chunk 125 optimal weight:    4.9990
   chunk 147 optimal weight:    0.8980
   chunk 166 optimal weight:    3.9990
   chunk 154 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN
B 228 ASN
H 115 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.123109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.099174 restraints weight = 35450.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 3.47
r_work: 0.3394 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  16972  Z= 0.189
  Angle     :  0.650  16.174  23016  Z= 0.342
  Chirality :  0.046   0.164   2552
  Planarity :  0.003   0.032   3008
  Dihedral  :  4.816  33.782   2264
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.80 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.20), residues: 2016
  helix:  0.21 (0.20), residues: 624
  sheet: -2.16 (0.45), residues: 144
  loop : -0.29 (0.20), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  56 
 TYR   0.025   0.002   TYR A 122 
 PHE   0.015   0.002   PHE E  47 
 TRP   0.020   0.003   TRP D  46 
 HIS   0.007   0.001   HIS D  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (16960)
  covalent geometry    : angle       0.64563 (22992)
  SS BOND              : bond        0.01026 (   12)
  SS BOND              : angle       2.30991 (   24)
  hydrogen bonds       : bond        0.02595 (  600)
  hydrogen bonds       : angle       5.33237 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 264
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7929 (tp30)
REVERT: A  222 GLU cc_start: 0.8122 (pp20) cc_final: 0.7858 (pp20)
REVERT: B   43 ASP cc_start: 0.8516 (t0) cc_final: 0.8277 (t0)
REVERT: B  114 GLU cc_start: 0.8540 (tt0) cc_final: 0.8148 (mt-10)
REVERT: B  157 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8695 (mmtt)
REVERT: B  166 ASN cc_start: 0.6393 (OUTLIER) cc_final: 0.6038 (p0)
REVERT: C   59 MET cc_start: 0.8662 (mtp) cc_final: 0.8329 (mtm)
REVERT: C  110 MET cc_start: 0.8320 (mtt) cc_final: 0.6916 (mtt)
REVERT: C  111 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7691 (mtp)
REVERT: C  114 GLU cc_start: 0.8560 (tt0) cc_final: 0.8087 (tt0)
REVERT: D   62 MET cc_start: 0.8354 (mtt) cc_final: 0.8142 (mtt)
REVERT: D  301 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6540 (m-80)
REVERT: E   62 MET cc_start: 0.8634 (mtt) cc_final: 0.8124 (mtt)
REVERT: F  132 CYS cc_start: 0.7484 (m) cc_final: 0.6950 (p)
REVERT: F  161 ASP cc_start: 0.8623 (m-30) cc_final: 0.8322 (m-30)
REVERT: F  216 TYR cc_start: 0.8972 (m-80) cc_final: 0.8694 (m-80)
REVERT: G   43 ASP cc_start: 0.8409 (t70) cc_final: 0.8164 (t0)
REVERT: G  297 LEU cc_start: 0.8933 (mm) cc_final: 0.8491 (mt)
REVERT: H   87 GLU cc_start: 0.7924 (pm20) cc_final: 0.7710 (pm20)
REVERT: H  120 LEU cc_start: 0.9269 (mt) cc_final: 0.9026 (mt)
REVERT: H  182 VAL cc_start: 0.6165 (OUTLIER) cc_final: 0.5781 (m)
REVERT: H  195 GLN cc_start: 0.8476 (pp30) cc_final: 0.8219 (pp30)
  outliers start: 55
  outliers final: 26
  residues processed: 304
  average time/residue: 0.1204
  time to fit residues: 54.1203
Evaluate side-chains
  270 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 240
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain D residue   27 ASP
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  150 HIS
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  301 TYR
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  295 VAL
Chi-restraints excluded: chain F residue   56 ARG
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain G residue   23 ILE
Chi-restraints excluded: chain G residue  104 VAL
Chi-restraints excluded: chain G residue  152 VAL
Chi-restraints excluded: chain G residue  295 VAL
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   26 PHE
Chi-restraints excluded: chain H residue   27 ASP
Chi-restraints excluded: chain H residue  150 HIS
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain H residue  249 LEU
Chi-restraints excluded: chain H residue  295 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 158 optimal weight:    0.3980
   chunk 55 optimal weight:    0.3980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 119 optimal weight:    3.9990
   chunk 126 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 160 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
B 166 ASN
B 195 GLN
C  81 HIS
E  81 HIS
G 228 ASN
H 228 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.124038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.099271 restraints weight = 35244.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 3.61
