Starting phenix.real_space_refine
on Thu Jul 31 07:13:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vam_21143/07_2025/6vam_21143.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vam_21143/07_2025/6vam_21143.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vam_21143/07_2025/6vam_21143.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vam_21143/07_2025/6vam_21143.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vam_21143/07_2025/6vam_21143.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vam_21143/07_2025/6vam_21143.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.045 sd=   0.520
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     152      5.16       5
     C    8704      2.51       5
     N    2248      2.21       5
     O    2256      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13360
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1670
          Classifications: {'peptide': 214}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 10, 'TRANS': 203}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
  Restraints were copied for chains:
    C, B, E, D, G, F, H
  Time building chain proxies: 5.14, per 1000 atoms: 0.38
  Number of scatterers: 13360
  At special positions: 0
  Unit cell: (119.78, 119.78, 96.46, 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     152     16.00
     O    2256      8.00
     N    2248      7.00
     C    8704      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A 126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  41 " - pdb=" SG  CYS C 126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  41 " - pdb=" SG  CYS E 126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  41 " - pdb=" SG  CYS D 126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  41 " - pdb=" SG  CYS G 126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F  41 " - pdb=" SG  CYS F 126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 126 " distance=2.02

  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: 3.36
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3280

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      78.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 35
    Processing helix  chain 'A' and resid 48 through 70
      removed outlier: 3.920A  pdb=" N   LEU A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      Proline residue:  A  59  - end of helix
      removed outlier: 3.772A  pdb=" N   PHE A  68 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 83
      removed outlier: 4.556A  pdb=" N   MET A  76 " --> pdb=" O   ASN A  72 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG A  83 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 107
      removed outlier: 3.841A  pdb=" N   GLN A 104 " --> pdb=" O   CYS A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 121
      removed outlier: 3.695A  pdb=" N   ALA A 111 " --> pdb=" O   MET A 107 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL A 112 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 128
    Processing helix  chain 'A' and resid 147 through 157
    Processing helix  chain 'A' and resid 171 through 201
      removed outlier: 3.535A  pdb=" N   LEU A 178 " --> pdb=" O   ALA A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 246
      removed outlier: 3.715A  pdb=" N   ASP A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN A 246 " --> pdb=" O   LYS A 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 35
    Processing helix  chain 'B' and resid 48 through 70
      removed outlier: 3.920A  pdb=" N   LEU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY B  54 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      Proline residue:  B  59  - end of helix
      removed outlier: 3.772A  pdb=" N   PHE B  68 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 83
      removed outlier: 4.556A  pdb=" N   MET B  76 " --> pdb=" O   ASN B  72 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG B  83 " --> pdb=" O   GLU B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 107
      removed outlier: 3.841A  pdb=" N   GLN B 104 " --> pdb=" O   CYS B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 121
      removed outlier: 3.696A  pdb=" N   ALA B 111 " --> pdb=" O   MET B 107 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL B 112 " --> pdb=" O   ILE B 108 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY B 121 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 128
    Processing helix  chain 'B' and resid 147 through 157
    Processing helix  chain 'B' and resid 171 through 201
      removed outlier: 3.535A  pdb=" N   LEU B 178 " --> pdb=" O   ALA B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 246
      removed outlier: 3.715A  pdb=" N   ASP B 223 " --> pdb=" O   SER B 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN B 246 " --> pdb=" O   LYS B 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 35
    Processing helix  chain 'C' and resid 48 through 70
      removed outlier: 3.920A  pdb=" N   LEU C  53 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY C  54 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
      Proline residue:  C  59  - end of helix
      removed outlier: 3.772A  pdb=" N   PHE C  68 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 83
      removed outlier: 4.556A  pdb=" N   MET C  76 " --> pdb=" O   ASN C  72 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG C  83 " --> pdb=" O   GLU C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 107
      removed outlier: 3.841A  pdb=" N   GLN C 104 " --> pdb=" O   CYS C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 121
      removed outlier: 3.695A  pdb=" N   ALA C 111 " --> pdb=" O   MET C 107 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL C 112 " --> pdb=" O   ILE C 108 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY C 121 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 128
    Processing helix  chain 'C' and resid 147 through 157
    Processing helix  chain 'C' and resid 171 through 201
      removed outlier: 3.535A  pdb=" N   LEU C 178 " --> pdb=" O   ALA C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 246
      removed outlier: 3.715A  pdb=" N   ASP C 223 " --> pdb=" O   SER C 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN C 246 " --> pdb=" O   LYS C 242 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 35
    Processing helix  chain 'D' and resid 48 through 70
      removed outlier: 3.920A  pdb=" N   LEU D  53 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY D  54 " --> pdb=" O   ALA D  50 " (cutoff:3.500A)
      Proline residue:  D  59  - end of helix
      removed outlier: 3.771A  pdb=" N   PHE D  68 " --> pdb=" O   PHE D  64 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 83
      removed outlier: 4.556A  pdb=" N   MET D  76 " --> pdb=" O   ASN D  72 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG D  83 " --> pdb=" O   GLU D  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 107
      removed outlier: 3.841A  pdb=" N   GLN D 104 " --> pdb=" O   CYS D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 121