r_work: 0.3430 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16972  Z= 0.134
  Angle     :  0.600   9.055  23016  Z= 0.318
  Chirality :  0.045   0.157   2552
  Planarity :  0.003   0.029   3008
  Dihedral  :  4.623  34.964   2264
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 18.07 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.20), residues: 2016
  helix:  0.40 (0.20), residues: 624
  sheet: -2.20 (0.44), residues: 144
  loop : -0.30 (0.20), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  88 
 TYR   0.020   0.002   TYR G 294 
 PHE   0.010   0.001   PHE G 141 
 TRP   0.019   0.003   TRP E  46 
 HIS   0.006   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (16960)
  covalent geometry    : angle       0.59737 (22992)
  SS BOND              : bond        0.00617 (   12)
  SS BOND              : angle       1.77753 (   24)
  hydrogen bonds       : bond        0.02496 (  600)
  hydrogen bonds       : angle       5.25222 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 269
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7917 (tp30)
REVERT: A  219 ILE cc_start: 0.8981 (mm) cc_final: 0.8679 (mm)
REVERT: A  222 GLU cc_start: 0.8051 (pp20) cc_final: 0.7761 (pp20)
REVERT: B   43 ASP cc_start: 0.8547 (t0) cc_final: 0.8277 (t0)
REVERT: B  114 GLU cc_start: 0.8368 (tt0) cc_final: 0.8124 (mt-10)
REVERT: B  115 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8871 (mp10)
REVERT: B  157 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8662 (mmtt)
REVERT: C   59 MET cc_start: 0.8589 (mtp) cc_final: 0.8263 (mtm)
REVERT: C  110 MET cc_start: 0.8307 (mtt) cc_final: 0.7156 (mtt)
REVERT: C  111 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7679 (mtp)
REVERT: C  114 GLU cc_start: 0.8545 (tt0) cc_final: 0.8070 (tt0)
REVERT: C  195 GLN cc_start: 0.8558 (mp10) cc_final: 0.8192 (mp10)
REVERT: C  290 GLU cc_start: 0.8195 (tp30) cc_final: 0.7712 (tp30)
REVERT: D   62 MET cc_start: 0.8275 (mtt) cc_final: 0.8037 (mtt)
REVERT: D  146 GLN cc_start: 0.8659 (tp40) cc_final: 0.7988 (pm20)
REVERT: D  301 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.6534 (m-80)
REVERT: F  161 ASP cc_start: 0.8360 (m-30) cc_final: 0.8079 (m-30)
REVERT: F  216 TYR cc_start: 0.8955 (m-80) cc_final: 0.8725 (m-80)
REVERT: F  291 TYR cc_start: 0.7385 (t80) cc_final: 0.7111 (t80)
REVERT: G   43 ASP cc_start: 0.8395 (t70) cc_final: 0.8145 (t0)
REVERT: G  195 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8067 (mm-40)
REVERT: G  297 LEU cc_start: 0.8922 (mm) cc_final: 0.8481 (mt)
REVERT: H  182 VAL cc_start: 0.6164 (OUTLIER) cc_final: 0.5832 (m)
  outliers start: 41
  outliers final: 24
  residues processed: 296
  average time/residue: 0.1231
  time to fit residues: 54.4912
Evaluate side-chains
  277 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 249
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  134 ASN
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain B residue  115 GLN
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   27 ASP
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  301 TYR
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  295 VAL
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   56 ARG
Chi-restraints excluded: chain G residue   87 GLU
Chi-restraints excluded: chain G residue  104 VAL
Chi-restraints excluded: chain G residue  136 LYS
Chi-restraints excluded: chain G residue  152 VAL
Chi-restraints excluded: chain G residue  295 VAL
Chi-restraints excluded: chain H residue   26 PHE
Chi-restraints excluded: chain H residue  150 HIS
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain H residue  295 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 185 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 163 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   chunk 174 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 GLN
** C  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 150 HIS
** G  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.119500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.094600 restraints weight = 35236.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 3.54
r_work: 0.3344 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  16972  Z= 0.200
  Angle     :  0.648  10.623  23016  Z= 0.343
  Chirality :  0.046   0.165   2552
  Planarity :  0.003   0.027   3008
  Dihedral  :  4.806  28.805   2264
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.43 %
    Favored  : 77.65 %
  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 are not related in a simple way.