      removed outlier: 3.695A  pdb=" N   ALA D 111 " --> pdb=" O   MET D 107 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL D 112 " --> pdb=" O   ILE D 108 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY D 121 " --> pdb=" O   THR D 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 128
    Processing helix  chain 'D' and resid 147 through 157
    Processing helix  chain 'D' and resid 171 through 201
      removed outlier: 3.535A  pdb=" N   LEU D 178 " --> pdb=" O   ALA D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 246
      removed outlier: 3.715A  pdb=" N   ASP D 223 " --> pdb=" O   SER D 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN D 246 " --> pdb=" O   LYS D 242 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 23 through 35
    Processing helix  chain 'E' and resid 48 through 70
      removed outlier: 3.920A  pdb=" N   LEU E  53 " --> pdb=" O   LEU E  49 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY E  54 " --> pdb=" O   ALA E  50 " (cutoff:3.500A)
      Proline residue:  E  59  - end of helix
      removed outlier: 3.772A  pdb=" N   PHE E  68 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 72 through 83
      removed outlier: 4.556A  pdb=" N   MET E  76 " --> pdb=" O   ASN E  72 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG E  83 " --> pdb=" O   GLU E  79 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 93 through 107
      removed outlier: 3.841A  pdb=" N   GLN E 104 " --> pdb=" O   CYS E 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 107 through 121
      removed outlier: 3.695A  pdb=" N   ALA E 111 " --> pdb=" O   MET E 107 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL E 112 " --> pdb=" O   ILE E 108 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY E 121 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 128
    Processing helix  chain 'E' and resid 147 through 157
    Processing helix  chain 'E' and resid 171 through 201
      removed outlier: 3.535A  pdb=" N   LEU E 178 " --> pdb=" O   ALA E 174 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 246
      removed outlier: 3.715A  pdb=" N   ASP E 223 " --> pdb=" O   SER E 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN E 246 " --> pdb=" O   LYS E 242 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 35
    Processing helix  chain 'F' and resid 48 through 70
      removed outlier: 3.920A  pdb=" N   LEU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLY F  54 " --> pdb=" O   ALA F  50 " (cutoff:3.500A)
      Proline residue:  F  59  - end of helix
      removed outlier: 3.772A  pdb=" N   PHE F  68 " --> pdb=" O   PHE F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 72 through 83
      removed outlier: 4.556A  pdb=" N   MET F  76 " --> pdb=" O   ASN F  72 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG F  83 " --> pdb=" O   GLU F  79 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 107
      removed outlier: 3.841A  pdb=" N   GLN F 104 " --> pdb=" O   CYS F 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 107 through 121
      removed outlier: 3.696A  pdb=" N   ALA F 111 " --> pdb=" O   MET F 107 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL F 112 " --> pdb=" O   ILE F 108 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY F 121 " --> pdb=" O   THR F 117 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 121 through 128
    Processing helix  chain 'F' and resid 147 through 157
    Processing helix  chain 'F' and resid 171 through 201
      removed outlier: 3.535A  pdb=" N   LEU F 178 " --> pdb=" O   ALA F 174 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 208 through 246
      removed outlier: 3.715A  pdb=" N   ASP F 223 " --> pdb=" O   SER F 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN F 246 " --> pdb=" O   LYS F 242 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 23 through 35
    Processing helix  chain 'G' and resid 48 through 70
      removed outlier: 3.920A  pdb=" N   LEU G  53 " --> pdb=" O   LEU G  49 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY G  54 " --> pdb=" O   ALA G  50 " (cutoff:3.500A)
      Proline residue:  G  59  - end of helix
      removed outlier: 3.772A  pdb=" N   PHE G  68 " --> pdb=" O   PHE G  64 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 72 through 83
      removed outlier: 4.556A  pdb=" N   MET G  76 " --> pdb=" O   ASN G  72 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG G  83 " --> pdb=" O   GLU G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 107
      removed outlier: 3.842A  pdb=" N   GLN G 104 " --> pdb=" O   CYS G 100 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 107 through 121
      removed outlier: 3.695A  pdb=" N   ALA G 111 " --> pdb=" O   MET G 107 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL G 112 " --> pdb=" O   ILE G 108 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY G 121 " --> pdb=" O   THR G 117 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 121 through 128
    Processing helix  chain 'G' and resid 147 through 157
    Processing helix  chain 'G' and resid 171 through 201
      removed outlier: 3.536A  pdb=" N   LEU G 178 " --> pdb=" O   ALA G 174 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 208 through 246
      removed outlier: 3.715A  pdb=" N   ASP G 223 " --> pdb=" O   SER G 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN G 246 " --> pdb=" O   LYS G 242 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 23 through 35
    Processing helix  chain 'H' and resid 48 through 70
      removed outlier: 3.920A  pdb=" N   LEU H  53 " --> pdb=" O   LEU H  49 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY H  54 " --> pdb=" O   ALA H  50 " (cutoff:3.500A)
      Proline residue:  H  59  - end of helix
      removed outlier: 3.772A  pdb=" N   PHE H  68 " --> pdb=" O   PHE H  64 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 72 through 83
      removed outlier: 4.556A  pdb=" N   MET H  76 " --> pdb=" O   ASN H  72 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG H  83 " --> pdb=" O   GLU H  79 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 93 through 107
      removed outlier: 3.841A  pdb=" N   GLN H 104 " --> pdb=" O   CYS H 100 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 107 through 121
      removed outlier: 3.695A  pdb=" N   ALA H 111 " --> pdb=" O   MET H 107 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL H 112 " --> pdb=" O   ILE H 108 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY H 121 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 121 through 128
    Processing helix  chain 'H' and resid 147 through 157
    Processing helix  chain 'H' and resid 171 through 201
      removed outlier: 3.536A  pdb=" N   LEU H 178 " --> pdb=" O   ALA H 174 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 208 through 246
      removed outlier: 3.715A  pdb=" N   ASP H 223 " --> pdb=" O   SER H 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN H 246 " --> pdb=" O   LYS H 242 " (cutoff:3.500A)

    929 hydrogen bonds defined for protein.
    2787 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.34

  Time building geometry restraints manager: 3.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4184
        1.34 -     1.46: 2675
        1.46 -     1.57: 6597
        1.57 -     1.69: 0
        1.69 -     1.81: 200
  Bond restraints: 13656
  Sorted by residual:
  bond pdb=" N   PRO C 146 "
       pdb=" CD  PRO C 146 "
    ideal  model  delta    sigma   weight residual
    1.473  1.521 -0.048 1.40e-02 5.10e+03 1.20e+01
  bond pdb=" N   PRO E 146 "
       pdb=" CD  PRO E 146 "
    ideal  model  delta    sigma   weight residual
    1.473  1.521 -0.048 1.40e-02 5.10e+03 1.20e+01
  bond pdb=" N   PRO A 146 "
       pdb=" CD  PRO A 146 "
    ideal  model  delta    sigma   weight residual
    1.473  1.521 -0.048 1.40e-02 5.10e+03 1.20e+01
  bond pdb=" N   PRO B 146 "
       pdb=" CD  PRO B 146 "
    ideal  model  delta    sigma   weight residual
    1.473  1.521 -0.048 1.40e-02 5.10e+03 1.19e+01
  bond pdb=" N   PRO F 146 "
       pdb=" CD  PRO F 146 "
    ideal  model  delta    sigma   weight residual
    1.473  1.521 -0.048 1.40e-02 5.10e+03 1.19e+01
  ... (remaining 13651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 18171
        2.57 -     5.14: 309
        5.14 -     7.71: 40
        7.71 -    10.28: 0
       10.28 -    12.85: 16
  Bond angle restraints: 18536
  Sorted by residual:
  angle pdb=" C   LEU B 203 "
        pdb=" N   ARG B 204 "
        pdb=" CA  ARG B 204 "
      ideal   model   delta    sigma   weight residual
     120.06  132.91  -12.85 1.19e+00 7.06e-01 1.17e+02
  angle pdb=" C   LEU F 203 "
        pdb=" N   ARG F 204 "
        pdb=" CA  ARG F 204 "
      ideal   model   delta    sigma   weight residual
     120.06  132.90  -12.84 1.19e+00 7.06e-01 1.16e+02
  angle pdb=" C   LEU A 203 "
        pdb=" N   ARG A 204 "
        pdb=" CA  ARG A 204 "
      ideal   model   delta    sigma   weight residual
     120.06  132.88  -12.82 1.19e+00 7.06e-01 1.16e+02
  angle pdb=" C   LEU C 203 "
        pdb=" N   ARG C 204 "
        pdb=" CA  ARG C 204 "
      ideal   model   delta    sigma   weight residual
     120.06  132.88  -12.82 1.19e+00 7.06e-01 1.16e+02
  angle pdb=" C   LEU E 203 "
        pdb=" N   ARG E 204 "
        pdb=" CA  ARG E 204 "
      ideal   model   delta    sigma   weight residual
     120.06  132.88  -12.82 1.19e+00 7.06e-01 1.16e+02
  ... (remaining 18531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 7232
       16.29 -    32.59: 760
       32.59 -    48.88: 120
       48.88 -    65.17: 24
       65.17 -    81.47: 48
  Dihedral angle restraints: 8184
    sinusoidal: 3152
      harmonic: 5032
  Sorted by residual:
  dihedral pdb=" CB  CYS G  41 "
           pdb=" SG  CYS G  41 "
           pdb=" SG  CYS G 126 "
           pdb=" CB  CYS G 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.76   69.76     1      1.00e+01 1.00e-02 6.28e+01
  dihedral pdb=" CB  CYS H  41 "
           pdb=" SG  CYS H  41 "
           pdb=" SG  CYS H 126 "
           pdb=" CB  CYS H 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.75   69.75     1      1.00e+01 1.00e-02 6.28e+01
  dihedral pdb=" CB  CYS D  41 "
           pdb=" SG  CYS D  41 "
           pdb=" SG  CYS D 126 "
           pdb=" CB  CYS D 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.75   69.75     1      1.00e+01 1.00e-02 6.28e+01
  ... (remaining 8181 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1375
       0.034 -    0.068: 620
       0.068 -    0.102: 109
       0.102 -    0.136: 41
       0.136 -    0.170: 15
  Chirality restraints: 2160
  Sorted by residual:
  chirality pdb=" CA  ILE B 169 "
            pdb=" N   ILE B 169 "
            pdb=" C   ILE B 169 "
            pdb=" CB  ILE B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.20e-01
  chirality pdb=" CA  ILE F 169 "
            pdb=" N   ILE F 169 "
            pdb=" C   ILE F 169 "
            pdb=" CB  ILE F 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.20e-01
  chirality pdb=" CA  ILE H 169 "
            pdb=" N   ILE H 169 "
            pdb=" C   ILE H 169 "
            pdb=" CB  ILE H 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.20e-01
  ... (remaining 2157 not shown)

  Planarity restraints: 2296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D  59 "    0.035 5.00e-02 4.00e+02   5.26e-02 4.43e+00
        pdb=" N   PRO D  60 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO D  60 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D  60 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C  59 "    0.035 5.00e-02 4.00e+02   5.25e-02 4.42e+00
        pdb=" N   PRO C  60 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO C  60 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C  60 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E  59 "    0.035 5.00e-02 4.00e+02   5.25e-02 4.42e+00
        pdb=" N   PRO E  60 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO E  60 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E  60 "    0.030 5.00e-02 4.00e+02
  ... (remaining 2293 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3850
        2.81 -     3.33: 13724
        3.33 -     3.86: 20744
        3.86 -     4.38: 21377
        4.38 -     4.90: 37590
  Nonbonded interactions: 97285
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU F 225 "
            pdb=" NH1 ARG F 226 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OE1 GLU B 225 "
            pdb=" NH1 ARG B 226 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OE1 GLU A 225 "
            pdb=" NH1 ARG A 226 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OE1 GLU G 225 "
            pdb=" NH1 ARG G 226 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OE1 GLU C 225 "
            pdb=" NH1 ARG C 226 "
     model   vdw
     2.290 3.120
  ... (remaining 97280 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.150
  Process input model:                     28.110
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
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      :  0.005   0.048  13664  Z= 0.251
  Angle     :  0.844  12.848  18552  Z= 0.538
  Chirality :  0.041   0.170   2160
  Planarity :  0.005   0.053   2296
  Dihedral  : 14.629  81.467   4880
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.19), residues: 1664
  helix: -0.64 (0.12), residues: 1304
  sheet:  None (None), residues: 0
  loop : -3.16 (0.35), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP F 218 
 HIS   0.001   0.000   HIS B 236 
 PHE   0.008   0.001   PHE H 229 
 TYR   0.014   0.002   TYR H  97 
 ARG   0.001   0.000   ARG D 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08586 (  929)
  hydrogen bonds       : angle       4.32021 ( 2787)
  SS BOND              : bond        0.00656 (    8)
  SS BOND              : angle       1.59915 (   16)
  covalent geometry    : bond        0.00534 (13656)
  covalent geometry    : angle       0.84314 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 1.539 
Fit side-chains
REVERT: A  102 MET cc_start: 0.8083 (ttp) cc_final: 0.7852 (ttm)
REVERT: B   26 MET cc_start: 0.7340 (mmm) cc_final: 0.6989 (tpt)
REVERT: B  235 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8523 (mm-30)