  whole: -0.46 (0.20), residues: 2016
  helix:  0.37 (0.20), residues: 624
  sheet: -2.36 (0.42), residues: 144
  loop : -0.32 (0.20), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  56 
 TYR   0.021   0.002   TYR G 294 
 PHE   0.017   0.002   PHE B 168 
 TRP   0.018   0.003   TRP D  46 
 HIS   0.009   0.001   HIS D  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (16960)
  covalent geometry    : angle       0.64580 (22992)
  SS BOND              : bond        0.00577 (   12)
  SS BOND              : angle       1.70757 (   24)
  hydrogen bonds       : bond        0.02635 (  600)
  hydrogen bonds       : angle       5.34691 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 252
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7781 (tp30)
REVERT: A  222 GLU cc_start: 0.8140 (pp20) cc_final: 0.7904 (pp20)
REVERT: B   43 ASP cc_start: 0.8549 (t0) cc_final: 0.8286 (t0)
REVERT: B   73 GLN cc_start: 0.8225 (tp40) cc_final: 0.7958 (tp-100)
REVERT: B  196 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8151 (pp)
REVERT: C   59 MET cc_start: 0.8780 (mtp) cc_final: 0.8389 (mtm)
REVERT: C  110 MET cc_start: 0.8320 (mtt) cc_final: 0.7082 (mtt)
REVERT: C  111 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7649 (mtp)
REVERT: C  114 GLU cc_start: 0.8591 (tt0) cc_final: 0.8234 (tt0)
REVERT: C  195 GLN cc_start: 0.8678 (mp10) cc_final: 0.8203 (mp10)
REVERT: C  290 GLU cc_start: 0.8257 (tp30) cc_final: 0.7821 (tp30)
REVERT: D  120 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8886 (mm)
REVERT: E   62 MET cc_start: 0.8545 (mtt) cc_final: 0.8132 (mtt)
REVERT: F  146 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8981 (mm-40)
REVERT: F  161 ASP cc_start: 0.8410 (m-30) cc_final: 0.8091 (m-30)
REVERT: G   43 ASP cc_start: 0.8579 (t70) cc_final: 0.8314 (t0)
REVERT: G  160 LEU cc_start: 0.8864 (tp) cc_final: 0.8634 (mp)
REVERT: G  195 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8146 (mm-40)
REVERT: G  222 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7430 (pm20)
REVERT: H   59 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8573 (mtt)
REVERT: H  116 LEU cc_start: 0.9025 (tp) cc_final: 0.8617 (tp)
REVERT: H  290 GLU cc_start: 0.8167 (tp30) cc_final: 0.7673 (mm-30)
  outliers start: 54
  outliers final: 36
  residues processed: 292
  average time/residue: 0.1313
  time to fit residues: 56.1184
Evaluate side-chains
  281 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 240
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  134 ASN
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   27 ASP
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  150 HIS
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  295 VAL
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   56 ARG
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   23 ILE
Chi-restraints excluded: chain G residue   87 GLU
Chi-restraints excluded: chain G residue  104 VAL
Chi-restraints excluded: chain G residue  136 LYS
Chi-restraints excluded: chain G residue  152 VAL
Chi-restraints excluded: chain G residue  222 GLU
Chi-restraints excluded: chain G residue  295 VAL
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   26 PHE
Chi-restraints excluded: chain H residue   27 ASP
Chi-restraints excluded: chain H residue   59 MET
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  249 LEU
Chi-restraints excluded: chain H residue  295 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9980
   chunk 126 optimal weight:    0.1980
   chunk 137 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0020
   chunk 17 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9980
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
B 166 ASN
B 195 GLN
C  81 HIS
D  81 HIS
** G  81 HIS ** 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 = 0.3953 r_free = 0.3953 target = 0.121783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.097822 restraints weight = 35177.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 3.49
r_work: 0.3402 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16972  Z= 0.135
  Angle     :  0.624  11.168  23016  Z= 0.330
  Chirality :  0.045   0.172   2552
  Planarity :  0.003   0.040   3008
  Dihedral  :  4.691  29.575   2264
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.56 %
    Favored  : 77.00 %
  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 are not related in a simple way.
  whole: -0.41 (0.20), residues: 2016
  helix:  0.47 (0.21), residues: 624
  sheet: -2.36 (0.42), residues: 144
  loop : -0.33 (0.20), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  88 
 TYR   0.018   0.002   TYR G 294 
 PHE   0.018   0.001   PHE A 141 
 TRP   0.017   0.003   TRP E  46 
 HIS   0.007   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (16960)
  covalent geometry    : angle       0.62238 (22992)
  SS BOND              : bond        0.00801 (   12)
  SS BOND              : angle       1.70339 (   24)
  hydrogen bonds       : bond        0.02547 (  600)
  hydrogen bonds       : angle       5.28847 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 263
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7789 (tp30)
REVERT: A  219 ILE cc_start: 0.8969 (mm) cc_final: 0.8640 (mm)
REVERT: A  222 GLU cc_start: 0.8040 (pp20) cc_final: 0.7745 (pp20)
REVERT: B   43 ASP cc_start: 0.8541 (t0) cc_final: 0.8269 (t0)
REVERT: B  115 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8913 (mp10)
REVERT: B  196 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8076 (pp)
REVERT: C  111 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7670 (mtp)
REVERT: C  150 HIS cc_start: 0.8227 (t70) cc_final: 0.8010 (t70)
REVERT: C  290 GLU cc_start: 0.8235 (tp30) cc_final: 0.7835 (tp30)
REVERT: D   94 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8814 (mp)
REVERT: E   59 MET cc_start: 0.8056 (ttm) cc_final: 0.7816 (mtt)
REVERT: E   62 MET cc_start: 0.8490 (mtt) cc_final: 0.8090 (mtt)
REVERT: F  110 MET cc_start: 0.8276 (mtt) cc_final: 0.7661 (mtm)
REVERT: F  146 GLN cc_start: 0.9249 (mm-40) cc_final: 0.9018 (mm-40)
REVERT: F  161 ASP cc_start: 0.8335 (m-30) cc_final: 0.8061 (m-30)
REVERT: F  216 TYR cc_start: 0.8976 (m-80) cc_final: 0.8487 (m-80)
REVERT: G   43 ASP cc_start: 0.8537 (t70) cc_final: 0.8259 (t0)
REVERT: G  222 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7425 (pm20)
REVERT: H  116 LEU cc_start: 0.8740 (tp) cc_final: 0.8374 (tp)
REVERT: H  290 GLU cc_start: 0.8019 (tp30) cc_final: 0.7733 (mm-30)
  outliers start: 45
  outliers final: 29
  residues processed: 295
  average time/residue: 0.1239
  time to fit residues: 54.5356
Evaluate side-chains
  274 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 240
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  134 ASN
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   23 ILE
Chi-restraints excluded: chain B residue  115 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue   43 ASP
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  150 HIS
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  295 VAL
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   56 ARG
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue  104 VAL
Chi-restraints excluded: chain G residue  136 LYS
Chi-restraints excluded: chain G residue  152 VAL
Chi-restraints excluded: chain G residue  222 GLU
Chi-restraints excluded: chain H residue   26 PHE
Chi-restraints excluded: chain H residue   27 ASP
Chi-restraints excluded: chain H residue  295 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 99 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 170 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 137 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN
C  81 HIS
D  85 ASN
D 150 HIS
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  81 HIS ** 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 = 0.3929 r_free = 0.3929 target = 0.120085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.095868 restraints weight = 35287.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 3.50
r_work: 0.3366 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  16972  Z= 0.168
  Angle     :  0.649  10.278  23016  Z= 0.343
  Chirality :  0.046   0.164   2552
  Planarity :  0.003   0.038   3008
  Dihedral  :  4.763  32.594   2264
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.49 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.62 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.20), residues: 2016
  helix:  0.46 (0.20), residues: 624
  sheet: -2.39 (0.41), residues: 144
  loop : -0.37 (0.20), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  88 
 TYR   0.017   0.002   TYR G 294 
 PHE   0.011   0.001   PHE E  47 
 TRP   0.016   0.003   TRP D  46 
 HIS   0.008   0.001   HIS F  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (16960)
  covalent geometry    : angle       0.64725 (22992)