REVERT: C  102 MET cc_start: 0.8084 (ttp) cc_final: 0.7851 (ttm)
REVERT: D   26 MET cc_start: 0.7335 (mmm) cc_final: 0.6978 (tpt)
REVERT: D  235 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8519 (mm-30)
REVERT: E  102 MET cc_start: 0.8081 (ttp) cc_final: 0.7847 (ttm)
REVERT: F   26 MET cc_start: 0.7331 (mmm) cc_final: 0.6980 (tpt)
REVERT: F  235 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8515 (mm-30)
REVERT: G  102 MET cc_start: 0.8081 (ttp) cc_final: 0.7846 (ttm)
REVERT: H   26 MET cc_start: 0.7333 (mmm) cc_final: 0.6985 (tpt)
REVERT: H  235 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8520 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.2382
  time to fit residues: 93.3920
Evaluate side-chains
  213 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 1.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    0.5980
   chunk 127 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 131 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 152 optimal weight:    4.9990
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  73 ASN
A 147 GLN
B  40 ASN
C  40 ASN
C  73 ASN
C 147 GLN
** D  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  40 ASN
E  73 ASN
E 147 GLN
F  40 ASN
G  40 ASN
G  73 ASN
H  40 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.111301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.091802 restraints weight = 29456.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.094517 restraints weight = 14723.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.096436 restraints weight = 9669.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  13664  Z= 0.210
  Angle     :  0.670   5.889  18552  Z= 0.364
  Chirality :  0.040   0.178   2160
  Planarity :  0.005   0.054   2296
  Dihedral  :  5.408  21.420   1856
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 16.08 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.21), residues: 1664
  helix:  0.58 (0.13), residues: 1344
  sheet:  None (None), residues: 0
  loop : -2.41 (0.40), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 218 
 HIS   0.001   0.000   HIS F 220 
 PHE   0.008   0.001   PHE E 229 
 TYR   0.013   0.002   TYR A  34 
 ARG   0.002   0.000   ARG E 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04592 (  929)
  hydrogen bonds       : angle       3.77422 ( 2787)
  SS BOND              : bond        0.00528 (    8)
  SS BOND              : angle       1.41674 (   16)
  covalent geometry    : bond        0.00512 (13656)
  covalent geometry    : angle       0.66943 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 242
  time to evaluate  : 1.452 
Fit side-chains
REVERT: A   32 GLN cc_start: 0.7654 (mt0) cc_final: 0.7368 (mt0)
REVERT: A   76 MET cc_start: 0.8762 (ttp) cc_final: 0.8532 (ppp)
REVERT: A  166 GLN cc_start: 0.8311 (pp30) cc_final: 0.7810 (pp30)
REVERT: B   26 MET cc_start: 0.5765 (mmm) cc_final: 0.5352 (tpt)
REVERT: B  147 GLN cc_start: 0.8268 (tp40) cc_final: 0.8046 (tp-100)
REVERT: B  166 GLN cc_start: 0.8375 (pp30) cc_final: 0.7894 (pp30)
REVERT: B  235 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8636 (mm-30)
REVERT: C   32 GLN cc_start: 0.7750 (mt0) cc_final: 0.7458 (mt0)
REVERT: C   76 MET cc_start: 0.8761 (ttp) cc_final: 0.8533 (ppp)
REVERT: C  166 GLN cc_start: 0.8314 (pp30) cc_final: 0.7811 (pp30)
REVERT: D   26 MET cc_start: 0.5771 (mmm) cc_final: 0.5356 (tpt)
REVERT: D  147 GLN cc_start: 0.8269 (tp40) cc_final: 0.8047 (tp-100)
REVERT: D  166 GLN cc_start: 0.8376 (pp30) cc_final: 0.7899 (pp30)
REVERT: D  235 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8644 (mm-30)
REVERT: E   32 GLN cc_start: 0.7741 (mt0) cc_final: 0.7450 (mt0)
REVERT: E   76 MET cc_start: 0.8761 (ttp) cc_final: 0.8534 (ppp)
REVERT: E  166 GLN cc_start: 0.8310 (pp30) cc_final: 0.7810 (pp30)
REVERT: F   26 MET cc_start: 0.5859 (mmm) cc_final: 0.5464 (tpt)
REVERT: F  147 GLN cc_start: 0.8289 (tp40) cc_final: 0.8065 (tp-100)
REVERT: F  166 GLN cc_start: 0.8366 (pp30) cc_final: 0.7893 (pp30)
REVERT: F  235 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8624 (mm-30)
REVERT: G   32 GLN cc_start: 0.7659 (mt0) cc_final: 0.7361 (mt0)
REVERT: G   76 MET cc_start: 0.8761 (ttp) cc_final: 0.8534 (ppp)
REVERT: G  166 GLN cc_start: 0.8308 (pp30) cc_final: 0.7811 (pp30)
REVERT: H   26 MET cc_start: 0.5847 (mmm) cc_final: 0.5453 (tpt)
REVERT: H  147 GLN cc_start: 0.8278 (tp40) cc_final: 0.8055 (tp-100)
REVERT: H  166 GLN cc_start: 0.8372 (pp30) cc_final: 0.7895 (pp30)
REVERT: H  235 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8625 (mm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 242
  average time/residue: 0.2244
  time to fit residues: 80.7599
Evaluate side-chains
  244 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 236
  time to evaluate  : 1.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain F residue  243 VAL
Chi-restraints excluded: chain G residue  243 VAL
Chi-restraints excluded: chain H residue  243 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 119 optimal weight:    0.9980
   chunk 138 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 155 optimal weight:    0.6980
   chunk 161 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 124 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.113610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.094526 restraints weight = 28848.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.097318 restraints weight = 13825.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.099344 restraints weight = 8818.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13664  Z= 0.146
  Angle     :  0.596   5.509  18552  Z= 0.322
  Chirality :  0.038   0.175   2160
  Planarity :  0.005   0.055   2296
  Dihedral  :  5.109  21.265   1856
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 16.01 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.21), residues: 1664
  helix:  1.22 (0.14), residues: 1344
  sheet:  None (None), residues: 0
  loop : -2.31 (0.42), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 218 
 HIS   0.000   0.000   HIS F 236 
 PHE   0.007   0.001   PHE B 229 
 TYR   0.009   0.001   TYR H  97 
 ARG   0.001   0.000   ARG E 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04081 (  929)
  hydrogen bonds       : angle       3.40691 ( 2787)
  SS BOND              : bond        0.00292 (    8)
  SS BOND              : angle       1.04176 (   16)
  covalent geometry    : bond        0.00355 (13656)
  covalent geometry    : angle       0.59597 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 246
  time to evaluate  : 1.510 
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   76 MET cc_start: 0.8850 (ttp) cc_final: 0.8560 (ppp)
REVERT: A  147 GLN cc_start: 0.8327 (tp40) cc_final: 0.8106 (tp-100)
REVERT: B   26 MET cc_start: 0.5682 (mmm) cc_final: 0.5322 (tpt)
REVERT: B   76 MET cc_start: 0.8503 (ppp) cc_final: 0.8090 (ppp)
REVERT: B  147 GLN cc_start: 0.8311 (tp40) cc_final: 0.8026 (tp-100)
REVERT: B  235 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8604 (mm-30)
REVERT: C   76 MET cc_start: 0.8852 (ttp) cc_final: 0.8568 (ppp)
REVERT: C  147 GLN cc_start: 0.8321 (tp40) cc_final: 0.8106 (tp-100)
REVERT: D   26 MET cc_start: 0.5665 (mmm) cc_final: 0.5311 (tpt)
REVERT: D   76 MET cc_start: 0.8448 (ppp) cc_final: 0.8040 (ppp)
REVERT: D  147 GLN cc_start: 0.8335 (tp40) cc_final: 0.8046 (tp-100)
REVERT: D  235 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8607 (mm-30)
REVERT: E   76 MET cc_start: 0.8849 (ttp) cc_final: 0.8566 (ppp)
REVERT: E  147 GLN cc_start: 0.8329 (tp40) cc_final: 0.8111 (tp-100)
REVERT: F   26 MET cc_start: 0.5686 (mmm) cc_final: 0.5330 (tpt)
REVERT: F   76 MET cc_start: 0.8502 (ppp) cc_final: 0.8098 (ppp)
REVERT: F  147 GLN cc_start: 0.8349 (tp40) cc_final: 0.8057 (tp-100)
REVERT: F  235 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8601 (mm-30)
REVERT: G   76 MET cc_start: 0.8849 (ttp) cc_final: 0.8562 (ppp)
REVERT: H   26 MET cc_start: 0.5685 (mmm) cc_final: 0.5327 (tpt)
REVERT: H   76 MET cc_start: 0.8501 (ppp) cc_final: 0.8096 (ppp)
REVERT: H  147 GLN cc_start: 0.8345 (tp40) cc_final: 0.8056 (tp-100)
REVERT: H  235 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8601 (mm-30)
  outliers start: 12
  outliers final: 12
  residues processed: 254
  average time/residue: 0.2218
  time to fit residues: 85.0529
Evaluate side-chains
  248 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 236
  time to evaluate  : 1.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain F residue  134 VAL
Chi-restraints excluded: chain F residue  243 VAL
Chi-restraints excluded: chain G residue  243 VAL
Chi-restraints excluded: chain H residue  134 VAL
Chi-restraints excluded: chain H residue  243 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 119 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 161 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 13 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.118195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.098972 restraints weight = 27245.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.101855 restraints weight = 13260.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.103940 restraints weight = 8526.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13664  Z= 0.148
  Angle     :  0.596   7.745  18552  Z= 0.318
  Chirality :  0.037   0.173   2160
  Planarity :  0.005   0.055   2296
  Dihedral  :  4.865  20.142   1856
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 17.35 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.21), residues: 1664
  helix:  1.62 (0.14), residues: 1344
  sheet:  None (None), residues: 0
  loop : -2.37 (0.40), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 218 
 HIS   0.000   0.000   HIS D 236 
 PHE   0.006   0.001   PHE C 229 
 TYR   0.010   0.001   TYR B  97 
 ARG   0.001   0.000   ARG E 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  929)
  hydrogen bonds       : angle       3.29969 ( 2787)
  SS BOND              : bond        0.00313 (    8)
  SS BOND              : angle       1.07834 (   16)
  covalent geometry    : bond        0.00358 (13656)
  covalent geometry    : angle       0.59589 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 246
  time to evaluate  : 1.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 MET cc_start: 0.8845 (ttp) cc_final: 0.8614 (ppp)
REVERT: A  147 GLN cc_start: 0.8232 (tp40) cc_final: 0.7964 (tp-100)
REVERT: B   26 MET cc_start: 0.5749 (mmm) cc_final: 0.5376 (tpt)
REVERT: B   76 MET cc_start: 0.8539 (ppp) cc_final: 0.8156 (ppp)
REVERT: B  147 GLN cc_start: 0.8276 (tp40) cc_final: 0.7976 (tp-100)
REVERT: B  235 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8555 (mm-30)
REVERT: C   76 MET cc_start: 0.8868 (ttp) cc_final: 0.8633 (ppp)
REVERT: C  147 GLN cc_start: 0.8287 (tp40) cc_final: 0.8016 (tp-100)
REVERT: D   26 MET cc_start: 0.5733 (mmm) cc_final: 0.5352 (tpt)
REVERT: D   76 MET cc_start: 0.8517 (ppp) cc_final: 0.8138 (ppp)
REVERT: D  147 GLN cc_start: 0.8278 (tp40) cc_final: 0.7978 (tp-100)
REVERT: D  235 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8548 (mm-30)
REVERT: E   76 MET cc_start: 0.8847 (ttp) cc_final: 0.8621 (ppp)
REVERT: E  147 GLN cc_start: 0.8220 (tp40) cc_final: 0.7955 (tp-100)
REVERT: F   26 MET cc_start: 0.5761 (mmm) cc_final: 0.5390 (tpt)
REVERT: F   76 MET cc_start: 0.8540 (ppp) cc_final: 0.8182 (ppp)
REVERT: F  147 GLN cc_start: 0.8273 (tp40) cc_final: 0.7977 (tp-100)
REVERT: F  235 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8556 (mm-30)
REVERT: G   76 MET cc_start: 0.8879 (ttp) cc_final: 0.8623 (ppp)
REVERT: H   26 MET cc_start: 0.5765 (mmm) cc_final: 0.5391 (tpt)
REVERT: H   76 MET cc_start: 0.8520 (ppp) cc_final: 0.8165 (ppp)
REVERT: H  147 GLN cc_start: 0.8252 (tp40) cc_final: 0.7955 (tp-100)
REVERT: H  235 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8539 (mm-30)
  outliers start: 24
  outliers final: 12
  residues processed: 266
  average time/residue: 0.2095
  time to fit residues: 84.6135
Evaluate side-chains
  247 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 235
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain F residue  134 VAL
Chi-restraints excluded: chain F residue  243 VAL
Chi-restraints excluded: chain G residue  243 VAL
Chi-restraints excluded: chain H residue  134 VAL
Chi-restraints excluded: chain H residue  243 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 105 optimal weight:   20.0000
   chunk 150 optimal weight:    0.0010
   chunk 42 optimal weight:   30.0000
   chunk 128 optimal weight:    0.0370
   chunk 153 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.5666

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  48 ASN
B 236 HIS
** C  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  48 ASN
D 236 HIS
** E  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  48 ASN
F 236 HIS
** G  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  48 ASN
H 236 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.126986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.107964 restraints weight = 28714.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.111036 restraints weight = 13706.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.113238 restraints weight = 8693.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13664  Z= 0.114
  Angle     :  0.559   6.368  18552  Z= 0.293
  Chirality :  0.037   0.173   2160
  Planarity :  0.004   0.054   2296
  Dihedral  :  4.580  20.161   1856
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 19.94 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.21), residues: 1664
  helix:  1.93 (0.14), residues: 1392
  sheet:  None (None), residues: 0
  loop : -2.00 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 218 
 HIS   0.001   0.000   HIS G 236 
 PHE   0.005   0.001   PHE G 229 
 TYR   0.005   0.001   TYR H 221 
 ARG   0.001   0.000   ARG G 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03227 (  929)
  hydrogen bonds       : angle       3.00970 ( 2787)
  SS BOND              : bond        0.00471 (    8)
  SS BOND              : angle       1.05805 (   16)
  covalent geometry    : bond        0.00262 (13656)
  covalent geometry    : angle       0.55809 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 265