  SS BOND              : bond        0.00621 (   12)
  SS BOND              : angle       1.69625 (   24)
  hydrogen bonds       : bond        0.02629 (  600)
  hydrogen bonds       : angle       5.31549 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 250
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7840 (tp30)
REVERT: A  222 GLU cc_start: 0.8063 (pp20) cc_final: 0.7819 (pp20)
REVERT: B   43 ASP cc_start: 0.8554 (t0) cc_final: 0.8267 (t0)
REVERT: B  196 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8125 (pp)
REVERT: C   59 MET cc_start: 0.8643 (mtp) cc_final: 0.8250 (mtm)
REVERT: C  195 GLN cc_start: 0.8727 (mp10) cc_final: 0.8347 (mp10)
REVERT: C  290 GLU cc_start: 0.8263 (tp30) cc_final: 0.7854 (tp30)
REVERT: D   91 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8668 (ttpp)
REVERT: D   94 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8826 (mp)
REVERT: E   62 MET cc_start: 0.8520 (mtt) cc_final: 0.8192 (mtt)
REVERT: E   82 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7599 (mt)
REVERT: F  110 MET cc_start: 0.8271 (mtt) cc_final: 0.7747 (mtm)
REVERT: F  146 GLN cc_start: 0.9280 (mm-40) cc_final: 0.9059 (mm-40)
REVERT: F  161 ASP cc_start: 0.8385 (m-30) cc_final: 0.8097 (m-30)
REVERT: G   43 ASP cc_start: 0.8568 (t70) cc_final: 0.8302 (t0)
REVERT: G  222 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7434 (pm20)
REVERT: H  116 LEU cc_start: 0.8763 (tp) cc_final: 0.8407 (tp)
REVERT: H  290 GLU cc_start: 0.8239 (tp30) cc_final: 0.7633 (mm-30)
  outliers start: 55
  outliers final: 40
  residues processed: 290
  average time/residue: 0.1253
  time to fit residues: 53.8735
Evaluate side-chains
  284 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 240
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   23 ILE
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  115 GLN
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  150 HIS
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  295 VAL
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   56 ARG
Chi-restraints excluded: chain F residue   76 MET
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   23 ILE
Chi-restraints excluded: chain G residue   87 GLU
Chi-restraints excluded: chain G residue  104 VAL
Chi-restraints excluded: chain G residue  136 LYS
Chi-restraints excluded: chain G residue  152 VAL
Chi-restraints excluded: chain G residue  222 GLU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   23 ILE
Chi-restraints excluded: chain H residue   26 PHE
Chi-restraints excluded: chain H residue   27 ASP
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  249 LEU
Chi-restraints excluded: chain H residue  295 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 170 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 121 optimal weight:    0.6980
   chunk 138 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 151 optimal weight:    0.8980
   chunk 164 optimal weight:    0.6980
   chunk 90 optimal weight:    0.4980
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN
C  81 HIS
D 150 HIS
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 195 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.121306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.096758 restraints weight = 35391.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 3.59
r_work: 0.3384 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.4228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16972  Z= 0.143
  Angle     :  0.659  11.197  23016  Z= 0.345
  Chirality :  0.046   0.169   2552
  Planarity :  0.003   0.038   3008
  Dihedral  :  4.765  32.787   2264
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.34 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 20.83 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.20), residues: 2016
  helix:  0.49 (0.20), residues: 624
  sheet: -1.44 (0.37), residues: 216
  loop : -0.44 (0.21), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  88 
 TYR   0.018   0.002   TYR B 137 
 PHE   0.012   0.001   PHE A 141 
 TRP   0.018   0.003   TRP D  46 
 HIS   0.010   0.001   HIS D  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (16960)
  covalent geometry    : angle       0.65548 (22992)
  SS BOND              : bond        0.00765 (   12)
  SS BOND              : angle       2.11351 (   24)
  hydrogen bonds       : bond        0.02690 (  600)
  hydrogen bonds       : angle       5.31829 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 263