  time to evaluate  : 1.463 
Fit side-chains
REVERT: A  147 GLN cc_start: 0.8106 (tp40) cc_final: 0.7829 (tp-100)
REVERT: A  228 LEU cc_start: 0.9107 (tp) cc_final: 0.8889 (tt)
REVERT: B   26 MET cc_start: 0.5569 (mmm) cc_final: 0.5307 (tpt)
REVERT: B   76 MET cc_start: 0.8586 (ppp) cc_final: 0.8274 (ppp)
REVERT: B  107 MET cc_start: 0.8526 (ttt) cc_final: 0.8161 (ttp)
REVERT: B  117 THR cc_start: 0.9491 (t) cc_final: 0.9269 (t)
REVERT: B  147 GLN cc_start: 0.8058 (tp40) cc_final: 0.7774 (tp-100)
REVERT: B  231 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8485 (mm-30)
REVERT: B  235 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8493 (mm-30)
REVERT: C  147 GLN cc_start: 0.8098 (tp40) cc_final: 0.7821 (tp-100)
REVERT: C  228 LEU cc_start: 0.9107 (tp) cc_final: 0.8889 (tt)
REVERT: D   26 MET cc_start: 0.5602 (mmm) cc_final: 0.5339 (tpt)
REVERT: D   76 MET cc_start: 0.8590 (ppp) cc_final: 0.8278 (ppp)
REVERT: D  107 MET cc_start: 0.8529 (ttt) cc_final: 0.8162 (ttp)
REVERT: D  117 THR cc_start: 0.9492 (t) cc_final: 0.9271 (t)
REVERT: D  147 GLN cc_start: 0.8068 (tp40) cc_final: 0.7780 (tp-100)
REVERT: D  231 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8478 (mm-30)
REVERT: D  235 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8491 (mm-30)
REVERT: E  147 GLN cc_start: 0.8092 (tp40) cc_final: 0.7818 (tp-100)
REVERT: F   26 MET cc_start: 0.5611 (mmm) cc_final: 0.5352 (tpt)
REVERT: F   76 MET cc_start: 0.8520 (ppp) cc_final: 0.8183 (ppp)
REVERT: F  107 MET cc_start: 0.8525 (ttt) cc_final: 0.8160 (ttp)
REVERT: F  117 THR cc_start: 0.9495 (t) cc_final: 0.9273 (t)
REVERT: F  147 GLN cc_start: 0.8059 (tp40) cc_final: 0.7776 (tp-100)
REVERT: F  231 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8466 (mm-30)
REVERT: F  235 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8476 (mm-30)
REVERT: H   26 MET cc_start: 0.5554 (mmm) cc_final: 0.5297 (tpt)
REVERT: H   76 MET cc_start: 0.8525 (ppp) cc_final: 0.8245 (ppp)
REVERT: H  107 MET cc_start: 0.8525 (ttt) cc_final: 0.8157 (ttp)
REVERT: H  117 THR cc_start: 0.9493 (t) cc_final: 0.9271 (t)
REVERT: H  147 GLN cc_start: 0.8053 (tp40) cc_final: 0.7770 (tp-100)
REVERT: H  231 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8475 (mm-30)
REVERT: H  235 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8477 (mm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 273
  average time/residue: 0.2136
  time to fit residues: 88.2308
Evaluate side-chains
  250 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 246
  time to evaluate  : 1.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain G residue  243 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 34 optimal weight:    0.1980
   chunk 72 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 79 optimal weight:    6.9990
   chunk 136 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 236 HIS
C 236 HIS
E 236 HIS
G 236 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.127129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108036 restraints weight = 29026.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.111017 restraints weight = 13774.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.113236 restraints weight = 8810.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13664  Z= 0.117
  Angle     :  0.553   6.136  18552  Z= 0.293
  Chirality :  0.037   0.162   2160
  Planarity :  0.004   0.054   2296
  Dihedral  :  4.414  18.784   1856
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.19 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.21), residues: 1664
  helix:  2.20 (0.14), residues: 1384
  sheet:  None (None), residues: 0
  loop : -2.33 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP H 218 
 HIS   0.001   0.000   HIS B 220 
 PHE   0.004   0.001   PHE D 229 
 TYR   0.009   0.001   TYR H  47 
 ARG   0.001   0.000   ARG D 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 (  929)
  hydrogen bonds       : angle       2.97310 ( 2787)
  SS BOND              : bond        0.00461 (    8)
  SS BOND              : angle       1.57209 (   16)
  covalent geometry    : bond        0.00273 (13656)
  covalent geometry    : angle       0.55167 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 GLN cc_start: 0.8142 (tp40) cc_final: 0.7858 (tp-100)
REVERT: B   26 MET cc_start: 0.5564 (mmm) cc_final: 0.5300 (tpt)
REVERT: B   76 MET cc_start: 0.8441 (ppp) cc_final: 0.8169 (ppp)
REVERT: B  231 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8487 (mm-30)
REVERT: B  235 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8471 (mm-30)
REVERT: C  147 GLN cc_start: 0.8142 (tp40) cc_final: 0.7860 (tp-100)
REVERT: D   26 MET cc_start: 0.5541 (mmm) cc_final: 0.5273 (tpt)
REVERT: D   38 ASP cc_start: 0.7879 (t0) cc_final: 0.7631 (t0)
REVERT: D   76 MET cc_start: 0.8443 (ppp) cc_final: 0.8166 (ppp)
REVERT: D  231 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8485 (mm-30)
REVERT: D  235 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8470 (mm-30)
REVERT: E  147 GLN cc_start: 0.8139 (tp40) cc_final: 0.7856 (tp-100)
REVERT: F   26 MET cc_start: 0.5571 (mmm) cc_final: 0.5312 (tpt)
REVERT: F   76 MET cc_start: 0.8455 (ppp) cc_final: 0.8162 (ppp)
REVERT: F  231 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8465 (mm-30)
REVERT: F  235 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8465 (mm-30)
REVERT: H   26 MET cc_start: 0.5558 (mmm) cc_final: 0.5296 (tpt)
REVERT: H   76 MET cc_start: 0.8448 (ppp) cc_final: 0.8167 (ppp)
REVERT: H  231 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8471 (mm-30)
REVERT: H  235 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8464 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.2096
  time to fit residues: 85.5307
Evaluate side-chains
  248 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:   30.0000
   chunk 53 optimal weight:    0.6980
   chunk 116 optimal weight:    2.9990
   chunk 165 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 125 optimal weight:    7.9990
   chunk 152 optimal weight:    0.0770
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9540

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

Flipped N/Q/H residues before XYZ refinement:
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.126957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.107919 restraints weight = 28933.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.110939 restraints weight = 13719.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.113111 restraints weight = 8764.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13664  Z= 0.124
  Angle     :  0.603   8.528  18552  Z= 0.306
  Chirality :  0.039   0.252   2160
  Planarity :  0.004   0.053   2296
  Dihedral  :  4.303  17.600   1856
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 22.26 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.21), residues: 1664
  helix:  2.32 (0.14), residues: 1384
  sheet:  None (None), residues: 0
  loop : -2.39 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 218 
 HIS   0.001   0.000   HIS C 236 
 PHE   0.004   0.001   PHE G 229 
 TYR   0.015   0.002   TYR E 163 
 ARG   0.001   0.000   ARG D 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03439 (  929)
  hydrogen bonds       : angle       3.04505 ( 2787)
  SS BOND              : bond        0.00117 (    8)
  SS BOND              : angle       1.21877 (   16)
  covalent geometry    : bond        0.00295 (13656)
  covalent geometry    : angle       0.60249 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 254
  time to evaluate  : 1.488 
Fit side-chains
REVERT: A  147 GLN cc_start: 0.8123 (tp40) cc_final: 0.7870 (tp-100)
REVERT: A  193 MET cc_start: 0.7679 (tpp) cc_final: 0.7147 (tpt)
REVERT: B   76 MET cc_start: 0.8435 (ppp) cc_final: 0.8034 (ppp)
REVERT: B  231 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8463 (mm-30)
REVERT: B  235 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8482 (mm-30)
REVERT: C  147 GLN cc_start: 0.8115 (tp40) cc_final: 0.7867 (tp-100)
REVERT: C  193 MET cc_start: 0.7680 (tpp) cc_final: 0.7157 (tpt)
REVERT: D   26 MET cc_start: 0.5665 (mmm) cc_final: 0.5465 (tpt)
REVERT: D   76 MET cc_start: 0.8438 (ppp) cc_final: 0.8035 (ppp)
REVERT: D  235 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8477 (mm-30)
REVERT: E  147 GLN cc_start: 0.8119 (tp40) cc_final: 0.7870 (tp-100)
REVERT: E  193 MET cc_start: 0.7685 (tpp) cc_final: 0.7160 (tpt)
REVERT: F   76 MET cc_start: 0.8429 (ppp) cc_final: 0.8137 (ppp)
REVERT: F  235 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8422 (mm-30)
REVERT: G  193 MET cc_start: 0.7678 (tpp) cc_final: 0.7153 (tpt)
REVERT: H   76 MET cc_start: 0.8416 (ppp) cc_final: 0.8029 (ppp)
REVERT: H  235 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8423 (mm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 262
  average time/residue: 0.2348
  time to fit residues: 94.3203
Evaluate side-chains
  233 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 226
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  203 LEU
Chi-restraints excluded: chain G residue  117 THR
Chi-restraints excluded: chain G residue  203 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 63 optimal weight:   20.0000
   chunk 5 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 158 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   chunk 118 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
G 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.125026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.105926 restraints weight = 29208.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.108840 restraints weight = 13850.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.110960 restraints weight = 8897.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13664  Z= 0.143
  Angle     :  0.629   9.603  18552  Z= 0.323
  Chirality :  0.040   0.184   2160
  Planarity :  0.004   0.053   2296
  Dihedral  :  4.357  17.725   1856
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 23.31 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.21), residues: 1664
  helix:  2.23 (0.14), residues: 1384
  sheet:  None (None), residues: 0
  loop : -2.35 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 218 
 HIS   0.001   0.000   HIS E 236 
 PHE   0.005   0.001   PHE G 229 
 TYR   0.019   0.002   TYR A 163 
 ARG   0.001   0.000   ARG E 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  929)
  hydrogen bonds       : angle       3.23543 ( 2787)
  SS BOND              : bond        0.00224 (    8)
  SS BOND              : angle       0.67017 (   16)
  covalent geometry    : bond        0.00352 (13656)
  covalent geometry    : angle       0.62851 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 233
  time to evaluate  : 1.447 
Fit side-chains
REVERT: A  147 GLN cc_start: 0.8236 (tp40) cc_final: 0.8000 (tp-100)
REVERT: B  231 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8493 (mm-30)
REVERT: B  235 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8487 (mm-30)
REVERT: C  147 GLN cc_start: 0.8239 (tp40) cc_final: 0.8003 (tp-100)
REVERT: D   26 MET cc_start: 0.5650 (mmm) cc_final: 0.5417 (tpt)
REVERT: D  235 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8494 (mm-30)
REVERT: E  147 GLN cc_start: 0.8242 (tp40) cc_final: 0.8005 (tp-100)
REVERT: F   76 MET cc_start: 0.8461 (ppp) cc_final: 0.8170 (ppp)
REVERT: F  235 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8427 (mm-30)
REVERT: H   76 MET cc_start: 0.8359 (ppp) cc_final: 0.8159 (ppp)
REVERT: H  235 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8426 (mm-30)
  outliers start: 18
  outliers final: 11
  residues processed: 241
  average time/residue: 0.2218
  time to fit residues: 80.1055
Evaluate side-chains
  244 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 233
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain E residue   76 MET
Chi-restraints excluded: chain E residue  203 LEU
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain G residue  203 LEU
Chi-restraints excluded: chain G residue  243 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 162 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 152 optimal weight:    5.9990
   chunk 145 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0000
   overall best weight:    1.1390

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

Flipped N/Q/H residues before XYZ refinement:
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.126350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.107347 restraints weight = 28949.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.110334 restraints weight = 13829.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.112435 restraints weight = 8848.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13664  Z= 0.134
  Angle     :  0.619   9.904  18552  Z= 0.319
  Chirality :  0.039   0.155   2160
  Planarity :  0.004   0.054   2296
  Dihedral  :  4.341  18.761   1856
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 24.02 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.21), residues: 1664
  helix:  2.34 (0.14), residues: 1384
  sheet:  None (None), residues: 0
  loop : -2.21 (0.39), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 218 
 HIS   0.001   0.000   HIS E 236 
 PHE   0.004   0.001   PHE D 229 
 TYR   0.014   0.001   TYR A  34 
 ARG   0.001   0.000   ARG H 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03590 (  929)
  hydrogen bonds       : angle       3.15327 ( 2787)
  SS BOND              : bond        0.00148 (    8)
  SS BOND              : angle       0.63408 (   16)
  covalent geometry    : bond        0.00327 (13656)
  covalent geometry    : angle       0.61862 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 242
  time to evaluate  : 1.540 
Fit side-chains
REVERT: A   76 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8096 (ppp)
REVERT: A  147 GLN cc_start: 0.8293 (tp40) cc_final: 0.8064 (tp-100)
REVERT: A  193 MET cc_start: 0.7702 (tpp) cc_final: 0.7164 (tpt)
REVERT: B  231 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8495 (mm-30)
REVERT: B  235 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8459 (mm-30)
REVERT: C   76 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8115 (ppp)