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7914 (tp30)
REVERT: A  222 GLU cc_start: 0.8054 (pp20) cc_final: 0.7787 (pp20)
REVERT: A  301 TYR cc_start: 0.8167 (t80) cc_final: 0.7834 (t80)
REVERT: B   43 ASP cc_start: 0.8563 (t0) cc_final: 0.8283 (t0)
REVERT: B  222 GLU cc_start: 0.7297 (pm20) cc_final: 0.7093 (pm20)
REVERT: C   59 MET cc_start: 0.8666 (mtp) cc_final: 0.8307 (mtm)
REVERT: C  110 MET cc_start: 0.7880 (mtt) cc_final: 0.7510 (mtm)
REVERT: C  114 GLU cc_start: 0.8585 (tt0) cc_final: 0.8137 (tt0)
REVERT: C  195 GLN cc_start: 0.8641 (mp10) cc_final: 0.8260 (mp10)
REVERT: C  290 GLU cc_start: 0.8232 (tp30) cc_final: 0.7795 (tp30)
REVERT: D   59 MET cc_start: 0.8408 (tpp) cc_final: 0.8160 (mtm)
REVERT: D   94 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8768 (mp)
REVERT: E   59 MET cc_start: 0.8122 (ttm) cc_final: 0.7792 (mtt)
REVERT: E   62 MET cc_start: 0.8503 (mtt) cc_final: 0.8192 (mtt)
REVERT: E  176 GLU cc_start: 0.6793 (mp0) cc_final: 0.6577 (mp0)
REVERT: F  110 MET cc_start: 0.8249 (mtt) cc_final: 0.7746 (mtm)
REVERT: F  146 GLN cc_start: 0.9286 (mm-40) cc_final: 0.9056 (mm-40)
REVERT: F  161 ASP cc_start: 0.8384 (m-30) cc_final: 0.8075 (m-30)
REVERT: G   43 ASP cc_start: 0.8546 (t70) cc_final: 0.8268 (t0)
REVERT: G  222 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7443 (pm20)
REVERT: H  116 LEU cc_start: 0.8713 (tp) cc_final: 0.8422 (tp)
REVERT: H  290 GLU cc_start: 0.8214 (tp30) cc_final: 0.7598 (mm-30)
  outliers start: 46
  outliers final: 37
  residues processed: 296
  average time/residue: 0.1214
  time to fit residues: 53.0183
Evaluate side-chains
  281 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 242
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   23 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  115 GLN
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   43 ASP
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  150 HIS
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   75 LYS
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  295 VAL
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   56 ARG
Chi-restraints excluded: chain F residue   76 MET
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   87 GLU
Chi-restraints excluded: chain G residue  104 VAL
Chi-restraints excluded: chain G residue  136 LYS
Chi-restraints excluded: chain G residue  152 VAL
Chi-restraints excluded: chain G residue  195 GLN
Chi-restraints excluded: chain G residue  222 GLU
Chi-restraints excluded: chain H residue   23 ILE
Chi-restraints excluded: chain H residue   26 PHE
Chi-restraints excluded: chain H residue  249 LEU
Chi-restraints excluded: chain H residue  295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 132 optimal weight:    1.9990
   chunk 188 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 113 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 134 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 195 GLN
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 GLN
** C  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 102 GLN
G 195 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.119898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.095578 restraints weight = 35219.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 3.51
r_work: 0.3363 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  16972  Z= 0.177
  Angle     :  0.693  10.024  23016  Z= 0.361
  Chirality :  0.047   0.253   2552
  Planarity :  0.003   0.037   3008
  Dihedral  :  4.842  32.508   2264
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.49 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 20.94 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.20), residues: 2016
  helix:  0.39 (0.20), residues: 632
  sheet: -2.38 (0.42), residues: 144
  loop : -0.49 (0.20), residues: 1240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  88 
 TYR   0.018   0.002   TYR B 137 
 PHE   0.011   0.001   PHE E  47 
 TRP   0.019   0.003   TRP D  46 
 HIS   0.010   0.001   HIS F  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (16960)
  covalent geometry    : angle       0.69067 (22992)
  SS BOND              : bond        0.00686 (   12)
  SS BOND              : angle       1.90628 (   24)
  hydrogen bonds       : bond        0.02787 (  600)
  hydrogen bonds       : angle       5.38536 ( 1560)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 249
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 HIS cc_start: 0.8177 (m-70) cc_final: 0.7945 (m-70)