REVERT: C  147 GLN cc_start: 0.8298 (tp40) cc_final: 0.8070 (tp-100)
REVERT: C  193 MET cc_start: 0.7706 (tpp) cc_final: 0.7170 (tpt)
REVERT: D  235 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8475 (mm-30)
REVERT: E   76 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8102 (ppp)
REVERT: E  147 GLN cc_start: 0.8297 (tp40) cc_final: 0.8066 (tp-100)
REVERT: E  193 MET cc_start: 0.7708 (tpp) cc_final: 0.7170 (tpt)
REVERT: F   38 ASP cc_start: 0.7908 (t0) cc_final: 0.7659 (t0)
REVERT: F   76 MET cc_start: 0.8445 (ppp) cc_final: 0.8170 (ppp)
REVERT: F  235 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8417 (mm-30)
REVERT: G   76 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8095 (ppp)
REVERT: G  193 MET cc_start: 0.7704 (tpp) cc_final: 0.7163 (tpt)
REVERT: H   38 ASP cc_start: 0.7902 (t0) cc_final: 0.7654 (t0)
REVERT: H   76 MET cc_start: 0.8406 (ppp) cc_final: 0.8068 (ppp)
REVERT: H  235 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8406 (mm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 247
  average time/residue: 0.2276
  time to fit residues: 84.0758
Evaluate side-chains
  240 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 231
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain E residue   76 MET
Chi-restraints excluded: chain E residue  203 LEU
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain G residue   76 MET
Chi-restraints excluded: chain G residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 115 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 139 optimal weight:    0.0170
   chunk 79 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 134 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
C  48 ASN
G  48 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.132619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.111130 restraints weight = 29141.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.114525 restraints weight = 14046.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.116862 restraints weight = 8895.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13664  Z= 0.124
  Angle     :  0.596   9.822  18552  Z= 0.305
  Chirality :  0.038   0.158   2160
  Planarity :  0.004   0.054   2296
  Dihedral  :  4.189  16.698   1856
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 24.72 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.21), residues: 1664
  helix:  2.53 (0.14), residues: 1384
  sheet:  None (None), residues: 0
  loop : -2.24 (0.39), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 218 
 HIS   0.000   0.000   HIS A 236 
 PHE   0.004   0.001   PHE D 229 
 TYR   0.015   0.001   TYR E 163 
 ARG   0.001   0.000   ARG E 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03317 (  929)
  hydrogen bonds       : angle       3.06454 ( 2787)
  SS BOND              : bond        0.00239 (    8)
  SS BOND              : angle       0.49363 (   16)
  covalent geometry    : bond        0.00296 (13656)
  covalent geometry    : angle       0.59644 (18536)

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

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

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3328 Ramachandran restraints generated.
    1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 242
  time to evaluate  : 1.468 
Fit side-chains
REVERT: A   76 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8199 (ppp)
REVERT: A  147 GLN cc_start: 0.8427 (tp40) cc_final: 0.8191 (tp-100)
REVERT: B   38 ASP cc_start: 0.7972 (t0) cc_final: 0.7752 (t0)
REVERT: B  107 MET cc_start: 0.8552 (ttt) cc_final: 0.8238 (ttp)
REVERT: B  231 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8516 (mm-30)
REVERT: B  235 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8495 (mm-30)
REVERT: C   76 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8212 (ppp)
REVERT: C  147 GLN cc_start: 0.8417 (tp40) cc_final: 0.8180 (tp-100)
REVERT: D   38 ASP cc_start: 0.7918 (t0) cc_final: 0.7690 (t0)
REVERT: D  107 MET cc_start: 0.8503 (ttt) cc_final: 0.8184 (ttp)
REVERT: D  235 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8467 (mm-30)
REVERT: E   76 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8204 (ppp)
REVERT: E  147 GLN cc_start: 0.8408 (tp40) cc_final: 0.8170 (tp-100)
REVERT: F   38 ASP cc_start: 0.7988 (t0) cc_final: 0.7737 (t0)
REVERT: F   76 MET cc_start: 0.8508 (ppp) cc_final: 0.8234 (ppp)
REVERT: F  107 MET cc_start: 0.8547 (ttt) cc_final: 0.8234 (ttp)
REVERT: F  235 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8414 (mm-30)
REVERT: G   76 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8197 (ppp)
REVERT: H   38 ASP cc_start: 0.7984 (t0) cc_final: 0.7739 (t0)
REVERT: H   76 MET cc_start: 0.8427 (ppp) cc_final: 0.8215 (ppp)
REVERT: H  107 MET cc_start: 0.8504 (ttt) cc_final: 0.8175 (ttp)
REVERT: H  235 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8437 (mm-30)
  outliers start: 8
  outliers final: 4
  residues processed: 246
  average time/residue: 0.2276
  time to fit residues: 83.5914
Evaluate side-chains
  239 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 231
  time to evaluate  : 1.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain E residue   76 MET
Chi-restraints excluded: chain E residue  203 LEU
Chi-restraints excluded: chain G residue   76 MET
Chi-restraints excluded: chain G residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 164 optimal weight:    4.9990
   chunk 90 optimal weight:    9.9990
   chunk 110 optimal weight:    6.9990
   chunk 142 optimal weight:    1.9990
   chunk 162 optimal weight:    2.9990
   chunk 147 optimal weight:   30.0000
   chunk 59 optimal weight:    0.9980
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  48 ASN
** F  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.123859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.103028 restraints weight = 28210.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.106169 restraints weight = 14037.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.108392 restraints weight = 9041.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13664  Z= 0.186
  Angle     :  0.665   9.745  18552  Z= 0.347
  Chirality :  0.042   0.163   2160
  Planarity :  0.005   0.053   2296
  Dihedral  :  4.504  18.540   1856
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 25.07 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.21), residues: 1664
  helix:  2.31 (0.13), residues: 1344
  sheet:  None (None), residues: 0
  loop : -2.54 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 218 
 HIS   0.001   0.000   HIS F 220 
 PHE   0.007   0.001   PHE D 229 
 TYR   0.020   0.002   TYR G  34 
 ARG   0.001   0.000   ARG G 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04288 (  929)
  hydrogen bonds       : angle       3.44746 ( 2787)
  SS BOND              : bond        0.00564 (    8)
  SS BOND              : angle       0.74979 (   16)
  covalent geometry    : bond        0.00455 (13656)
  covalent geometry    : angle       0.66459 (18536)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3767.85 seconds
wall clock time: 66 minutes 20.42 seconds (3980.42 seconds total)