REVERT: A  125 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8099 (tp30)
REVERT: A  222 GLU cc_start: 0.8097 (pp20) cc_final: 0.7847 (pp20)
REVERT: A  289 GLU cc_start: 0.7587 (pm20) cc_final: 0.7368 (pm20)
REVERT: B   43 ASP cc_start: 0.8528 (t0) cc_final: 0.8261 (t0)
REVERT: B  222 GLU cc_start: 0.7291 (pm20) cc_final: 0.7086 (pm20)
REVERT: B  234 ILE cc_start: 0.9136 (mm) cc_final: 0.8910 (tt)
REVERT: C   59 MET cc_start: 0.8714 (mtp) cc_final: 0.8382 (mtm)
REVERT: C  195 GLN cc_start: 0.8647 (mp10) cc_final: 0.8261 (mp10)
REVERT: C  290 GLU cc_start: 0.8229 (tp30) cc_final: 0.7790 (tp30)
REVERT: D   94 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8783 (mp)
REVERT: D  301 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6853 (m-80)
REVERT: E   59 MET cc_start: 0.8182 (ttm) cc_final: 0.7867 (mtt)
REVERT: E   62 MET cc_start: 0.8501 (mtt) cc_final: 0.8203 (mtt)
REVERT: E  176 GLU cc_start: 0.6805 (mp0) cc_final: 0.6585 (mp0)
REVERT: F  110 MET cc_start: 0.8289 (mtt) cc_final: 0.7778 (mtm)
REVERT: F  161 ASP cc_start: 0.8378 (m-30) cc_final: 0.8121 (m-30)
REVERT: G   43 ASP cc_start: 0.8550 (t70) cc_final: 0.8279 (t0)
REVERT: G  222 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7478 (pm20)
REVERT: G  290 GLU cc_start: 0.8475 (tp30) cc_final: 0.8198 (tp30)
REVERT: H  116 LEU cc_start: 0.8731 (tp) cc_final: 0.8430 (tp)
REVERT: H  290 GLU cc_start: 0.8421 (tp30) cc_final: 0.7851 (mm-30)
  outliers start: 46
  outliers final: 36
  residues processed: 281
  average time/residue: 0.1214
  time to fit residues: 51.0922
Evaluate side-chains
  279 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 240
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   23 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  115 GLN
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   43 ASP
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  301 TYR
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   75 LYS
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  295 VAL
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   56 ARG
Chi-restraints excluded: chain F residue   76 MET
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   23 ILE
Chi-restraints excluded: chain G residue   87 GLU
Chi-restraints excluded: chain G residue  104 VAL
Chi-restraints excluded: chain G residue  152 VAL
Chi-restraints excluded: chain G residue  195 GLN
Chi-restraints excluded: chain G residue  222 GLU
Chi-restraints excluded: chain H residue   23 ILE
Chi-restraints excluded: chain H residue   26 PHE
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  249 LEU
Chi-restraints excluded: chain H residue  295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 163 optimal weight:    0.8980
   chunk 149 optimal weight:    1.9990
   chunk 157 optimal weight:    0.3980
   chunk 67 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0270
   chunk 37 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 120 optimal weight:    0.8980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 195 GLN
** H 195 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 = 0.3951 r_free = 0.3951 target = 0.121368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.097932 restraints weight = 35141.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 3.49
r_work: 0.3404 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16972  Z= 0.141
  Angle     :  0.672   9.927  23016  Z= 0.351
  Chirality :  0.046   0.213   2552
  Planarity :  0.003   0.038   3008
  Dihedral  :  4.747  31.978   2264
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.04 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.54 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.20), residues: 2016
  helix:  0.40 (0.20), residues: 632
  sheet: -1.42 (0.37), residues: 216
  loop : -0.55 (0.21), residues: 1168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  88 
 TYR   0.019   0.001   TYR B 137 
 PHE   0.010   0.001   PHE A 141 
 TRP   0.017   0.003   TRP D  46 
 HIS   0.007   0.001   HIS F  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (16960)
  covalent geometry    : angle       0.67024 (22992)
  SS BOND              : bond        0.00713 (   12)
  SS BOND              : angle       1.77614 (   24)
  hydrogen bonds       : bond        0.02781 (  600)
  hydrogen bonds       : angle       5.42655 ( 1560)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3603.53 seconds
wall clock time: 62 minutes 54.92 seconds (3774.92 seconds total)